Starting phenix.real_space_refine on Fri Aug 22 20:41:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6irt_9722/08_2025/6irt_9722_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6irt_9722/08_2025/6irt_9722.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6irt_9722/08_2025/6irt_9722_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6irt_9722/08_2025/6irt_9722_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6irt_9722/08_2025/6irt_9722.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6irt_9722/08_2025/6irt_9722.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 27 5.16 5 C 4815 2.51 5 N 1173 2.21 5 O 1331 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7348 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3650 Classifications: {'peptide': 469} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 446} Chain: "B" Number of atoms: 3479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3479 Classifications: {'peptide': 457} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 432} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 3, 'ASN:plan1': 2, 'PHE:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 107 Unusual residues: {'3PH': 2, 'AUU': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 1.67, per 1000 atoms: 0.23 Number of scatterers: 7348 At special positions: 0 Unit cell: (82.916, 84.007, 124.374, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 27 16.00 P 2 15.00 O 1331 8.00 N 1173 7.00 C 4815 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 211 " - pdb=" SG CYS B 164 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG C 1 " - " ASN A 507 " " NAG D 1 " - " ASN A 366 " " NAG E 1 " - " ASN A 382 " " NAG F 1 " - " ASN A 425 " Time building additional restraints: 0.65 Conformation dependent library (CDL) restraints added in 327.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1704 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 3 sheets defined 58.4% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 168 through 175 removed outlier: 3.604A pdb=" N LYS A 172 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N VAL A 173 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 185 Processing helix chain 'A' and resid 185 through 208 removed outlier: 3.616A pdb=" N PHE A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TRP A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET A 197 " --> pdb=" O GLY A 193 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY A 200 " --> pdb=" O GLY A 196 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ILE A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE A 205 " --> pdb=" O ALA A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 222 removed outlier: 3.735A pdb=" N HIS A 221 " --> pdb=" O LYS A 218 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A 222 " --> pdb=" O TRP A 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 218 through 222' Processing helix chain 'A' and resid 230 through 235 Processing helix chain 'A' and resid 241 through 246 Processing helix chain 'A' and resid 248 through 256 removed outlier: 3.876A pdb=" N SER A 254 " --> pdb=" O ASP A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 301 removed outlier: 3.866A pdb=" N LYS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 342 removed outlier: 4.203A pdb=" N GLU A 336 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A 339 " --> pdb=" O LEU A 335 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 354 Processing helix chain 'A' and resid 356 through 370 removed outlier: 3.768A pdb=" N PHE A 360 " --> pdb=" O ASP A 356 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU A 361 " --> pdb=" O ALA A 357 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA A 362 " --> pdb=" O SER A 358 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU A 363 " --> pdb=" O SER A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 393 removed outlier: 3.665A pdb=" N LEU A 392 " --> pdb=" O GLN A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 428 removed outlier: 3.787A pdb=" N GLN A 422 " --> pdb=" O SER A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 461 removed outlier: 3.522A pdb=" N GLN A 455 " --> pdb=" O LEU A 451 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LEU A 456 " --> pdb=" O ARG A 452 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N MET A 457 " --> pdb=" O LEU A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 497 removed outlier: 4.405A pdb=" N PHE A 497 " --> pdb=" O GLU A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 514 Processing helix chain 'A' and resid 519 through 532 removed outlier: 3.595A pdb=" N ARG A 526 " --> pdb=" O SER A 522 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER A 532 " --> pdb=" O SER A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 540 removed outlier: 3.784A pdb=" N HIS A 539 " --> pdb=" O ARG A 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 63 removed outlier: 4.369A pdb=" N ALA B 57 " --> pdb=" O LEU B 53 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ILE B 58 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE B 59 " --> pdb=" O GLY B 55 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE B 63 " --> pdb=" O ILE B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 74 removed outlier: 4.759A pdb=" N THR B 71 " --> pdb=" O ILE B 68 " (cutoff:3.500A) Proline residue: B 72 - end of helix Processing helix chain 'B' and resid 81 through 110 removed outlier: 3.607A pdb=" N LEU B 86 " --> pdb=" O PRO B 82 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL B 87 " --> pdb=" O GLY B 83 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TRP B 89 " --> pdb=" O ALA B 85 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY B 93 " --> pdb=" O TRP B 89 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR B 108 " --> pdb=" O ALA B 104 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ILE B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 124 removed outlier: 3.569A pdb=" N VAL B 123 " --> pdb=" O TYR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 139 Processing helix chain 'B' and resid 139 through 158 removed outlier: 3.581A pdb=" N SER B 143 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN B 145 " --> pdb=" O ARG B 141 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE B 147 " --> pdb=" O SER B 143 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N VAL B 148 " --> pdb=" O SER B 144 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA B 153 " --> pdb=" O ALA B 149 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU B 156 " --> pdb=" O PHE B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 187 removed outlier: 4.333A pdb=" N LEU B 173 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL B 174 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA B 175 " --> pdb=" O ALA B 171 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU B 177 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU B 181 " --> pdb=" O LEU B 177 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU B 182 " --> pdb=" O CYS B 178 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA B 184 " --> pdb=" O LEU B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 199 removed outlier: 4.151A pdb=" N ARG B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 222 removed outlier: 3.544A pdb=" N LEU B 213 " --> pdb=" O ALA B 209 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLN B 218 " --> pdb=" O LEU B 214 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE B 219 " --> pdb=" O GLY B 215 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY B 222 " --> pdb=" O GLN B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 235 removed outlier: 4.399A pdb=" N GLU B 234 " --> pdb=" O PHE B 231 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLY B 235 " --> pdb=" O SER B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 251 removed outlier: 3.633A pdb=" N SER B 249 " --> pdb=" O LEU B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 263 removed outlier: 3.727A pdb=" N VAL B 263 " --> pdb=" O LEU B 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 260 through 263' Processing helix chain 'B' and resid 264 through 269 removed outlier: 4.079A pdb=" N ILE B 268 " --> pdb=" O THR B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 300 removed outlier: 3.694A pdb=" N ALA B 277 " --> pdb=" O ASN B 273 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE B 279 " --> pdb=" O PRO B 275 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE B 280 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B 282 " --> pdb=" O ILE B 278 " (cutoff:3.500A) Proline residue: B 283 - end of helix removed outlier: 3.730A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 308 Processing helix chain 'B' and resid 310 through 320 removed outlier: 4.029A pdb=" N ASP B 314 " --> pdb=" O ALA B 310 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N HIS B 319 " --> pdb=" O PHE B 315 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU B 320 " --> pdb=" O GLY B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 333 Processing helix chain 'B' and resid 334 through 339 removed outlier: 3.550A pdb=" N VAL B 339 " --> pdb=" O CYS B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 343 Processing helix chain 'B' and resid 344 through 355 removed outlier: 3.954A pdb=" N ARG B 348 " --> pdb=" O PHE B 344 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU B 349 " --> pdb=" O THR B 345 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE B 350 " --> pdb=" O SER B 346 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE B 351 " --> pdb=" O SER B 347 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL B 352 " --> pdb=" O ARG B 348 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG B 355 " --> pdb=" O PHE B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 386 removed outlier: 3.675A pdb=" N PHE B 379 " --> pdb=" O PRO B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 390 Processing helix chain 'B' and resid 393 through 421 removed outlier: 3.509A pdb=" N PHE B 399 " --> pdb=" O SER B 395 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE B 402 " --> pdb=" O ASN B 398 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N PHE B 403 " --> pdb=" O PHE B 399 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TRP B 405 " --> pdb=" O SER B 401 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE B 412 " --> pdb=" O VAL B 408 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG B 419 " --> pdb=" O MET B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 453 removed outlier: 3.808A pdb=" N ALA B 442 " --> pdb=" O PHE B 438 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE B 445 " --> pdb=" O LEU B 441 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU B 446 " --> pdb=" O ALA B 442 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE B 447 " --> pdb=" O CYS B 443 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER B 450 " --> pdb=" O LEU B 446 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE B 451 " --> pdb=" O ILE B 447 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N TRP B 452 " --> pdb=" O ALA B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 466 removed outlier: 4.293A pdb=" N CYS B 458 " --> pdb=" O THR B 454 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ILE B 460 " --> pdb=" O VAL B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 476 Processing helix chain 'B' and resid 484 through 501 removed outlier: 3.950A pdb=" N PHE B 490 " --> pdb=" O LEU B 486 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 400 through 401 removed outlier: 6.562A pdb=" N PHE A 346 " --> pdb=" O ILE A 378 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N VAL A 305 " --> pdb=" O GLY A 345 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N GLN A 347 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU A 307 " --> pdb=" O GLN A 347 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR A 226 " --> pdb=" O GLY A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 266 through 268 Processing sheet with id=AA3, first strand: chain 'A' and resid 541 through 545 removed outlier: 4.700A pdb=" N SER A 553 " --> pdb=" O PHE A 545 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG A 556 " --> pdb=" O PHE A 564 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ARG A 626 " --> pdb=" O LEU A 596 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N LEU A 596 " --> pdb=" O ARG A 626 " (cutoff:3.500A) 297 hydrogen bonds defined for protein. 852 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: 1.07 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2069 1.33 - 1.45: 1333 1.45 - 1.57: 4077 1.57 - 1.69: 3 1.69 - 1.81: 42 Bond restraints: 7524 Sorted by residual: bond pdb=" C06 AUU B 603 " pdb=" C08 AUU B 603 " ideal model delta sigma weight residual 1.531 1.707 -0.176 2.00e-02 2.50e+03 7.77e+01 bond pdb=" C04 AUU B 603 " pdb=" C09 AUU B 603 " ideal model delta sigma weight residual 1.535 1.362 0.173 2.00e-02 2.50e+03 7.53e+01 bond pdb=" C04 AUU B 603 " pdb=" C08 AUU B 603 " ideal model delta sigma weight residual 1.533 1.699 -0.166 2.00e-02 2.50e+03 6.89e+01 bond pdb=" C06 AUU B 603 " pdb=" C07 AUU B 603 " ideal model delta sigma weight residual 1.534 1.370 0.164 2.00e-02 2.50e+03 6.71e+01 bond pdb=" C06 AUU B 603 " pdb=" C11 AUU B 603 " ideal model delta sigma weight residual 1.537 1.383 0.154 2.00e-02 2.50e+03 5.94e+01 ... (remaining 7519 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 9548 2.19 - 4.39: 554 4.39 - 6.58: 79 6.58 - 8.78: 35 8.78 - 10.97: 13 Bond angle restraints: 10229 Sorted by residual: angle pdb=" N HIS B 319 " pdb=" CA HIS B 319 " pdb=" C HIS B 319 " ideal model delta sigma weight residual 111.36 122.33 -10.97 1.09e+00 8.42e-01 1.01e+02 angle pdb=" C SER A 176 " pdb=" N PRO A 177 " pdb=" CA PRO A 177 " ideal model delta sigma weight residual 119.84 128.89 -9.05 1.25e+00 6.40e-01 5.24e+01 angle pdb=" N LEU B 320 " pdb=" CA LEU B 320 " pdb=" C LEU B 320 " ideal model delta sigma weight residual 108.34 116.69 -8.35 1.31e+00 5.83e-01 4.07e+01 angle pdb=" C PHE B 161 " pdb=" N PRO B 162 " pdb=" CD PRO B 162 " ideal model delta sigma weight residual 120.60 109.75 10.85 2.20e+00 2.07e-01 2.43e+01 angle pdb=" CA LEU B 469 " pdb=" C LEU B 469 " pdb=" N PRO B 470 " ideal model delta sigma weight residual 120.81 116.58 4.23 8.60e-01 1.35e+00 2.42e+01 ... (remaining 10224 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.14: 4295 21.14 - 42.28: 211 42.28 - 63.42: 34 63.42 - 84.56: 12 84.56 - 105.70: 10 Dihedral angle restraints: 4562 sinusoidal: 1909 harmonic: 2653 Sorted by residual: dihedral pdb=" CB CYS A 211 " pdb=" SG CYS A 211 " pdb=" SG CYS B 164 " pdb=" CB CYS B 164 " ideal model delta sinusoidal sigma weight residual -86.00 -157.02 71.02 1 1.00e+01 1.00e-02 6.48e+01 dihedral pdb=" CA VAL B 322 " pdb=" C VAL B 322 " pdb=" N MET B 323 " pdb=" CA MET B 323 " ideal model delta harmonic sigma weight residual 180.00 153.31 26.69 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA GLN A 323 " pdb=" C GLN A 323 " pdb=" N VAL A 324 " pdb=" CA VAL A 324 " ideal model delta harmonic sigma weight residual 180.00 -154.11 -25.89 0 5.00e+00 4.00e-02 2.68e+01 ... (remaining 4559 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.277: 1194 0.277 - 0.553: 7 0.553 - 0.830: 0 0.830 - 1.106: 0 1.106 - 1.383: 2 Chirality restraints: 1203 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 507 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.02 -1.38 2.00e-01 2.50e+01 4.78e+01 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 382 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.10 -1.30 2.00e-01 2.50e+01 4.22e+01 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 366 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.88 0.48 2.00e-01 2.50e+01 5.74e+00 ... (remaining 1200 not shown) Planarity restraints: 1259 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 366 " 0.102 2.00e-02 2.50e+03 2.65e-01 8.75e+02 pdb=" CG ASN A 366 " -0.080 2.00e-02 2.50e+03 pdb=" OD1 ASN A 366 " 0.153 2.00e-02 2.50e+03 pdb=" ND2 ASN A 366 " -0.471 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " 0.296 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 382 " -0.123 2.00e-02 2.50e+03 2.00e-01 5.00e+02 pdb=" CG ASN A 382 " 0.059 2.00e-02 2.50e+03 pdb=" OD1 ASN A 382 " -0.058 2.00e-02 2.50e+03 pdb=" ND2 ASN A 382 " 0.353 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " -0.231 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 507 " -0.072 2.00e-02 2.50e+03 8.36e-02 8.74e+01 pdb=" CG ASN A 507 " 0.031 2.00e-02 2.50e+03 pdb=" OD1 ASN A 507 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 507 " 0.139 2.00e-02 2.50e+03 pdb=" C1 NAG C 1 " -0.098 2.00e-02 2.50e+03 ... (remaining 1256 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1762 2.77 - 3.30: 6596 3.30 - 3.84: 11683 3.84 - 4.37: 13661 4.37 - 4.90: 22977 Nonbonded interactions: 56679 Sorted by model distance: nonbonded pdb=" OG1 THR A 460 " pdb=" OH TYR A 554 " model vdw 2.241 3.040 nonbonded pdb=" OG SER A 599 " pdb=" OE2 GLU A 621 " model vdw 2.284 3.040 nonbonded pdb=" O ASP A 516 " pdb=" OG SER A 522 " model vdw 2.284 3.040 nonbonded pdb=" O THR A 460 " pdb=" NH1 ARG A 556 " model vdw 2.291 3.120 nonbonded pdb=" O GLY B 107 " pdb=" OG SER B 111 " model vdw 2.300 3.040 ... (remaining 56674 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.470 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 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 : 0.012 0.176 7533 Z= 0.539 Angle : 1.297 17.404 10255 Z= 0.657 Chirality : 0.088 1.383 1203 Planarity : 0.008 0.063 1255 Dihedral : 14.319 105.703 2855 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.76 % Allowed : 9.22 % Favored : 90.02 % Rotamer: Outliers : 3.01 % Allowed : 6.54 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.53 (0.19), residues: 922 helix: -4.19 (0.12), residues: 470 sheet: -1.95 (0.65), residues: 49 loop : -3.07 (0.26), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 227 TYR 0.036 0.004 TYR A 454 PHE 0.024 0.003 PHE A 552 TRP 0.031 0.004 TRP B 417 HIS 0.009 0.004 HIS A 620 Details of bonding type rmsd covalent geometry : bond 0.01162 ( 7524) covalent geometry : angle 1.23364 (10229) SS BOND : bond 0.00530 ( 1) SS BOND : angle 1.23577 ( 2) hydrogen bonds : bond 0.31282 ( 297) hydrogen bonds : angle 10.07666 ( 852) link_BETA1-4 : bond 0.01414 ( 4) link_BETA1-4 : angle 3.79315 ( 12) link_NAG-ASN : bond 0.05936 ( 4) link_NAG-ASN : angle 11.21040 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 226 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 GLU cc_start: 0.7413 (mm-30) cc_final: 0.7077 (mm-30) REVERT: B 146 TYR cc_start: 0.8686 (t80) cc_final: 0.8121 (t80) REVERT: B 195 ARG cc_start: 0.8020 (mtm110) cc_final: 0.7690 (ptt180) REVERT: B 218 GLN cc_start: 0.8445 (tp40) cc_final: 0.8213 (tp40) REVERT: B 315 PHE cc_start: 0.8297 (t80) cc_final: 0.8064 (t80) REVERT: B 419 ARG cc_start: 0.8107 (mtp85) cc_final: 0.7342 (mmp-170) REVERT: B 440 ILE cc_start: 0.9232 (mt) cc_final: 0.9008 (mt) REVERT: B 466 LEU cc_start: 0.8515 (mp) cc_final: 0.8275 (tp) REVERT: B 478 TRP cc_start: 0.6616 (t-100) cc_final: 0.6280 (t-100) REVERT: B 501 GLN cc_start: 0.8096 (tt0) cc_final: 0.7827 (tm-30) outliers start: 23 outliers final: 5 residues processed: 234 average time/residue: 0.0965 time to fit residues: 29.5109 Evaluate side-chains 139 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 134 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 490 MET Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 131 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 7.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN A 221 HIS A 232 GLN A 268 ASN A 388 GLN A 483 GLN A 561 ASN A 620 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.122317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.095702 restraints weight = 13370.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.099364 restraints weight = 6909.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.101745 restraints weight = 4747.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.103260 restraints weight = 3794.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.104154 restraints weight = 3299.822| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7533 Z= 0.172 Angle : 0.879 12.859 10255 Z= 0.416 Chirality : 0.051 0.658 1203 Planarity : 0.006 0.043 1255 Dihedral : 12.738 89.954 1274 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.70 % Favored : 92.08 % Rotamer: Outliers : 2.88 % Allowed : 13.61 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.02 (0.22), residues: 922 helix: -2.56 (0.17), residues: 491 sheet: -1.91 (0.62), residues: 60 loop : -2.76 (0.29), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 355 TYR 0.014 0.002 TYR B 318 PHE 0.022 0.002 PHE B 95 TRP 0.021 0.002 TRP B 134 HIS 0.006 0.001 HIS B 319 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 7524) covalent geometry : angle 0.84407 (10229) SS BOND : bond 0.00179 ( 1) SS BOND : angle 0.97073 ( 2) hydrogen bonds : bond 0.06056 ( 297) hydrogen bonds : angle 5.56462 ( 852) link_BETA1-4 : bond 0.00512 ( 4) link_BETA1-4 : angle 2.43175 ( 12) link_NAG-ASN : bond 0.01053 ( 4) link_NAG-ASN : angle 6.82898 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 174 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.7777 (ttp) cc_final: 0.7568 (mmp) REVERT: A 279 LEU cc_start: 0.8051 (pp) cc_final: 0.7766 (pp) REVERT: B 120 MET cc_start: 0.9078 (tpp) cc_final: 0.8818 (tpp) REVERT: B 146 TYR cc_start: 0.8633 (t80) cc_final: 0.8106 (t80) REVERT: B 195 ARG cc_start: 0.7976 (mtm110) cc_final: 0.7703 (ptt180) REVERT: B 218 GLN cc_start: 0.8709 (tp40) cc_final: 0.8435 (tp-100) REVERT: B 254 TYR cc_start: 0.8741 (m-80) cc_final: 0.8277 (m-80) REVERT: B 352 VAL cc_start: 0.9407 (t) cc_final: 0.9069 (t) REVERT: B 466 LEU cc_start: 0.8596 (mp) cc_final: 0.8288 (tp) REVERT: B 478 TRP cc_start: 0.6524 (t-100) cc_final: 0.6254 (t-100) REVERT: B 499 LEU cc_start: 0.9120 (tt) cc_final: 0.8886 (tt) outliers start: 22 outliers final: 10 residues processed: 187 average time/residue: 0.0671 time to fit residues: 17.8857 Evaluate side-chains 151 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 141 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 467 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 51 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 44 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 76 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 317 ASN B 497 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.122311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.095113 restraints weight = 13315.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.098887 restraints weight = 6792.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.101338 restraints weight = 4635.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.102833 restraints weight = 3693.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.103833 restraints weight = 3223.197| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7533 Z= 0.144 Angle : 0.777 11.096 10255 Z= 0.366 Chirality : 0.047 0.451 1203 Planarity : 0.005 0.039 1255 Dihedral : 10.931 88.832 1267 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.27 % Favored : 92.41 % Rotamer: Outliers : 3.53 % Allowed : 15.71 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.81 (0.25), residues: 922 helix: -1.38 (0.21), residues: 488 sheet: -1.15 (0.67), residues: 54 loop : -2.54 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 272 TYR 0.016 0.002 TYR B 119 PHE 0.022 0.001 PHE B 95 TRP 0.016 0.001 TRP B 405 HIS 0.004 0.001 HIS B 367 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 7524) covalent geometry : angle 0.74501 (10229) SS BOND : bond 0.00168 ( 1) SS BOND : angle 0.66283 ( 2) hydrogen bonds : bond 0.04949 ( 297) hydrogen bonds : angle 5.07096 ( 852) link_BETA1-4 : bond 0.00748 ( 4) link_BETA1-4 : angle 2.55135 ( 12) link_NAG-ASN : bond 0.00835 ( 4) link_NAG-ASN : angle 6.05194 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 151 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.7815 (ttp) cc_final: 0.7587 (mmp) REVERT: A 534 GLU cc_start: 0.6960 (mm-30) cc_final: 0.6356 (mt-10) REVERT: B 146 TYR cc_start: 0.8637 (t80) cc_final: 0.8086 (t80) REVERT: B 195 ARG cc_start: 0.7955 (mtm110) cc_final: 0.7647 (ptt180) REVERT: B 218 GLN cc_start: 0.8776 (tp40) cc_final: 0.8501 (tp-100) REVERT: B 248 TYR cc_start: 0.8489 (m-10) cc_final: 0.8281 (m-10) REVERT: B 254 TYR cc_start: 0.8762 (m-80) cc_final: 0.8295 (m-80) REVERT: B 318 TYR cc_start: 0.6876 (t80) cc_final: 0.6661 (t80) REVERT: B 352 VAL cc_start: 0.9253 (t) cc_final: 0.8307 (t) REVERT: B 356 GLU cc_start: 0.7194 (mp0) cc_final: 0.6993 (mp0) REVERT: B 466 LEU cc_start: 0.8631 (mp) cc_final: 0.8310 (tp) outliers start: 27 outliers final: 15 residues processed: 166 average time/residue: 0.0603 time to fit residues: 14.6971 Evaluate side-chains 150 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 135 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 427 ARG Chi-restraints excluded: chain B residue 467 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 27 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 83 optimal weight: 0.0020 chunk 10 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 overall best weight: 0.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 317 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.124429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.096792 restraints weight = 13656.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.100695 restraints weight = 6841.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.103237 restraints weight = 4638.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.104804 restraints weight = 3688.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.105579 restraints weight = 3209.797| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7533 Z= 0.147 Angle : 0.742 11.189 10255 Z= 0.349 Chirality : 0.046 0.420 1203 Planarity : 0.004 0.040 1255 Dihedral : 9.891 88.004 1264 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.48 % Favored : 92.30 % Rotamer: Outliers : 3.27 % Allowed : 16.49 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.25 (0.26), residues: 922 helix: -0.83 (0.22), residues: 500 sheet: -0.93 (0.66), residues: 55 loop : -2.46 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 272 TYR 0.017 0.002 TYR A 405 PHE 0.023 0.001 PHE B 95 TRP 0.016 0.001 TRP B 405 HIS 0.004 0.001 HIS B 367 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 7524) covalent geometry : angle 0.71475 (10229) SS BOND : bond 0.00130 ( 1) SS BOND : angle 0.57333 ( 2) hydrogen bonds : bond 0.04372 ( 297) hydrogen bonds : angle 4.76227 ( 852) link_BETA1-4 : bond 0.00785 ( 4) link_BETA1-4 : angle 2.48453 ( 12) link_NAG-ASN : bond 0.00598 ( 4) link_NAG-ASN : angle 5.41850 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 145 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 555 ILE cc_start: 0.9121 (OUTLIER) cc_final: 0.8873 (pt) REVERT: B 146 TYR cc_start: 0.8662 (t80) cc_final: 0.8185 (t80) REVERT: B 195 ARG cc_start: 0.7948 (mtm110) cc_final: 0.7673 (ptt180) REVERT: B 254 TYR cc_start: 0.8777 (m-80) cc_final: 0.8245 (m-80) REVERT: B 352 VAL cc_start: 0.9243 (t) cc_final: 0.8323 (t) REVERT: B 466 LEU cc_start: 0.8624 (mp) cc_final: 0.8305 (tp) REVERT: B 500 MET cc_start: 0.8678 (mtt) cc_final: 0.8442 (mtp) REVERT: B 501 GLN cc_start: 0.8619 (tm-30) cc_final: 0.7919 (tm-30) outliers start: 25 outliers final: 17 residues processed: 156 average time/residue: 0.0622 time to fit residues: 13.9380 Evaluate side-chains 156 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 138 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 467 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.2874 > 50: distance: 36 - 37: 4.516 distance: 36 - 39: 12.176 distance: 37 - 38: 11.421 distance: 37 - 41: 8.691 distance: 39 - 40: 9.718 distance: 41 - 42: 11.160 distance: 42 - 43: 5.582 distance: 42 - 45: 9.823 distance: 43 - 44: 7.726 distance: 43 - 49: 7.166 distance: 45 - 46: 6.883 distance: 46 - 47: 3.836 distance: 46 - 48: 10.615 distance: 49 - 50: 9.588 distance: 50 - 51: 8.759 distance: 50 - 53: 6.238 distance: 51 - 52: 5.774 distance: 51 - 57: 4.712 distance: 53 - 54: 4.295 distance: 54 - 55: 9.369 distance: 57 - 58: 25.896 distance: 57 - 63: 28.759 distance: 58 - 59: 21.067 distance: 58 - 61: 32.116 distance: 59 - 60: 7.469 distance: 59 - 64: 7.427 distance: 61 - 62: 23.161 distance: 62 - 63: 26.178 distance: 64 - 65: 9.054 distance: 65 - 66: 8.438 distance: 65 - 68: 16.311 distance: 66 - 67: 11.392 distance: 66 - 69: 4.610 distance: 69 - 70: 4.969 distance: 70 - 71: 3.698 distance: 70 - 73: 9.896 distance: 71 - 72: 27.196 distance: 71 - 75: 19.001 distance: 73 - 74: 12.425 distance: 76 - 77: 15.798 distance: 77 - 78: 11.987 distance: 77 - 80: 17.626 distance: 80 - 81: 11.931 distance: 81 - 82: 30.527 distance: 81 - 84: 23.201 distance: 82 - 83: 27.120 distance: 82 - 86: 33.923 distance: 84 - 85: 8.690 distance: 86 - 87: 19.780 distance: 87 - 88: 30.255 distance: 87 - 90: 24.595 distance: 88 - 89: 23.113 distance: 88 - 94: 21.175 distance: 90 - 91: 17.295 distance: 91 - 92: 11.459 distance: 91 - 93: 21.520 distance: 94 - 95: 15.844 distance: 94 - 100: 21.158 distance: 95 - 96: 11.662 distance: 95 - 98: 21.498 distance: 96 - 97: 19.554 distance: 96 - 101: 4.403 distance: 98 - 99: 21.277 distance: 99 - 100: 25.511