Starting phenix.real_space_refine on Thu Jul 2 12:38:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7t54_25694/07_2026/7t54_25694.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t54_25694/07_2026/7t54_25694.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7t54_25694/07_2026/7t54_25694.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7t54_25694/07_2026/7t54_25694.cif" model { file = "/net/cci-nas-00/data/ceres_data/7t54_25694/07_2026/7t54_25694.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t54_25694/07_2026/7t54_25694.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7t54_25694/07_2026/7t54_25694.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t54_25694/07_2026/7t54_25694.map" } resolution = 4.5 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= 0.001 sd= 0.034 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 6 5.49 5 S 20 5.16 5 C 5310 2.51 5 N 1570 2.21 5 O 1646 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8552 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 708, 4245 Classifications: {'peptide': 708} Incomplete info: {'truncation_to_alanine': 386} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 694} Chain breaks: 1 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 1336 Unresolved non-hydrogen angles: 1697 Unresolved non-hydrogen dihedrals: 1098 Unresolved non-hydrogen chiralities: 144 Planarities with less than four sites: {'TYR:plan': 15, 'ARG:plan': 12, 'GLN:plan1': 12, 'ASP:plan': 33, 'GLU:plan': 19, 'ASN:plan1': 22, 'HIS:plan': 5, 'PHE:plan': 22, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 629 Chain: "B" Number of atoms: 4245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 708, 4245 Classifications: {'peptide': 708} Incomplete info: {'truncation_to_alanine': 386} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 694} Chain breaks: 1 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 1336 Unresolved non-hydrogen angles: 1697 Unresolved non-hydrogen dihedrals: 1098 Unresolved non-hydrogen chiralities: 144 Planarities with less than four sites: {'TYR:plan': 15, 'ARG:plan': 12, 'GLN:plan1': 12, 'ASP:plan': 33, 'GLU:plan': 19, 'ASN:plan1': 22, 'HIS:plan': 5, 'PHE:plan': 22, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 629 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.79, per 1000 atoms: 0.21 Number of scatterers: 8552 At special positions: 0 Unit cell: (128.75, 87.55, 135.96, 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 20 16.00 P 6 15.00 O 1646 8.00 N 1570 7.00 C 5310 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: 0.69 Conformation dependent library (CDL) restraints added in 384.6 milliseconds 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2628 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 11 sheets defined 62.7% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 21 through 33 Processing helix chain 'A' and resid 38 through 47 removed outlier: 4.059A pdb=" N ILE A 42 " --> pdb=" O SER A 38 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLY A 47 " --> pdb=" O ARG A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 66 removed outlier: 3.592A pdb=" N LEU A 58 " --> pdb=" O ASN A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 96 No H-bonds generated for 'chain 'A' and resid 94 through 96' Processing helix chain 'A' and resid 124 through 132 removed outlier: 3.784A pdb=" N CYS A 129 " --> pdb=" O MET A 125 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N SER A 130 " --> pdb=" O ASP A 126 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N TRP A 132 " --> pdb=" O PHE A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 163 Processing helix chain 'A' and resid 165 through 197 Processing helix chain 'A' and resid 202 through 250 removed outlier: 3.509A pdb=" N SER A 248 " --> pdb=" O MET A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 261 removed outlier: 3.636A pdb=" N PHE A 258 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 272 removed outlier: 4.337A pdb=" N ARG A 269 " --> pdb=" O GLU A 265 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE A 270 " --> pdb=" O ILE A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 305 removed outlier: 3.934A pdb=" N ILE A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN A 278 " --> pdb=" O SER A 274 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE A 299 " --> pdb=" O VAL A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 326 removed outlier: 3.864A pdb=" N PHE A 326 " --> pdb=" O ILE A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 354 removed outlier: 3.912A pdb=" N ILE A 330 " --> pdb=" O PHE A 326 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N GLN A 331 " --> pdb=" O ASN A 327 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN A 332 " --> pdb=" O LYS A 328 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLN A 336 " --> pdb=" O ASN A 332 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU A 350 " --> pdb=" O SER A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 361 removed outlier: 3.604A pdb=" N PHE A 361 " --> pdb=" O THR A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 418 removed outlier: 3.845A pdb=" N THR A 371 " --> pdb=" O THR A 367 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR A 389 " --> pdb=" O GLU A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 446 Proline residue: A 438 - end of helix Processing helix chain 'A' and resid 448 through 463 removed outlier: 3.762A pdb=" N VAL A 454 " --> pdb=" O GLN A 450 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLU A 461 " --> pdb=" O ASN A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 533 removed outlier: 3.811A pdb=" N LEU A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 553 Processing helix chain 'A' and resid 554 through 561 Processing helix chain 'A' and resid 576 through 582 Processing helix chain 'A' and resid 588 through 599 removed outlier: 3.584A pdb=" N ILE A 592 " --> pdb=" O ASP A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 608 removed outlier: 4.251A pdb=" N LYS A 607 " --> pdb=" O ASP A 603 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU A 608 " --> pdb=" O PHE A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 639 removed outlier: 3.673A pdb=" N LYS A 639 " --> pdb=" O ARG A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 669 removed outlier: 3.812A pdb=" N HIS A 660 " --> pdb=" O ILE A 656 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N ALA A 664 " --> pdb=" O HIS A 660 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU A 669 " --> pdb=" O ILE A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 711 removed outlier: 3.579A pdb=" N LYS A 711 " --> pdb=" O LEU A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 722 Processing helix chain 'B' and resid 20 through 34 removed outlier: 4.050A pdb=" N ALA B 24 " --> pdb=" O ASP B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 47 removed outlier: 3.611A pdb=" N ILE B 42 " --> pdb=" O SER B 38 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY B 47 " --> pdb=" O ARG B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 66 removed outlier: 3.648A pdb=" N LEU B 58 " --> pdb=" O ASN B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 96 No H-bonds generated for 'chain 'B' and resid 94 through 96' Processing helix chain 'B' and resid 124 through 132 removed outlier: 3.926A pdb=" N TRP B 132 " --> pdb=" O PHE B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 163 Processing helix chain 'B' and resid 165 through 197 Processing helix chain 'B' and resid 202 through 252 removed outlier: 3.574A pdb=" N LEU B 206 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR B 226 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 261 removed outlier: 3.866A pdb=" N PHE B 258 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 272 removed outlier: 4.271A pdb=" N ARG B 269 " --> pdb=" O GLU B 265 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE B 270 " --> pdb=" O ILE B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 305 removed outlier: 3.712A pdb=" N ILE B 276 " --> pdb=" O ASP B 272 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN B 278 " --> pdb=" O SER B 274 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU B 285 " --> pdb=" O SER B 281 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE B 299 " --> pdb=" O VAL B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 354 removed outlier: 4.679A pdb=" N LYS B 328 " --> pdb=" O THR B 324 " (cutoff:3.500A) Proline residue: B 329 - end of helix removed outlier: 3.728A pdb=" N ASN B 332 " --> pdb=" O LYS B 328 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLN B 336 " --> pdb=" O ASN B 332 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU B 339 " --> pdb=" O ARG B 335 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS B 343 " --> pdb=" O GLU B 339 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU B 350 " --> pdb=" O SER B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 361 Processing helix chain 'B' and resid 363 through 418 removed outlier: 3.508A pdb=" N SER B 382 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TYR B 389 " --> pdb=" O GLU B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 446 Proline residue: B 438 - end of helix Processing helix chain 'B' and resid 448 through 460 removed outlier: 3.691A pdb=" N VAL B 454 " --> pdb=" O GLN B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 470 removed outlier: 4.186A pdb=" N GLU B 470 " --> pdb=" O ALA B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 533 removed outlier: 3.825A pdb=" N LEU B 532 " --> pdb=" O LEU B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 553 Processing helix chain 'B' and resid 554 through 561 Processing helix chain 'B' and resid 576 through 582 Processing helix chain 'B' and resid 588 through 599 removed outlier: 3.546A pdb=" N ILE B 592 " --> pdb=" O ASP B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 607 removed outlier: 4.320A pdb=" N LYS B 607 " --> pdb=" O ASP B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 639 removed outlier: 3.592A pdb=" N LYS B 639 " --> pdb=" O ARG B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 657 Processing helix chain 'B' and resid 658 through 669 removed outlier: 4.985A pdb=" N ALA B 664 " --> pdb=" O HIS B 660 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU B 669 " --> pdb=" O ILE B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 711 removed outlier: 3.565A pdb=" N LYS B 711 " --> pdb=" O LEU B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 722 Processing sheet with id=AA1, first strand: chain 'A' and resid 67 through 68 Processing sheet with id=AA2, first strand: chain 'A' and resid 71 through 72 removed outlier: 3.951A pdb=" N ILE A 88 " --> pdb=" O VAL A 137 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 111 through 115 Processing sheet with id=AA4, first strand: chain 'A' and resid 502 through 505 removed outlier: 4.066A pdb=" N ASN A 504 " --> pdb=" O VAL A 491 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL A 491 " --> pdb=" O ASN A 504 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL A 491 " --> pdb=" O LYS A 540 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LYS A 540 " --> pdb=" O VAL A 491 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 643 through 646 removed outlier: 6.609A pdb=" N LEU A 644 " --> pdb=" O ILE A 675 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ILE A 677 " --> pdb=" O LEU A 644 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU A 646 " --> pdb=" O ILE A 677 " (cutoff:3.500A) removed outlier: 8.729A pdb=" N TYR A 691 " --> pdb=" O THR A 514 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ALA A 516 " --> pdb=" O TYR A 691 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N LEU A 693 " --> pdb=" O ALA A 516 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N VAL A 518 " --> pdb=" O LEU A 693 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE A 690 " --> pdb=" O SER A 701 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N SER A 701 " --> pdb=" O ILE A 690 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N LEU A 692 " --> pdb=" O VAL A 699 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 574 through 575 removed outlier: 3.688A pdb=" N GLY A 574 " --> pdb=" O LEU A 616 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 71 through 72 removed outlier: 3.899A pdb=" N ILE B 88 " --> pdb=" O VAL B 137 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 111 through 113 removed outlier: 4.072A pdb=" N ILE B 111 " --> pdb=" O TYR B 123 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYR B 123 " --> pdb=" O ILE B 111 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL B 113 " --> pdb=" O VAL B 121 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 502 through 505 removed outlier: 4.063A pdb=" N ASN B 504 " --> pdb=" O VAL B 491 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL B 491 " --> pdb=" O ASN B 504 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL B 491 " --> pdb=" O LYS B 540 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LYS B 540 " --> pdb=" O VAL B 491 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 643 through 646 removed outlier: 8.724A pdb=" N TYR B 691 " --> pdb=" O THR B 514 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ALA B 516 " --> pdb=" O TYR B 691 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N LEU B 693 " --> pdb=" O ALA B 516 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N VAL B 518 " --> pdb=" O LEU B 693 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE B 690 " --> pdb=" O SER B 701 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N SER B 701 " --> pdb=" O ILE B 690 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N LEU B 692 " --> pdb=" O VAL B 699 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 574 through 575 655 hydrogen bonds defined for protein. 1908 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: 1.10 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3042 1.34 - 1.46: 748 1.46 - 1.58: 4780 1.58 - 1.69: 12 1.69 - 1.81: 36 Bond restraints: 8618 Sorted by residual: bond pdb=" N ILE B 656 " pdb=" CA ILE B 656 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.85e+00 bond pdb=" N ILE A 656 " pdb=" CA ILE A 656 " ideal model delta sigma weight residual 1.461 1.495 -0.035 1.19e-02 7.06e+03 8.48e+00 bond pdb=" N VAL A 250 " pdb=" CA VAL A 250 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.25e-02 6.40e+03 7.12e+00 bond pdb=" N LEU A 653 " pdb=" CA LEU A 653 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.22e-02 6.72e+03 6.53e+00 bond pdb=" N SER A 655 " pdb=" CA SER A 655 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.19e-02 7.06e+03 6.41e+00 ... (remaining 8613 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 11545 2.01 - 4.03: 245 4.03 - 6.04: 20 6.04 - 8.06: 8 8.06 - 10.07: 2 Bond angle restraints: 11820 Sorted by residual: angle pdb=" N PHE B 478 " pdb=" CA PHE B 478 " pdb=" C PHE B 478 " ideal model delta sigma weight residual 111.36 121.43 -10.07 1.09e+00 8.42e-01 8.53e+01 angle pdb=" N ASP B 477 " pdb=" CA ASP B 477 " pdb=" C ASP B 477 " ideal model delta sigma weight residual 109.07 118.60 -9.53 1.61e+00 3.86e-01 3.51e+01 angle pdb=" C ASP B 654 " pdb=" CA ASP B 654 " pdb=" CB ASP B 654 " ideal model delta sigma weight residual 117.23 111.55 5.68 1.36e+00 5.41e-01 1.74e+01 angle pdb=" C GLU B 648 " pdb=" CA GLU B 648 " pdb=" CB GLU B 648 " ideal model delta sigma weight residual 116.54 112.00 4.54 1.15e+00 7.56e-01 1.56e+01 angle pdb=" C GLU A 44 " pdb=" N MET A 45 " pdb=" CA MET A 45 " ideal model delta sigma weight residual 122.38 115.67 6.71 1.81e+00 3.05e-01 1.37e+01 ... (remaining 11815 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.13: 4781 16.13 - 32.26: 215 32.26 - 48.40: 39 48.40 - 64.53: 9 64.53 - 80.66: 2 Dihedral angle restraints: 5046 sinusoidal: 986 harmonic: 4060 Sorted by residual: dihedral pdb=" N SER B 481 " pdb=" C SER B 481 " pdb=" CA SER B 481 " pdb=" CB SER B 481 " ideal model delta harmonic sigma weight residual 122.80 133.61 -10.81 0 2.50e+00 1.60e-01 1.87e+01 dihedral pdb=" C SER B 481 " pdb=" N SER B 481 " pdb=" CA SER B 481 " pdb=" CB SER B 481 " ideal model delta harmonic sigma weight residual -122.60 -132.85 10.25 0 2.50e+00 1.60e-01 1.68e+01 dihedral pdb=" CA GLU B 339 " pdb=" C GLU B 339 " pdb=" N ASP B 340 " pdb=" CA ASP B 340 " ideal model delta harmonic sigma weight residual 180.00 163.06 16.94 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 5043 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1381 0.081 - 0.162: 123 0.162 - 0.242: 4 0.242 - 0.323: 1 0.323 - 0.404: 1 Chirality restraints: 1510 Sorted by residual: chirality pdb=" CA SER B 481 " pdb=" N SER B 481 " pdb=" C SER B 481 " pdb=" CB SER B 481 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.08e+00 chirality pdb=" CA PHE B 478 " pdb=" N PHE B 478 " pdb=" C PHE B 478 " pdb=" CB PHE B 478 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CA ASP B 477 " pdb=" N ASP B 477 " pdb=" C ASP B 477 " pdb=" CB ASP B 477 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 1507 not shown) Planarity restraints: 1578 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 475 " 0.017 2.00e-02 2.50e+03 3.50e-02 1.22e+01 pdb=" C SER B 475 " -0.060 2.00e-02 2.50e+03 pdb=" O SER B 475 " 0.023 2.00e-02 2.50e+03 pdb=" N ASP B 476 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 247 " 0.009 2.00e-02 2.50e+03 9.27e-03 1.72e+00 pdb=" CG TYR B 247 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR B 247 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR B 247 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR B 247 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR B 247 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 247 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 247 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 480 " -0.006 2.00e-02 2.50e+03 1.18e-02 1.40e+00 pdb=" C ILE B 480 " 0.020 2.00e-02 2.50e+03 pdb=" O ILE B 480 " -0.008 2.00e-02 2.50e+03 pdb=" N SER B 481 " -0.007 2.00e-02 2.50e+03 ... (remaining 1575 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 49 2.64 - 3.21: 8175 3.21 - 3.77: 12763 3.77 - 4.34: 14680 4.34 - 4.90: 24423 Nonbonded interactions: 60090 Sorted by model distance: nonbonded pdb=" O ASN A 622 " pdb=" ND2 ASN A 622 " model vdw 2.078 3.120 nonbonded pdb=" OH TYR B 246 " pdb=" OE2 GLU B 461 " model vdw 2.215 3.040 nonbonded pdb=" N SER B 68 " pdb=" O GLU B 140 " model vdw 2.360 3.120 nonbonded pdb=" NH1 ARG B 269 " pdb=" OD1 ASN B 457 " model vdw 2.418 3.120 nonbonded pdb=" OE2 GLU B 339 " pdb=" ND2 ASN B 457 " model vdw 2.426 3.120 ... (remaining 60085 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' } Set refine NCS operators NCS operators will be refined. 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: 1.480 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: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.750 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6402 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 : 0.004 0.041 8618 Z= 0.248 Angle : 0.696 10.069 11820 Z= 0.464 Chirality : 0.045 0.404 1510 Planarity : 0.003 0.038 1578 Dihedral : 10.838 80.661 2418 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.40 % Favored : 95.53 % Rotamer: Outliers : 0.68 % Allowed : 0.68 % Favored : 98.63 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 7.69 % 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: 0.70 (0.23), residues: 1408 helix: 2.25 (0.19), residues: 786 sheet: -1.46 (0.43), residues: 146 loop : -2.09 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 498 TYR 0.022 0.001 TYR B 247 PHE 0.009 0.001 PHE B 270 TRP 0.001 0.000 TRP A 718 HIS 0.003 0.001 HIS B 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.25 ( 8618) covalent geometry : angle 0.69597 / 0.46 (11820) hydrogen bonds : bond 0.14559 / 11.30 ( 655) hydrogen bonds : angle 4.72044 / 3.59 ( 1908) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 54 time to evaluate : 0.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 57 average time/residue: 0.0652 time to fit residues: 4.6255 Evaluate side-chains 29 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 30.0000 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.0270 chunk 124 optimal weight: 0.0030 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 9.9990 chunk 55 optimal weight: 0.4980 overall best weight: 1.9052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.038723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.031581 restraints weight = 60641.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.031970 restraints weight = 50319.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.032209 restraints weight = 43712.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.032511 restraints weight = 39304.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.032629 restraints weight = 35951.211| |-----------------------------------------------------------------------------| r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.4309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8618 Z= 0.165 Angle : 0.590 8.219 11820 Z= 0.355 Chirality : 0.042 0.173 1510 Planarity : 0.003 0.055 1578 Dihedral : 5.042 50.750 1456 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.12 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.43 % 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: 1.12 (0.23), residues: 1408 helix: 2.47 (0.18), residues: 828 sheet: -0.70 (0.49), residues: 132 loop : -2.31 (0.25), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.002 ARG A 372 TYR 0.009 0.001 TYR A 536 PHE 0.011 0.001 PHE B 361 TRP 0.001 0.000 TRP B 718 HIS 0.005 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.17 ( 8618) covalent geometry : angle 0.58990 / 0.36 (11820) hydrogen bonds : bond 0.08426 / 6.08 ( 655) hydrogen bonds : angle 3.76379 / 2.89 ( 1908) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 536 TYR cc_start: 0.8657 (m-10) cc_final: 0.8131 (m-80) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0603 time to fit residues: 2.3336 Evaluate side-chains 25 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 10 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 89 optimal weight: 30.0000 chunk 82 optimal weight: 30.0000 chunk 51 optimal weight: 0.9990 chunk 24 optimal weight: 0.3980 chunk 128 optimal weight: 9.9990 chunk 126 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 64 optimal weight: 0.0050 chunk 48 optimal weight: 0.0000 overall best weight: 1.0802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 567 GLN B 652 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.038479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.031480 restraints weight = 60582.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.031874 restraints weight = 51005.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.032154 restraints weight = 44834.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.032293 restraints weight = 40618.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.032472 restraints weight = 38177.183| |-----------------------------------------------------------------------------| r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.4853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8618 Z= 0.111 Angle : 0.515 9.205 11820 Z= 0.300 Chirality : 0.040 0.139 1510 Planarity : 0.002 0.027 1578 Dihedral : 5.047 68.062 1456 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.12 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: 1.58 (0.23), residues: 1408 helix: 2.75 (0.18), residues: 832 sheet: 0.12 (0.55), residues: 106 loop : -2.07 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 458 TYR 0.007 0.001 TYR A 691 PHE 0.016 0.001 PHE A 257 TRP 0.003 0.001 TRP A 718 HIS 0.004 0.001 HIS B 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00197 / 0.11 ( 8618) covalent geometry : angle 0.51524 / 0.30 (11820) hydrogen bonds : bond 0.04911 / 3.62 ( 655) hydrogen bonds : angle 3.37572 / 2.59 ( 1908) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 MET cc_start: 0.8876 (tpt) cc_final: 0.8672 (tpp) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0571 time to fit residues: 2.1384 Evaluate side-chains 25 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 62 optimal weight: 0.9990 chunk 23 optimal weight: 8.9990 chunk 31 optimal weight: 0.0270 chunk 106 optimal weight: 1.9990 chunk 40 optimal weight: 20.0000 chunk 127 optimal weight: 9.9990 chunk 132 optimal weight: 0.7980 chunk 116 optimal weight: 8.9990 chunk 138 optimal weight: 0.0020 chunk 134 optimal weight: 30.0000 chunk 45 optimal weight: 7.9990 overall best weight: 0.7650 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 652 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.038550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.031329 restraints weight = 59530.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.031690 restraints weight = 50746.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.031916 restraints weight = 44840.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.032154 restraints weight = 40907.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.032154 restraints weight = 38005.650| |-----------------------------------------------------------------------------| r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.5092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8618 Z= 0.096 Angle : 0.480 7.589 11820 Z= 0.282 Chirality : 0.040 0.137 1510 Planarity : 0.002 0.022 1578 Dihedral : 5.078 69.286 1456 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.69 % Favored : 96.02 % Rotamer: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: 1.72 (0.24), residues: 1408 helix: 2.80 (0.18), residues: 836 sheet: 0.24 (0.54), residues: 106 loop : -1.96 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 559 TYR 0.009 0.001 TYR B 536 PHE 0.008 0.001 PHE B 257 TRP 0.002 0.000 TRP A 718 HIS 0.003 0.001 HIS B 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00176 / 0.10 ( 8618) covalent geometry : angle 0.48017 / 0.28 (11820) hydrogen bonds : bond 0.03642 / 2.73 ( 655) hydrogen bonds : angle 3.22967 / 2.46 ( 1908) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.101 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0623 time to fit residues: 2.4941 Evaluate side-chains 23 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 4.9990 chunk 48 optimal weight: 0.2980 chunk 68 optimal weight: 0.9990 chunk 79 optimal weight: 30.0000 chunk 53 optimal weight: 9.9990 chunk 57 optimal weight: 9.9990 chunk 128 optimal weight: 20.0000 chunk 92 optimal weight: 0.8980 chunk 60 optimal weight: 0.0000 chunk 11 optimal weight: 20.0000 chunk 77 optimal weight: 10.0000 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 652 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.037755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.030944 restraints weight = 61350.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.031269 restraints weight = 51254.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.031611 restraints weight = 45111.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.031823 restraints weight = 40353.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.031823 restraints weight = 37335.131| |-----------------------------------------------------------------------------| r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.5517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 8618 Z= 0.102 Angle : 0.487 6.398 11820 Z= 0.287 Chirality : 0.040 0.125 1510 Planarity : 0.002 0.020 1578 Dihedral : 4.966 69.026 1456 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.55 % Favored : 96.16 % Rotamer: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: 1.88 (0.24), residues: 1408 helix: 2.95 (0.18), residues: 836 sheet: 0.37 (0.55), residues: 106 loop : -1.94 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 489 TYR 0.005 0.001 TYR A 247 PHE 0.012 0.001 PHE A 535 TRP 0.003 0.001 TRP A 718 HIS 0.002 0.001 HIS B 602 Details of bonding type rmsd/Z covalent geometry : bond 0.00183 / 0.10 ( 8618) covalent geometry : angle 0.48728 / 0.29 (11820) hydrogen bonds : bond 0.03562 / 2.68 ( 655) hydrogen bonds : angle 3.26976 / 2.48 ( 1908) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.127 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 255 MET cc_start: 0.8911 (mtt) cc_final: 0.8689 (ptp) REVERT: A 598 MET cc_start: 0.8833 (tpp) cc_final: 0.8410 (tpt) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0337 time to fit residues: 1.2993 Evaluate side-chains 22 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 48 optimal weight: 0.8980 chunk 126 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 86 optimal weight: 20.0000 chunk 54 optimal weight: 0.5980 chunk 28 optimal weight: 40.0000 chunk 96 optimal weight: 7.9990 chunk 116 optimal weight: 5.9990 chunk 37 optimal weight: 0.0070 chunk 120 optimal weight: 6.9990 chunk 66 optimal weight: 0.0000 overall best weight: 0.4602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 652 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.038249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.031149 restraints weight = 61753.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.031554 restraints weight = 51412.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.031872 restraints weight = 44777.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.032042 restraints weight = 40248.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.032244 restraints weight = 37326.877| |-----------------------------------------------------------------------------| r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.5699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8618 Z= 0.093 Angle : 0.470 6.382 11820 Z= 0.276 Chirality : 0.040 0.127 1510 Planarity : 0.002 0.020 1578 Dihedral : 4.869 69.193 1456 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.55 % Favored : 96.16 % Rotamer: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: 1.92 (0.24), residues: 1408 helix: 2.91 (0.18), residues: 842 sheet: 0.46 (0.56), residues: 106 loop : -1.87 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 489 TYR 0.007 0.001 TYR A 247 PHE 0.007 0.001 PHE B 535 TRP 0.001 0.000 TRP B 718 HIS 0.001 0.000 HIS B 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00160 / 0.09 ( 8618) covalent geometry : angle 0.47020 / 0.28 (11820) hydrogen bonds : bond 0.03404 / 2.54 ( 655) hydrogen bonds : angle 3.22827 / 2.46 ( 1908) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 598 MET cc_start: 0.8762 (tpp) cc_final: 0.8301 (tpt) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.0514 time to fit residues: 2.0398 Evaluate side-chains 21 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 46 optimal weight: 40.0000 chunk 0 optimal weight: 50.0000 chunk 20 optimal weight: 20.0000 chunk 19 optimal weight: 20.0000 chunk 128 optimal weight: 0.0050 chunk 54 optimal weight: 5.9990 chunk 45 optimal weight: 20.0000 chunk 82 optimal weight: 40.0000 chunk 4 optimal weight: 30.0000 chunk 26 optimal weight: 8.9990 chunk 60 optimal weight: 0.2980 overall best weight: 7.0602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 567 GLN ** A 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.034625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.028326 restraints weight = 67547.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.028663 restraints weight = 60164.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.028842 restraints weight = 52888.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.029101 restraints weight = 44477.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.029199 restraints weight = 39984.852| |-----------------------------------------------------------------------------| r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.6870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 8618 Z= 0.285 Angle : 0.685 13.930 11820 Z= 0.401 Chirality : 0.042 0.138 1510 Planarity : 0.004 0.037 1578 Dihedral : 6.038 66.721 1456 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.26 % Favored : 94.46 % Rotamer: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: 1.64 (0.23), residues: 1408 helix: 2.83 (0.18), residues: 822 sheet: -0.30 (0.53), residues: 106 loop : -1.89 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 489 TYR 0.015 0.002 TYR A 612 PHE 0.024 0.003 PHE A 493 TRP 0.010 0.002 TRP A 718 HIS 0.007 0.002 HIS B 602 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.29 ( 8618) covalent geometry : angle 0.68499 / 0.40 (11820) hydrogen bonds : bond 0.04440 / 3.33 ( 655) hydrogen bonds : angle 4.24754 / 3.23 ( 1908) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.137 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0378 time to fit residues: 1.2712 Evaluate side-chains 19 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 67 optimal weight: 10.9990 chunk 91 optimal weight: 9.9990 chunk 128 optimal weight: 8.9990 chunk 96 optimal weight: 8.9990 chunk 68 optimal weight: 6.9990 chunk 77 optimal weight: 9.9990 chunk 108 optimal weight: 20.0000 chunk 87 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 28 optimal weight: 30.0000 chunk 61 optimal weight: 5.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.033406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.027502 restraints weight = 70403.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.027883 restraints weight = 59814.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.028025 restraints weight = 52149.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.028122 restraints weight = 44021.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.028190 restraints weight = 42342.013| |-----------------------------------------------------------------------------| r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.8263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 8618 Z= 0.297 Angle : 0.722 10.823 11820 Z= 0.428 Chirality : 0.042 0.148 1510 Planarity : 0.004 0.029 1578 Dihedral : 6.508 65.176 1456 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.96 % Favored : 92.90 % Rotamer: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: 0.96 (0.23), residues: 1408 helix: 2.17 (0.18), residues: 842 sheet: -1.01 (0.52), residues: 106 loop : -1.97 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 489 TYR 0.016 0.002 TYR B 495 PHE 0.034 0.004 PHE A 493 TRP 0.009 0.001 TRP A 718 HIS 0.004 0.002 HIS A 548 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.30 ( 8618) covalent geometry : angle 0.72189 / 0.43 (11820) hydrogen bonds : bond 0.04739 / 3.54 ( 655) hydrogen bonds : angle 4.62963 / 3.51 ( 1908) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.098 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 271 MET cc_start: 0.9831 (mmp) cc_final: 0.9550 (mmm) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0298 time to fit residues: 1.1137 Evaluate side-chains 19 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 46 optimal weight: 50.0000 chunk 67 optimal weight: 8.9990 chunk 39 optimal weight: 10.0000 chunk 108 optimal weight: 0.0970 chunk 88 optimal weight: 20.0000 chunk 51 optimal weight: 8.9990 chunk 89 optimal weight: 30.0000 chunk 98 optimal weight: 40.0000 chunk 68 optimal weight: 6.9990 chunk 128 optimal weight: 0.1980 chunk 84 optimal weight: 40.0000 overall best weight: 5.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.033690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.027676 restraints weight = 68292.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.027726 restraints weight = 56566.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.027922 restraints weight = 55353.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.028051 restraints weight = 47621.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.028225 restraints weight = 45304.423| |-----------------------------------------------------------------------------| r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.8328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8618 Z= 0.198 Angle : 0.595 6.523 11820 Z= 0.354 Chirality : 0.041 0.129 1510 Planarity : 0.003 0.023 1578 Dihedral : 6.060 65.664 1456 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.11 % Favored : 93.61 % Rotamer: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: 1.30 (0.24), residues: 1408 helix: 2.47 (0.18), residues: 846 sheet: -1.17 (0.49), residues: 108 loop : -1.87 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 489 TYR 0.012 0.001 TYR A 612 PHE 0.022 0.002 PHE B 535 TRP 0.006 0.001 TRP A 718 HIS 0.002 0.001 HIS B 548 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.20 ( 8618) covalent geometry : angle 0.59530 / 0.35 (11820) hydrogen bonds : bond 0.04200 / 3.14 ( 655) hydrogen bonds : angle 4.11621 / 3.13 ( 1908) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.115 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 271 MET cc_start: 0.9826 (mmp) cc_final: 0.9577 (mmm) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0362 time to fit residues: 1.2892 Evaluate side-chains 20 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 128 optimal weight: 5.9990 chunk 108 optimal weight: 8.9990 chunk 107 optimal weight: 0.0370 chunk 35 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 104 optimal weight: 7.9990 chunk 59 optimal weight: 7.9990 chunk 98 optimal weight: 30.0000 chunk 79 optimal weight: 30.0000 chunk 129 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 overall best weight: 2.9864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.033926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.027801 restraints weight = 66527.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.027972 restraints weight = 54421.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.028209 restraints weight = 49316.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.028274 restraints weight = 42962.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.028311 restraints weight = 41809.581| |-----------------------------------------------------------------------------| r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.8366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8618 Z= 0.137 Angle : 0.580 14.914 11820 Z= 0.327 Chirality : 0.040 0.125 1510 Planarity : 0.002 0.024 1578 Dihedral : 5.562 64.668 1456 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.11 % Favored : 94.60 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: 1.80 (0.24), residues: 1408 helix: 2.91 (0.18), residues: 848 sheet: -1.22 (0.49), residues: 110 loop : -1.71 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 489 TYR 0.013 0.001 TYR A 389 PHE 0.017 0.001 PHE B 535 TRP 0.003 0.001 TRP A 718 HIS 0.001 0.001 HIS B 548 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.14 ( 8618) covalent geometry : angle 0.58007 / 0.33 (11820) hydrogen bonds : bond 0.03877 / 2.90 ( 655) hydrogen bonds : angle 3.69864 / 2.81 ( 1908) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.096 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 271 MET cc_start: 0.9831 (mmp) cc_final: 0.9588 (mmm) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0255 time to fit residues: 0.9447 Evaluate side-chains 19 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 40 optimal weight: 20.0000 chunk 104 optimal weight: 5.9990 chunk 116 optimal weight: 30.0000 chunk 77 optimal weight: 10.0000 chunk 91 optimal weight: 0.7980 chunk 41 optimal weight: 20.0000 chunk 105 optimal weight: 0.9990 chunk 137 optimal weight: 10.0000 chunk 27 optimal weight: 30.0000 chunk 68 optimal weight: 0.2980 chunk 88 optimal weight: 20.0000 overall best weight: 3.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.033772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.027835 restraints weight = 67245.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.027834 restraints weight = 53881.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.028020 restraints weight = 53170.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.028088 restraints weight = 46420.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.028131 restraints weight = 45017.904| |-----------------------------------------------------------------------------| r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.8518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8618 Z= 0.153 Angle : 0.547 7.008 11820 Z= 0.323 Chirality : 0.040 0.124 1510 Planarity : 0.003 0.026 1578 Dihedral : 5.467 64.081 1456 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.82 % Favored : 93.89 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: 1.90 (0.24), residues: 1408 helix: 2.99 (0.18), residues: 852 sheet: -1.38 (0.48), residues: 112 loop : -1.64 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 489 TYR 0.013 0.001 TYR A 612 PHE 0.017 0.002 PHE A 535 TRP 0.005 0.001 TRP B 718 HIS 0.002 0.001 HIS B 548 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.15 ( 8618) covalent geometry : angle 0.54674 / 0.32 (11820) hydrogen bonds : bond 0.03814 / 2.85 ( 655) hydrogen bonds : angle 3.69916 / 2.81 ( 1908) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 835.66 seconds wall clock time: 15 minutes 6.54 seconds (906.54 seconds total)