Starting phenix.real_space_refine on Wed Feb 4 04:09:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n66_49050/02_2026/9n66_49050.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n66_49050/02_2026/9n66_49050.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9n66_49050/02_2026/9n66_49050.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n66_49050/02_2026/9n66_49050.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9n66_49050/02_2026/9n66_49050.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n66_49050/02_2026/9n66_49050.map" } resolution = 3.2 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= 0.018 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 39 5.16 5 C 5418 2.51 5 N 1475 2.21 5 O 1598 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8537 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 556, 4280 Classifications: {'peptide': 556} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 533} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 4197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4197 Classifications: {'peptide': 537} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 516} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 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: 2.37, per 1000 atoms: 0.28 Number of scatterers: 8537 At special positions: 0 Unit cell: (77.4, 89.44, 140.18, 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 39 16.00 P 5 15.00 Mg 2 11.99 O 1598 8.00 N 1475 7.00 C 5418 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: 0.72 Conformation dependent library (CDL) restraints added in 355.3 milliseconds 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2014 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 5 sheets defined 68.0% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 173 through 179 removed outlier: 3.541A pdb=" N GLY A 178 " --> pdb=" O ARG A 175 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N CYS A 179 " --> pdb=" O LEU A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 183 through 203 Processing helix chain 'A' and resid 229 through 271 removed outlier: 3.560A pdb=" N VAL A 240 " --> pdb=" O ILE A 236 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU A 241 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU A 242 " --> pdb=" O SER A 238 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 279 Processing helix chain 'A' and resid 280 through 319 removed outlier: 3.739A pdb=" N ASP A 291 " --> pdb=" O ARG A 287 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N THR A 292 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER A 293 " --> pdb=" O THR A 289 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N SER A 304 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LEU A 305 " --> pdb=" O GLU A 301 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE A 319 " --> pdb=" O CYS A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 334 Processing helix chain 'A' and resid 335 through 338 Processing helix chain 'A' and resid 339 through 345 Processing helix chain 'A' and resid 345 through 373 removed outlier: 3.886A pdb=" N TYR A 349 " --> pdb=" O VAL A 345 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLN A 350 " --> pdb=" O GLY A 346 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLN A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 380 Processing helix chain 'A' and resid 382 through 402 removed outlier: 3.665A pdb=" N LYS A 393 " --> pdb=" O LYS A 389 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU A 400 " --> pdb=" O GLU A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 436 removed outlier: 3.829A pdb=" N TYR A 408 " --> pdb=" O GLU A 404 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER A 416 " --> pdb=" O SER A 412 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER A 418 " --> pdb=" O THR A 414 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLY A 419 " --> pdb=" O THR A 415 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE A 426 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU A 427 " --> pdb=" O LYS A 423 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN A 432 " --> pdb=" O TYR A 428 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR A 435 " --> pdb=" O GLY A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 442 removed outlier: 4.525A pdb=" N GLY A 442 " --> pdb=" O VAL A 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 439 through 442' Processing helix chain 'A' and resid 443 through 463 removed outlier: 3.678A pdb=" N PHE A 447 " --> pdb=" O ASN A 443 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU A 449 " --> pdb=" O VAL A 445 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TYR A 450 " --> pdb=" O THR A 446 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL A 460 " --> pdb=" O GLN A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 475 Processing helix chain 'A' and resid 475 through 483 removed outlier: 3.805A pdb=" N ASP A 483 " --> pdb=" O PHE A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 552 Processing helix chain 'A' and resid 570 through 572 No H-bonds generated for 'chain 'A' and resid 570 through 572' Processing helix chain 'A' and resid 573 through 580 removed outlier: 3.695A pdb=" N HIS A 578 " --> pdb=" O HIS A 574 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG A 579 " --> pdb=" O ARG A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 600 removed outlier: 3.641A pdb=" N ALA A 600 " --> pdb=" O GLN A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 619 Processing helix chain 'A' and resid 621 through 626 Processing helix chain 'A' and resid 630 through 634 removed outlier: 3.704A pdb=" N THR A 634 " --> pdb=" O GLY A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 641 removed outlier: 3.593A pdb=" N SER A 641 " --> pdb=" O GLU A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 658 removed outlier: 3.595A pdb=" N ALA A 652 " --> pdb=" O ARG A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 687 Processing helix chain 'A' and resid 688 through 694 removed outlier: 4.345A pdb=" N TYR A 692 " --> pdb=" O PRO A 689 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG A 694 " --> pdb=" O ARG A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 707 Processing helix chain 'A' and resid 725 through 733 Processing helix chain 'A' and resid 734 through 741 Processing helix chain 'B' and resid 139 through 145 Processing helix chain 'B' and resid 148 through 178 removed outlier: 3.627A pdb=" N ALA B 154 " --> pdb=" O PRO B 150 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU B 161 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA B 162 " --> pdb=" O PHE B 158 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU B 168 " --> pdb=" O LEU B 164 " (cutoff:3.500A) Proline residue: B 170 - end of helix Processing helix chain 'B' and resid 187 through 234 removed outlier: 3.728A pdb=" N SER B 191 " --> pdb=" O HIS B 187 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER B 206 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N MET B 218 " --> pdb=" O PHE B 214 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER B 219 " --> pdb=" O THR B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 244 removed outlier: 3.784A pdb=" N GLU B 243 " --> pdb=" O GLY B 239 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR B 244 " --> pdb=" O PHE B 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 239 through 244' Processing helix chain 'B' and resid 245 through 262 removed outlier: 3.504A pdb=" N ASP B 256 " --> pdb=" O ARG B 252 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N THR B 257 " --> pdb=" O LEU B 253 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N THR B 258 " --> pdb=" O SER B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 282 removed outlier: 4.578A pdb=" N ASN B 269 " --> pdb=" O PRO B 265 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N VAL B 270 " --> pdb=" O LEU B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 299 Processing helix chain 'B' and resid 303 through 338 removed outlier: 3.558A pdb=" N GLY B 338 " --> pdb=" O GLU B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 345 removed outlier: 3.620A pdb=" N PHE B 345 " --> pdb=" O THR B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 394 removed outlier: 3.826A pdb=" N CYS B 394 " --> pdb=" O LEU B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 412 removed outlier: 3.965A pdb=" N PHE B 412 " --> pdb=" O SER B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 423 removed outlier: 3.586A pdb=" N SER B 421 " --> pdb=" O GLU B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 438 removed outlier: 3.620A pdb=" N VAL B 427 " --> pdb=" O VAL B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 448 removed outlier: 3.970A pdb=" N PHE B 444 " --> pdb=" O ALA B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 517 Processing helix chain 'B' and resid 535 through 537 No H-bonds generated for 'chain 'B' and resid 535 through 537' Processing helix chain 'B' and resid 538 through 545 removed outlier: 3.660A pdb=" N HIS B 543 " --> pdb=" O HIS B 539 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N SER B 544 " --> pdb=" O CYS B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 565 Processing helix chain 'B' and resid 572 through 583 Processing helix chain 'B' and resid 585 through 590 removed outlier: 3.544A pdb=" N ILE B 589 " --> pdb=" O ALA B 585 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN B 590 " --> pdb=" O ASP B 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 585 through 590' Processing helix chain 'B' and resid 594 through 597 Processing helix chain 'B' and resid 601 through 605 Processing helix chain 'B' and resid 608 through 622 Processing helix chain 'B' and resid 638 through 645 Processing helix chain 'B' and resid 662 through 666 Processing sheet with id=AA1, first strand: chain 'A' and resid 527 through 528 Processing sheet with id=AA2, first strand: chain 'A' and resid 581 through 583 removed outlier: 6.412A pdb=" N LEU A 664 " --> pdb=" O LEU A 697 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ILE A 699 " --> pdb=" O LEU A 664 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU A 666 " --> pdb=" O ILE A 699 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL A 533 " --> pdb=" O HIS A 711 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N LEU A 713 " --> pdb=" O VAL A 533 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ALA A 535 " --> pdb=" O LEU A 713 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N LEU A 715 " --> pdb=" O ALA A 535 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N VAL A 537 " --> pdb=" O LEU A 715 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE A 712 " --> pdb=" O GLY A 723 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLY A 723 " --> pdb=" O ILE A 712 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N PHE A 714 " --> pdb=" O ARG A 721 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA A 719 " --> pdb=" O GLU A 716 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 486 through 493 removed outlier: 7.046A pdb=" N LYS B 487 " --> pdb=" O SER B 474 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N SER B 474 " --> pdb=" O LYS B 487 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N LEU B 489 " --> pdb=" O ASP B 472 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL B 473 " --> pdb=" O GLY B 524 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N GLY B 524 " --> pdb=" O VAL B 473 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 546 through 549 removed outlier: 6.509A pdb=" N VAL B 498 " --> pdb=" O GLN B 671 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N LEU B 673 " --> pdb=" O VAL B 498 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ALA B 500 " --> pdb=" O LEU B 673 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N LEU B 675 " --> pdb=" O ALA B 500 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL B 502 " --> pdb=" O LEU B 675 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 558 through 559 502 hydrogen bonds defined for protein. 1452 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: 1.40 Time building geometry restraints manager: 0.98 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: 1661 1.33 - 1.45: 2014 1.45 - 1.57: 4946 1.57 - 1.69: 8 1.69 - 1.81: 64 Bond restraints: 8693 Sorted by residual: bond pdb=" CA LEU B 292 " pdb=" C LEU B 292 " ideal model delta sigma weight residual 1.524 1.465 0.059 1.29e-02 6.01e+03 2.08e+01 bond pdb=" C ILE A 204 " pdb=" N PRO A 205 " ideal model delta sigma weight residual 1.335 1.372 -0.037 9.40e-03 1.13e+04 1.51e+01 bond pdb=" CA SER B 635 " pdb=" CB SER B 635 " ideal model delta sigma weight residual 1.533 1.482 0.051 1.58e-02 4.01e+03 1.05e+01 bond pdb=" CA LYS A 606 " pdb=" C LYS A 606 " ideal model delta sigma weight residual 1.524 1.492 0.032 1.26e-02 6.30e+03 6.45e+00 bond pdb=" C LEU B 292 " pdb=" O LEU B 292 " ideal model delta sigma weight residual 1.237 1.206 0.030 1.19e-02 7.06e+03 6.43e+00 ... (remaining 8688 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 11541 1.99 - 3.98: 173 3.98 - 5.97: 61 5.97 - 7.96: 13 7.96 - 9.96: 10 Bond angle restraints: 11798 Sorted by residual: angle pdb=" N LEU B 292 " pdb=" CA LEU B 292 " pdb=" C LEU B 292 " ideal model delta sigma weight residual 111.36 104.78 6.58 1.09e+00 8.42e-01 3.64e+01 angle pdb=" N THR A 604 " pdb=" CA THR A 604 " pdb=" C THR A 604 " ideal model delta sigma weight residual 110.23 103.14 7.09 1.45e+00 4.76e-01 2.39e+01 angle pdb=" C LYS A 606 " pdb=" N PRO A 607 " pdb=" CA PRO A 607 " ideal model delta sigma weight residual 120.03 115.55 4.48 9.90e-01 1.02e+00 2.05e+01 angle pdb=" N LEU B 294 " pdb=" CA LEU B 294 " pdb=" C LEU B 294 " ideal model delta sigma weight residual 111.11 105.94 5.17 1.20e+00 6.94e-01 1.86e+01 angle pdb=" N PRO B 290 " pdb=" CA PRO B 290 " pdb=" C PRO B 290 " ideal model delta sigma weight residual 113.53 107.84 5.69 1.39e+00 5.18e-01 1.68e+01 ... (remaining 11793 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 4479 17.69 - 35.38: 554 35.38 - 53.07: 156 53.07 - 70.76: 29 70.76 - 88.44: 14 Dihedral angle restraints: 5232 sinusoidal: 2095 harmonic: 3137 Sorted by residual: dihedral pdb=" C4' ADP B 701 " pdb=" C5' ADP B 701 " pdb=" O5' ADP B 701 " pdb=" PA ADP B 701 " ideal model delta sinusoidal sigma weight residual 180.00 91.56 88.44 1 2.00e+01 2.50e-03 2.33e+01 dihedral pdb=" CA MET B 218 " pdb=" C MET B 218 " pdb=" N SER B 219 " pdb=" CA SER B 219 " ideal model delta harmonic sigma weight residual 180.00 160.01 19.99 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CG ARG A 487 " pdb=" CD ARG A 487 " pdb=" NE ARG A 487 " pdb=" CZ ARG A 487 " ideal model delta sinusoidal sigma weight residual 90.00 38.34 51.66 2 1.50e+01 4.44e-03 1.31e+01 ... (remaining 5229 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1204 0.061 - 0.122: 152 0.122 - 0.183: 10 0.183 - 0.244: 0 0.244 - 0.305: 1 Chirality restraints: 1367 Sorted by residual: chirality pdb=" CB ILE A 204 " pdb=" CA ILE A 204 " pdb=" CG1 ILE A 204 " pdb=" CG2 ILE A 204 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CG LEU B 161 " pdb=" CB LEU B 161 " pdb=" CD1 LEU B 161 " pdb=" CD2 LEU B 161 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 6.96e-01 chirality pdb=" CA ASP A 517 " pdb=" N ASP A 517 " pdb=" C ASP A 517 " pdb=" CB ASP A 517 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.47e-01 ... (remaining 1364 not shown) Planarity restraints: 1506 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 157 " 0.012 2.00e-02 2.50e+03 1.71e-02 5.11e+00 pdb=" CG PHE B 157 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE B 157 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE B 157 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE B 157 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 157 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 157 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 487 " -0.164 9.50e-02 1.11e+02 7.41e-02 4.10e+00 pdb=" NE ARG A 487 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG A 487 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A 487 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 487 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 447 " 0.011 2.00e-02 2.50e+03 1.50e-02 3.96e+00 pdb=" CG PHE A 447 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE A 447 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 447 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE A 447 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 447 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 447 " -0.000 2.00e-02 2.50e+03 ... (remaining 1503 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 41 2.56 - 3.14: 6442 3.14 - 3.73: 12890 3.73 - 4.31: 16836 4.31 - 4.90: 28742 Nonbonded interactions: 64951 Sorted by model distance: nonbonded pdb=" O2B ADP B 701 " pdb="MG MG B 702 " model vdw 1.974 2.170 nonbonded pdb=" OG SER B 510 " pdb="MG MG B 702 " model vdw 2.022 2.170 nonbonded pdb=" OE1 GLN A 586 " pdb="MG MG A 802 " model vdw 2.031 2.170 nonbonded pdb=" O3G ATP A 801 " pdb="MG MG A 802 " model vdw 2.053 2.170 nonbonded pdb=" OG SER A 545 " pdb="MG MG A 802 " model vdw 2.071 2.170 ... (remaining 64946 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: 5.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.970 Find NCS groups from input model: 0.060 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 8693 Z= 0.186 Angle : 0.730 9.955 11798 Z= 0.380 Chirality : 0.041 0.305 1367 Planarity : 0.005 0.074 1506 Dihedral : 17.307 88.444 3218 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.22 % Allowed : 21.24 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.22), residues: 1083 helix: -1.72 (0.16), residues: 661 sheet: 1.85 (0.65), residues: 76 loop : -1.03 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 487 TYR 0.010 0.001 TYR B 216 PHE 0.039 0.002 PHE B 157 TRP 0.024 0.001 TRP A 737 HIS 0.002 0.001 HIS B 314 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 8693) covalent geometry : angle 0.73046 (11798) hydrogen bonds : bond 0.27464 ( 502) hydrogen bonds : angle 7.55421 ( 1452) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 152 time to evaluate : 0.530 Fit side-chains REVERT: A 408 TYR cc_start: 0.8100 (t80) cc_final: 0.7882 (t80) outliers start: 2 outliers final: 1 residues processed: 153 average time/residue: 0.0931 time to fit residues: 20.0159 Evaluate side-chains 130 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 129 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 0.3980 chunk 106 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 ASN B 242 GLN B 424 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.106600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.082079 restraints weight = 16639.262| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.78 r_work: 0.2964 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8693 Z= 0.179 Angle : 0.643 10.332 11798 Z= 0.320 Chirality : 0.042 0.252 1367 Planarity : 0.004 0.034 1506 Dihedral : 7.353 84.135 1231 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.58 % Allowed : 21.24 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.26), residues: 1083 helix: 0.95 (0.20), residues: 673 sheet: 1.77 (0.64), residues: 76 loop : -0.82 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 487 TYR 0.012 0.001 TYR B 428 PHE 0.032 0.002 PHE B 156 TRP 0.008 0.001 TRP A 737 HIS 0.004 0.001 HIS B 299 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 8693) covalent geometry : angle 0.64252 (11798) hydrogen bonds : bond 0.06663 ( 502) hydrogen bonds : angle 4.31526 ( 1452) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 131 time to evaluate : 0.356 Fit side-chains REVERT: A 329 MET cc_start: 0.7122 (ptp) cc_final: 0.6711 (tpt) outliers start: 33 outliers final: 18 residues processed: 154 average time/residue: 0.0850 time to fit residues: 18.8974 Evaluate side-chains 141 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 413 MET Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 622 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 24 optimal weight: 0.0770 chunk 31 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 GLN A 401 ASN B 242 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.108218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.083769 restraints weight = 16720.825| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.79 r_work: 0.2996 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8693 Z= 0.128 Angle : 0.560 6.891 11798 Z= 0.278 Chirality : 0.040 0.185 1367 Planarity : 0.003 0.035 1506 Dihedral : 6.958 85.700 1228 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.71 % Allowed : 20.37 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.27), residues: 1083 helix: 1.68 (0.21), residues: 670 sheet: 1.72 (0.64), residues: 76 loop : -0.77 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 487 TYR 0.020 0.001 TYR A 408 PHE 0.024 0.001 PHE B 194 TRP 0.006 0.001 TRP B 263 HIS 0.002 0.000 HIS B 543 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 8693) covalent geometry : angle 0.56028 (11798) hydrogen bonds : bond 0.05506 ( 502) hydrogen bonds : angle 3.96088 ( 1452) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 0.343 Fit side-chains REVERT: B 272 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7957 (tt) REVERT: B 615 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8653 (mp) outliers start: 25 outliers final: 11 residues processed: 140 average time/residue: 0.0778 time to fit residues: 16.0607 Evaluate side-chains 129 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 413 MET Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 615 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 4 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 GLN A 401 ASN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.107078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.082528 restraints weight = 16920.881| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.81 r_work: 0.2969 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8693 Z= 0.154 Angle : 0.583 9.746 11798 Z= 0.283 Chirality : 0.041 0.197 1367 Planarity : 0.003 0.039 1506 Dihedral : 6.873 81.509 1228 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.60 % Allowed : 21.78 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.27), residues: 1083 helix: 1.93 (0.21), residues: 670 sheet: 1.53 (0.64), residues: 76 loop : -0.72 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 487 TYR 0.020 0.001 TYR B 422 PHE 0.028 0.002 PHE B 194 TRP 0.003 0.001 TRP B 367 HIS 0.002 0.001 HIS A 726 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 8693) covalent geometry : angle 0.58314 (11798) hydrogen bonds : bond 0.05375 ( 502) hydrogen bonds : angle 3.92123 ( 1452) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.355 Fit side-chains REVERT: A 573 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7922 (tt0) REVERT: B 272 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8028 (tt) REVERT: B 320 GLU cc_start: 0.8823 (mm-30) cc_final: 0.8531 (mm-30) REVERT: B 615 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8701 (mp) outliers start: 24 outliers final: 14 residues processed: 139 average time/residue: 0.0827 time to fit residues: 16.7687 Evaluate side-chains 136 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 573 GLU Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 197 CYS Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 413 MET Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 540 CYS Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 615 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 21 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 GLN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.104401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.079903 restraints weight = 17065.699| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.80 r_work: 0.2915 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 8693 Z= 0.240 Angle : 0.646 8.794 11798 Z= 0.317 Chirality : 0.044 0.204 1367 Planarity : 0.003 0.042 1506 Dihedral : 6.947 75.531 1228 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.58 % Allowed : 21.56 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.27), residues: 1083 helix: 1.86 (0.21), residues: 673 sheet: 1.27 (0.63), residues: 76 loop : -0.86 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 487 TYR 0.023 0.001 TYR B 422 PHE 0.032 0.002 PHE B 194 TRP 0.004 0.001 TRP A 737 HIS 0.003 0.001 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00558 ( 8693) covalent geometry : angle 0.64571 (11798) hydrogen bonds : bond 0.05976 ( 502) hydrogen bonds : angle 4.13826 ( 1452) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 125 time to evaluate : 0.335 Fit side-chains REVERT: A 301 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8531 (mm-30) REVERT: A 335 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8659 (tt) REVERT: B 272 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7958 (tt) REVERT: B 615 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8724 (mp) outliers start: 33 outliers final: 24 residues processed: 146 average time/residue: 0.0803 time to fit residues: 17.2825 Evaluate side-chains 148 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain B residue 197 CYS Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 384 HIS Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 413 MET Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 540 CYS Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 589 ILE Chi-restraints excluded: chain B residue 615 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 51 optimal weight: 0.0270 chunk 13 optimal weight: 0.6980 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 GLN B 242 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.105990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.081270 restraints weight = 16660.166| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.84 r_work: 0.2967 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8693 Z= 0.127 Angle : 0.574 7.214 11798 Z= 0.278 Chirality : 0.040 0.193 1367 Planarity : 0.003 0.041 1506 Dihedral : 6.832 77.650 1228 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.82 % Allowed : 22.64 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.27), residues: 1083 helix: 2.11 (0.21), residues: 669 sheet: 1.33 (0.64), residues: 76 loop : -0.78 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 487 TYR 0.011 0.001 TYR A 309 PHE 0.017 0.001 PHE B 194 TRP 0.004 0.001 TRP A 348 HIS 0.002 0.000 HIS B 543 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 8693) covalent geometry : angle 0.57405 (11798) hydrogen bonds : bond 0.05128 ( 502) hydrogen bonds : angle 3.81369 ( 1452) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 0.370 Fit side-chains REVERT: A 301 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8521 (mm-30) REVERT: A 335 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8624 (tt) REVERT: A 573 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7857 (tt0) REVERT: B 272 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7962 (tt) REVERT: B 320 GLU cc_start: 0.8794 (mm-30) cc_final: 0.8478 (mm-30) outliers start: 26 outliers final: 13 residues processed: 145 average time/residue: 0.0804 time to fit residues: 17.1888 Evaluate side-chains 137 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 573 GLU Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 589 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 50 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 25 optimal weight: 0.0370 chunk 60 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 82 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 GLN B 416 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.107684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.083344 restraints weight = 16892.146| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.79 r_work: 0.2984 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8693 Z= 0.122 Angle : 0.576 10.862 11798 Z= 0.272 Chirality : 0.040 0.189 1367 Planarity : 0.003 0.043 1506 Dihedral : 6.675 73.916 1228 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.60 % Allowed : 23.08 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.27), residues: 1083 helix: 2.26 (0.21), residues: 669 sheet: 1.29 (0.64), residues: 76 loop : -0.73 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 487 TYR 0.024 0.001 TYR B 422 PHE 0.022 0.001 PHE A 276 TRP 0.004 0.000 TRP A 348 HIS 0.002 0.000 HIS B 543 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 8693) covalent geometry : angle 0.57625 (11798) hydrogen bonds : bond 0.04791 ( 502) hydrogen bonds : angle 3.69234 ( 1452) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.346 Fit side-chains REVERT: A 301 GLU cc_start: 0.8766 (mm-30) cc_final: 0.8532 (mm-30) REVERT: A 335 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8625 (tt) REVERT: A 573 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7893 (tt0) REVERT: B 157 PHE cc_start: 0.8639 (t80) cc_final: 0.8136 (t80) REVERT: B 272 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.7988 (tt) REVERT: B 320 GLU cc_start: 0.8797 (mm-30) cc_final: 0.8442 (mm-30) outliers start: 24 outliers final: 17 residues processed: 142 average time/residue: 0.0789 time to fit residues: 16.5048 Evaluate side-chains 140 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 573 GLU Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 384 HIS Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 589 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 73 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 67 optimal weight: 0.0050 chunk 70 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 102 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 GLN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.107196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.082693 restraints weight = 16508.593| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.86 r_work: 0.2999 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8693 Z= 0.114 Angle : 0.572 9.843 11798 Z= 0.268 Chirality : 0.040 0.186 1367 Planarity : 0.003 0.043 1506 Dihedral : 6.575 72.594 1228 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.38 % Allowed : 23.19 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.27), residues: 1083 helix: 2.36 (0.21), residues: 670 sheet: 1.28 (0.63), residues: 76 loop : -0.67 (0.35), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 487 TYR 0.011 0.001 TYR A 309 PHE 0.016 0.001 PHE B 194 TRP 0.003 0.000 TRP A 348 HIS 0.001 0.000 HIS B 543 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 8693) covalent geometry : angle 0.57208 (11798) hydrogen bonds : bond 0.04540 ( 502) hydrogen bonds : angle 3.60249 ( 1452) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.359 Fit side-chains REVERT: A 301 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8501 (mm-30) REVERT: A 335 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8618 (tt) REVERT: A 573 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7903 (tt0) REVERT: B 157 PHE cc_start: 0.8685 (t80) cc_final: 0.8213 (t80) REVERT: B 272 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7974 (tt) REVERT: B 320 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8445 (mm-30) outliers start: 22 outliers final: 18 residues processed: 138 average time/residue: 0.0762 time to fit residues: 15.5545 Evaluate side-chains 140 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 573 GLU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 384 HIS Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 589 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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: 57.9501 > 50: distance: 13 - 17: 4.052 distance: 17 - 18: 9.052 distance: 17 - 23: 22.362 distance: 18 - 19: 5.467 distance: 18 - 21: 12.048 distance: 19 - 20: 19.195 distance: 19 - 24: 23.963 distance: 21 - 22: 22.447 distance: 22 - 23: 16.695 distance: 24 - 25: 13.881 distance: 25 - 26: 17.294 distance: 25 - 28: 9.845 distance: 26 - 27: 11.810 distance: 26 - 35: 16.005 distance: 28 - 29: 11.794 distance: 29 - 30: 13.046 distance: 30 - 31: 6.827 distance: 31 - 32: 8.341 distance: 32 - 33: 6.803 distance: 32 - 34: 4.792 distance: 35 - 36: 23.160 distance: 36 - 37: 7.359 distance: 36 - 39: 14.714 distance: 37 - 38: 3.993 distance: 37 - 43: 9.032 distance: 39 - 40: 6.931 distance: 40 - 41: 27.690 distance: 40 - 42: 34.485 distance: 43 - 44: 4.926 distance: 44 - 45: 16.462 distance: 44 - 47: 31.875 distance: 45 - 46: 37.324 distance: 45 - 50: 8.056 distance: 46 - 72: 22.086 distance: 47 - 48: 12.059 distance: 47 - 49: 39.319 distance: 50 - 51: 27.957 distance: 51 - 52: 20.729 distance: 51 - 54: 6.012 distance: 52 - 53: 31.382 distance: 52 - 58: 17.105 distance: 53 - 80: 24.403 distance: 54 - 55: 4.858 distance: 55 - 56: 44.777 distance: 55 - 57: 33.918 distance: 58 - 59: 13.250 distance: 59 - 60: 9.870 distance: 59 - 62: 23.466 distance: 60 - 61: 28.777 distance: 60 - 66: 5.036 distance: 61 - 88: 46.231 distance: 62 - 63: 35.573 distance: 63 - 64: 11.975 distance: 63 - 65: 20.589 distance: 66 - 67: 13.700 distance: 67 - 68: 36.201 distance: 67 - 70: 28.130 distance: 68 - 69: 11.658 distance: 70 - 71: 16.493 distance: 72 - 73: 8.440 distance: 73 - 74: 5.151 distance: 73 - 76: 12.680 distance: 74 - 75: 16.481 distance: 74 - 80: 13.007 distance: 76 - 77: 21.658 distance: 77 - 78: 10.156 distance: 77 - 79: 10.664 distance: 80 - 81: 8.633 distance: 81 - 82: 7.107 distance: 81 - 84: 5.591 distance: 82 - 83: 12.897 distance: 82 - 88: 10.515 distance: 84 - 85: 25.035 distance: 85 - 86: 5.018 distance: 85 - 87: 7.356 distance: 88 - 89: 8.342 distance: 89 - 90: 10.049 distance: 89 - 92: 8.560 distance: 90 - 91: 5.430 distance: 90 - 98: 29.140 distance: 92 - 93: 25.076 distance: 93 - 94: 21.537 distance: 93 - 95: 30.802 distance: 94 - 96: 20.176 distance: 95 - 97: 22.689 distance: 96 - 97: 22.120