Starting phenix.real_space_refine on Thu May 1 04:34:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6rah_4775/05_2025/6rah_4775.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rah_4775/05_2025/6rah_4775.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6rah_4775/05_2025/6rah_4775.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rah_4775/05_2025/6rah_4775.map" model { file = "/net/cci-nas-00/data/ceres_data/6rah_4775/05_2025/6rah_4775.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rah_4775/05_2025/6rah_4775.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 6 5.49 5 Mg 2 5.21 5 S 25 5.16 5 C 6549 2.51 5 N 1792 2.21 5 O 1787 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 10161 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 586, 4690 Classifications: {'peptide': 586} Link IDs: {'PTRANS': 24, 'TRANS': 561} Chain: "B" Number of atoms: 4506 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 570, 4499 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 18, 'TRANS': 551} Conformer: "B" Number of residues, atoms: 570, 4499 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 18, 'TRANS': 551} bond proxies already assigned to first conformer: 4579 Chain: "C" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 897 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} 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: 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: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 8.62, per 1000 atoms: 0.85 Number of scatterers: 10161 At special positions: 0 Unit cell: (103.392, 85.083, 155.088, 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 25 16.00 P 6 15.00 Mg 2 11.99 O 1787 8.00 N 1792 7.00 C 6549 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 50 " - pdb=" SG CYS C 108 " distance=2.07 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: 2.22 Conformation dependent library (CDL) restraints added in 1.8 seconds 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2338 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 6 sheets defined 65.2% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 12 through 23 removed outlier: 3.983A pdb=" N TYR A 21 " --> pdb=" O ARG A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 45 Processing helix chain 'A' and resid 45 through 59 Processing helix chain 'A' and resid 65 through 120 Processing helix chain 'A' and resid 121 through 128 removed outlier: 3.804A pdb=" N TYR A 125 " --> pdb=" O HIS A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 138 Processing helix chain 'A' and resid 140 through 151 removed outlier: 4.435A pdb=" N ILE A 144 " --> pdb=" O ASP A 140 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN A 145 " --> pdb=" O VAL A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 173 removed outlier: 3.789A pdb=" N PHE A 171 " --> pdb=" O GLY A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 222 removed outlier: 3.835A pdb=" N VAL A 179 " --> pdb=" O LYS A 175 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL A 183 " --> pdb=" O VAL A 179 " (cutoff:3.500A) Proline residue: A 185 - end of helix removed outlier: 3.521A pdb=" N LEU A 196 " --> pdb=" O THR A 192 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY A 197 " --> pdb=" O TRP A 193 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA A 210 " --> pdb=" O ARG A 206 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 230 removed outlier: 3.663A pdb=" N LEU A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 283 removed outlier: 3.553A pdb=" N ARG A 241 " --> pdb=" O GLU A 237 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU A 242 " --> pdb=" O LYS A 238 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE A 253 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N PHE A 261 " --> pdb=" O PHE A 257 " (cutoff:3.500A) Proline residue: A 262 - end of helix removed outlier: 3.687A pdb=" N ASP A 269 " --> pdb=" O GLY A 265 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY A 281 " --> pdb=" O TYR A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 332 removed outlier: 3.692A pdb=" N ASP A 298 " --> pdb=" O VAL A 294 " (cutoff:3.500A) Proline residue: A 306 - end of helix removed outlier: 3.977A pdb=" N ASP A 312 " --> pdb=" O GLN A 308 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG A 326 " --> pdb=" O ALA A 322 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL A 330 " --> pdb=" O ARG A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 407 Processing helix chain 'A' and resid 425 through 427 No H-bonds generated for 'chain 'A' and resid 425 through 427' Processing helix chain 'A' and resid 428 through 435 removed outlier: 3.683A pdb=" N HIS A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 455 Processing helix chain 'A' and resid 462 through 474 removed outlier: 3.503A pdb=" N VAL A 466 " --> pdb=" O PRO A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 481 Processing helix chain 'A' and resid 484 through 488 Processing helix chain 'A' and resid 498 through 513 Processing helix chain 'A' and resid 529 through 544 Processing helix chain 'A' and resid 578 through 586 Processing helix chain 'A' and resid 586 through 594 removed outlier: 3.724A pdb=" N ALA A 590 " --> pdb=" O GLY A 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 19 Proline residue: B 15 - end of helix Processing helix chain 'B' and resid 20 through 55 Proline residue: B 42 - end of helix Processing helix chain 'B' and resid 57 through 103 Processing helix chain 'B' and resid 106 through 113 removed outlier: 3.567A pdb=" N TYR B 110 " --> pdb=" O ASP B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 133 removed outlier: 3.805A pdb=" N ASP B 125 " --> pdb=" O ARG B 121 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LEU B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 158 Processing helix chain 'B' and resid 158 through 167 removed outlier: 3.528A pdb=" N ALA B 162 " --> pdb=" O ASN B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 207 removed outlier: 3.587A pdb=" N ARG B 177 " --> pdb=" O PHE B 173 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N PHE B 178 " --> pdb=" O LEU B 174 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU B 179 " --> pdb=" O ALA B 175 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU B 182 " --> pdb=" O PHE B 178 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP B 184 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG B 196 " --> pdb=" O GLU B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 214 Processing helix chain 'B' and resid 216 through 264 removed outlier: 3.605A pdb=" N VAL B 241 " --> pdb=" O ALA B 237 " (cutoff:3.500A) Proline residue: B 244 - end of helix removed outlier: 4.333A pdb=" N LEU B 249 " --> pdb=" O LEU B 245 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLY B 250 " --> pdb=" O HIS B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 269 removed outlier: 3.636A pdb=" N VAL B 268 " --> pdb=" O GLY B 264 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL B 269 " --> pdb=" O GLY B 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 264 through 269' Processing helix chain 'B' and resid 274 through 317 removed outlier: 4.554A pdb=" N TRP B 290 " --> pdb=" O ALA B 286 " (cutoff:3.500A) Proline residue: B 291 - end of helix removed outlier: 4.032A pdb=" N GLY B 296 " --> pdb=" O ILE B 292 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N TRP B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 383 Processing helix chain 'B' and resid 406 through 413 Processing helix chain 'B' and resid 427 through 433 Processing helix chain 'B' and resid 440 through 451 Processing helix chain 'B' and resid 453 through 458 Processing helix chain 'B' and resid 462 through 466 Processing helix chain 'B' and resid 476 through 491 removed outlier: 4.243A pdb=" N LYS B 491 " --> pdb=" O ARG B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 518 Processing helix chain 'B' and resid 532 through 537 Processing helix chain 'B' and resid 555 through 562 Processing helix chain 'B' and resid 564 through 573 removed outlier: 3.511A pdb=" N GLN B 573 " --> pdb=" O MET B 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 30 removed outlier: 3.560A pdb=" N LEU C 29 " --> pdb=" O GLY C 26 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ASP C 30 " --> pdb=" O SER C 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 26 through 30' Processing helix chain 'C' and resid 87 through 91 removed outlier: 4.086A pdb=" N THR C 91 " --> pdb=" O PRO C 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 374 through 383 removed outlier: 6.347A pdb=" N LEU A 360 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LYS A 377 " --> pdb=" O VAL A 358 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL A 358 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL A 379 " --> pdb=" O ARG A 356 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ARG A 356 " --> pdb=" O VAL A 379 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N PHE A 381 " --> pdb=" O GLU A 354 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLU A 354 " --> pdb=" O PHE A 381 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N PHE A 355 " --> pdb=" O PHE A 418 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N PHE A 418 " --> pdb=" O PHE A 355 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N ASP A 357 " --> pdb=" O CYS A 416 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N CYS A 416 " --> pdb=" O ASP A 357 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 436 through 439 removed outlier: 6.611A pdb=" N GLY A 437 " --> pdb=" O ILE A 520 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N ASP A 522 " --> pdb=" O GLY A 437 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL A 439 " --> pdb=" O ASP A 522 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LYS A 388 " --> pdb=" O ARG A 564 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N LEU A 566 " --> pdb=" O LYS A 388 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ALA A 390 " --> pdb=" O LEU A 566 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N PHE A 568 " --> pdb=" O ALA A 390 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL A 392 " --> pdb=" O PHE A 568 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU A 575 " --> pdb=" O VAL A 567 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ARG A 569 " --> pdb=" O LEU A 573 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N LEU A 573 " --> pdb=" O ARG A 569 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 351 through 361 removed outlier: 6.384A pdb=" N LEU B 353 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LYS B 347 " --> pdb=" O LEU B 353 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ARG B 355 " --> pdb=" O GLY B 345 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLY B 345 " --> pdb=" O ARG B 355 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N LEU B 357 " --> pdb=" O GLY B 343 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY B 343 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL B 344 " --> pdb=" O GLU B 392 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLU B 392 " --> pdb=" O VAL B 344 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 414 through 417 removed outlier: 6.459A pdb=" N THR B 366 " --> pdb=" O TRP B 541 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N ILE B 543 " --> pdb=" O THR B 366 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLY B 368 " --> pdb=" O ILE B 543 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N LEU B 545 " --> pdb=" O GLY B 368 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N THR B 370 " --> pdb=" O LEU B 545 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU B 552 " --> pdb=" O VAL B 544 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASP B 546 " --> pdb=" O ILE B 550 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ILE B 550 " --> pdb=" O ASP B 546 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA C 101 " --> pdb=" O VAL C 109 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 4 through 7 removed outlier: 3.563A pdb=" N THR C 78 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP C 73 " --> pdb=" O THR C 78 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 11 through 12 removed outlier: 5.675A pdb=" N ARG C 38 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N GLY C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) 649 hydrogen bonds defined for protein. 1907 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: 3.13 Time building geometry restraints manager: 2.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1602 1.29 - 1.42: 2713 1.42 - 1.55: 5982 1.55 - 1.68: 29 1.68 - 1.82: 45 Bond restraints: 10371 Sorted by residual: bond pdb=" N HIS B 111 " pdb=" CA BHIS B 111 " ideal model delta sigma weight residual 1.459 1.647 -0.187 1.21e-02 6.83e+03 2.40e+02 bond pdb=" C4 ATP B 601 " pdb=" C5 ATP B 601 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.97e+01 bond pdb=" N PRO C 110 " pdb=" CD PRO C 110 " ideal model delta sigma weight residual 1.473 1.358 0.115 1.40e-02 5.10e+03 6.71e+01 bond pdb=" C4 ATP A 701 " pdb=" C5 ATP A 701 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.08e+01 bond pdb=" N PRO C 88 " pdb=" CD PRO C 88 " ideal model delta sigma weight residual 1.473 1.375 0.098 1.40e-02 5.10e+03 4.87e+01 ... (remaining 10366 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.76: 13585 3.76 - 7.52: 417 7.52 - 11.28: 62 11.28 - 15.03: 8 15.03 - 18.79: 3 Bond angle restraints: 14075 Sorted by residual: angle pdb=" PB ATP A 701 " pdb=" O3B ATP A 701 " pdb=" PG ATP A 701 " ideal model delta sigma weight residual 139.87 121.08 18.79 1.00e+00 1.00e+00 3.53e+02 angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 124.23 15.64 1.00e+00 1.00e+00 2.45e+02 angle pdb=" N ALA C 28 " pdb=" CA ALA C 28 " pdb=" C ALA C 28 " ideal model delta sigma weight residual 113.21 131.11 -17.90 1.15e+00 7.56e-01 2.42e+02 angle pdb=" PA ATP B 601 " pdb=" O3A ATP B 601 " pdb=" PB ATP B 601 " ideal model delta sigma weight residual 136.83 121.95 14.88 1.00e+00 1.00e+00 2.21e+02 angle pdb=" PA ATP A 701 " pdb=" O3A ATP A 701 " pdb=" PB ATP A 701 " ideal model delta sigma weight residual 136.83 123.70 13.13 1.00e+00 1.00e+00 1.73e+02 ... (remaining 14070 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.25: 5882 16.25 - 32.50: 229 32.50 - 48.75: 55 48.75 - 65.00: 18 65.00 - 81.25: 9 Dihedral angle restraints: 6193 sinusoidal: 2539 harmonic: 3654 Sorted by residual: dihedral pdb=" C VAL A 59 " pdb=" N VAL A 59 " pdb=" CA VAL A 59 " pdb=" CB VAL A 59 " ideal model delta harmonic sigma weight residual -122.00 -137.97 15.97 0 2.50e+00 1.60e-01 4.08e+01 dihedral pdb=" N VAL C 99 " pdb=" C VAL C 99 " pdb=" CA VAL C 99 " pdb=" CB VAL C 99 " ideal model delta harmonic sigma weight residual 123.40 109.91 13.49 0 2.50e+00 1.60e-01 2.91e+01 dihedral pdb=" CA GLY A 151 " pdb=" C GLY A 151 " pdb=" N LEU A 152 " pdb=" CA LEU A 152 " ideal model delta harmonic sigma weight residual -180.00 -153.09 -26.91 0 5.00e+00 4.00e-02 2.90e+01 ... (remaining 6190 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1298 0.096 - 0.193: 214 0.193 - 0.289: 62 0.289 - 0.385: 24 0.385 - 0.482: 6 Chirality restraints: 1604 Sorted by residual: chirality pdb=" CA ILE A 54 " pdb=" N ILE A 54 " pdb=" C ILE A 54 " pdb=" CB ILE A 54 " both_signs ideal model delta sigma weight residual False 2.43 2.92 -0.48 2.00e-01 2.50e+01 5.80e+00 chirality pdb=" CA VAL C 99 " pdb=" N VAL C 99 " pdb=" C VAL C 99 " pdb=" CB VAL C 99 " both_signs ideal model delta sigma weight residual False 2.44 2.92 -0.48 2.00e-01 2.50e+01 5.79e+00 chirality pdb=" CA VAL C 109 " pdb=" N VAL C 109 " pdb=" C VAL C 109 " pdb=" CB VAL C 109 " both_signs ideal model delta sigma weight residual False 2.44 2.88 -0.44 2.00e-01 2.50e+01 4.80e+00 ... (remaining 1601 not shown) Planarity restraints: 1778 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 226 " -0.020 2.00e-02 2.50e+03 4.03e-02 1.62e+01 pdb=" C ASP B 226 " 0.070 2.00e-02 2.50e+03 pdb=" O ASP B 226 " -0.027 2.00e-02 2.50e+03 pdb=" N LEU B 227 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 69 " -0.019 2.00e-02 2.50e+03 3.89e-02 1.51e+01 pdb=" C ARG A 69 " 0.067 2.00e-02 2.50e+03 pdb=" O ARG A 69 " -0.026 2.00e-02 2.50e+03 pdb=" N PHE A 70 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 223 " -0.021 2.00e-02 2.50e+03 2.12e-02 1.12e+01 pdb=" CG TRP B 223 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 TRP B 223 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP B 223 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 223 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 223 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 223 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 223 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 223 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP B 223 " -0.000 2.00e-02 2.50e+03 ... (remaining 1775 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 63 2.60 - 3.17: 8040 3.17 - 3.75: 15536 3.75 - 4.32: 22067 4.32 - 4.90: 36913 Nonbonded interactions: 82619 Sorted by model distance: nonbonded pdb="MG MG A 702 " pdb=" O HOH A 802 " model vdw 2.022 2.170 nonbonded pdb=" OG1 THR A 400 " pdb="MG MG A 702 " model vdw 2.047 2.170 nonbonded pdb=" O2B ATP B 601 " pdb="MG MG B 602 " model vdw 2.094 2.170 nonbonded pdb=" O2G ATP A 701 " pdb="MG MG A 702 " model vdw 2.102 2.170 nonbonded pdb=" O2B ATP A 701 " pdb="MG MG A 702 " model vdw 2.110 2.170 ... (remaining 82614 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=0.50 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: 1.330 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: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 28.370 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:13.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.187 10373 Z= 0.568 Angle : 1.575 44.635 14079 Z= 1.096 Chirality : 0.091 0.482 1604 Planarity : 0.007 0.060 1778 Dihedral : 10.599 81.253 3849 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.12 % Favored : 97.72 % Rotamer: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Cbeta Deviations : 0.77 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.20), residues: 1272 helix: -1.58 (0.15), residues: 778 sheet: -0.29 (0.43), residues: 127 loop : -1.92 (0.27), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP B 223 HIS 0.008 0.002 HIS A 554 PHE 0.038 0.003 PHE A 229 TYR 0.019 0.002 TYR A 299 ARG 0.026 0.001 ARG B 88 Details of bonding type rmsd hydrogen bonds : bond 0.18035 ( 649) hydrogen bonds : angle 6.47260 ( 1907) SS BOND : bond 0.02729 ( 2) SS BOND : angle 22.38824 ( 4) covalent geometry : bond 0.00813 (10371) covalent geometry : angle 1.52933 (14075) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7814 (mtm-85) cc_final: 0.7570 (mtm110) REVERT: A 259 LEU cc_start: 0.8379 (tt) cc_final: 0.8174 (tp) REVERT: A 467 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7712 (mt-10) REVERT: A 477 GLU cc_start: 0.7534 (pt0) cc_final: 0.7194 (pt0) REVERT: A 534 LYS cc_start: 0.8332 (tttm) cc_final: 0.8129 (ttmt) REVERT: A 537 GLN cc_start: 0.7706 (mt0) cc_final: 0.7496 (mt0) REVERT: A 558 THR cc_start: 0.8439 (m) cc_final: 0.8142 (m) REVERT: B 50 ASP cc_start: 0.7870 (m-30) cc_final: 0.7661 (m-30) REVERT: B 63 LEU cc_start: 0.8028 (mt) cc_final: 0.7797 (mt) REVERT: B 164 TYR cc_start: 0.7160 (m-10) cc_final: 0.6876 (m-10) REVERT: B 184 ASP cc_start: 0.8204 (t0) cc_final: 0.7987 (t0) REVERT: B 299 MET cc_start: 0.7626 (mtm) cc_final: 0.7249 (mtt) REVERT: B 481 GLN cc_start: 0.8438 (mt0) cc_final: 0.8221 (mt0) REVERT: B 510 GLU cc_start: 0.7519 (tt0) cc_final: 0.7091 (tt0) REVERT: B 568 GLU cc_start: 0.7921 (tp30) cc_final: 0.7559 (tp30) outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 1.7692 time to fit residues: 469.3284 Evaluate side-chains 179 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/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-5669/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-5669/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-5669/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-5669/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-5669/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-5669/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-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/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-5669/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-5669/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-5669/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: 72.6877 > 50: distance: 90 - 95: 29.324 distance: 95 - 96: 21.316 distance: 96 - 97: 56.944 distance: 96 - 99: 42.889 distance: 97 - 98: 52.830 distance: 97 - 102: 57.111 distance: 99 - 100: 28.337 distance: 99 - 101: 30.515 distance: 102 - 103: 66.164 distance: 102 - 108: 44.386 distance: 103 - 104: 7.927 distance: 103 - 106: 40.819 distance: 104 - 105: 3.109 distance: 104 - 109: 68.327 distance: 106 - 107: 56.037 distance: 107 - 108: 43.817 distance: 109 - 110: 40.980 distance: 110 - 111: 8.901 distance: 110 - 113: 69.160 distance: 111 - 112: 45.741 distance: 111 - 120: 8.802 distance: 113 - 114: 44.826 distance: 114 - 115: 35.153 distance: 115 - 116: 24.914 distance: 116 - 117: 11.310 distance: 117 - 118: 31.503 distance: 117 - 119: 13.844 distance: 120 - 121: 54.401 distance: 121 - 122: 41.099 distance: 121 - 124: 57.329 distance: 122 - 123: 19.640 distance: 122 - 128: 40.645 distance: 124 - 125: 24.250 distance: 125 - 126: 41.596 distance: 125 - 127: 28.319 distance: 128 - 129: 37.599 distance: 129 - 132: 55.861 distance: 130 - 136: 43.361 distance: 132 - 133: 39.062 distance: 133 - 134: 27.968 distance: 133 - 135: 50.415 distance: 136 - 137: 21.566 distance: 137 - 138: 48.496 distance: 137 - 140: 64.800 distance: 138 - 139: 5.981 distance: 138 - 144: 57.577 distance: 140 - 141: 39.782 distance: 141 - 142: 5.147 distance: 141 - 143: 39.454 distance: 144 - 145: 18.797 distance: 144 - 150: 43.448 distance: 145 - 148: 42.299 distance: 146 - 147: 39.292 distance: 146 - 151: 41.422 distance: 148 - 149: 56.393 distance: 149 - 150: 50.441 distance: 151 - 152: 49.330 distance: 152 - 153: 21.639 distance: 152 - 155: 27.244 distance: 153 - 154: 53.165 distance: 153 - 157: 46.069 distance: 155 - 156: 62.047 distance: 157 - 158: 23.378 distance: 158 - 159: 27.608 distance: 158 - 161: 57.518 distance: 159 - 160: 39.940 distance: 159 - 166: 40.456 distance: 161 - 162: 55.142 distance: 162 - 163: 44.087 distance: 163 - 164: 16.712 distance: 163 - 165: 60.471 distance: 166 - 167: 43.319 distance: 167 - 168: 69.060 distance: 168 - 169: 39.872 distance: 168 - 170: 35.363