Starting phenix.real_space_refine on Tue Mar 3 21:05:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t54_25694/03_2026/7t54_25694.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t54_25694/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7t54_25694/03_2026/7t54_25694.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t54_25694/03_2026/7t54_25694.map" model { file = "/net/cci-nas-00/data/ceres_data/7t54_25694/03_2026/7t54_25694.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t54_25694/03_2026/7t54_25694.cif" } 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-5986/lib/python3.9/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: 2.31, per 1000 atoms: 0.27 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: 0.66 Conformation dependent library (CDL) restraints added in 477.2 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: 0.34 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: 1.47 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: 4793 16.13 - 32.26: 231 32.26 - 48.40: 58 48.40 - 64.53: 24 64.53 - 80.66: 2 Dihedral angle restraints: 5108 sinusoidal: 1048 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 5105 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: 0.02 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: 1.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.580 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 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 : 12.143 80.661 2480 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 covalent geometry : bond 0.00369 ( 8618) covalent geometry : angle 0.69597 (11820) hydrogen bonds : bond 0.14559 ( 655) hydrogen bonds : angle 4.72044 ( 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 : 0.128 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: 0.0781 time to fit residues: 5.5568 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 : 0.158 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** B 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3024 r_free = 0.3024 target = 0.038707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.031564 restraints weight = 60464.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.031946 restraints weight = 50500.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.032205 restraints weight = 44039.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.032461 restraints weight = 39800.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.032622 restraints weight = 36466.038| |-----------------------------------------------------------------------------| r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.4327 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= 0.160 Angle : 0.596 9.295 11820 Z= 0.358 Chirality : 0.041 0.147 1510 Planarity : 0.003 0.048 1578 Dihedral : 7.334 61.792 1518 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.97 % Favored : 94.89 % 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 : 0.58 % 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: 1.14 (0.23), residues: 1408 helix: 2.50 (0.18), residues: 828 sheet: -0.66 (0.49), residues: 132 loop : -2.35 (0.25), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG A 372 TYR 0.009 0.001 TYR B 536 PHE 0.006 0.001 PHE B 535 TRP 0.001 0.000 TRP A 718 HIS 0.004 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 8618) covalent geometry : angle 0.59647 (11820) hydrogen bonds : bond 0.07069 ( 655) hydrogen bonds : angle 3.73729 ( 1908) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 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 : 0.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 536 TYR cc_start: 0.8661 (m-10) cc_final: 0.8154 (m-80) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0796 time to fit residues: 3.1069 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 : 0.156 ------------------------------------------------------------------------------- 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: 10.9990 chunk 44 optimal weight: 1.9990 chunk 89 optimal weight: 30.0000 chunk 82 optimal weight: 30.0000 chunk 51 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 128 optimal weight: 0.4980 chunk 126 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 64 optimal weight: 30.0000 chunk 48 optimal weight: 0.0170 overall best weight: 0.8420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 567 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.040812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.034801 restraints weight = 63479.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.035338 restraints weight = 48254.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.035735 restraints weight = 39139.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.036040 restraints weight = 33256.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.036232 restraints weight = 29193.456| |-----------------------------------------------------------------------------| r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.4861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8618 Z= 0.108 Angle : 0.507 8.167 11820 Z= 0.306 Chirality : 0.040 0.134 1510 Planarity : 0.002 0.042 1578 Dihedral : 6.449 54.243 1518 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.69 % Favored : 95.17 % Rotamer: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % 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: 0.86 (0.23), residues: 1408 helix: 2.11 (0.18), residues: 832 sheet: 0.02 (0.54), residues: 106 loop : -2.29 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 635 TYR 0.007 0.001 TYR B 225 PHE 0.009 0.001 PHE B 535 TRP 0.002 0.000 TRP B 718 HIS 0.002 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00188 ( 8618) covalent geometry : angle 0.50670 (11820) hydrogen bonds : bond 0.03428 ( 655) hydrogen bonds : angle 3.34764 ( 1908) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 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 : 0.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 MET cc_start: 0.8872 (tpt) cc_final: 0.8647 (tpp) REVERT: A 536 TYR cc_start: 0.8306 (m-10) cc_final: 0.7873 (m-10) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0819 time to fit residues: 3.1682 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 : 0.148 ------------------------------------------------------------------------------- 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: 8.9990 chunk 23 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 40 optimal weight: 20.0000 chunk 127 optimal weight: 8.9990 chunk 132 optimal weight: 8.9990 chunk 116 optimal weight: 6.9990 chunk 138 optimal weight: 3.9990 chunk 134 optimal weight: 30.0000 chunk 45 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.037364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.031796 restraints weight = 68118.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.032462 restraints weight = 55548.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.032687 restraints weight = 42850.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.032936 restraints weight = 35014.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.033088 restraints weight = 30972.137| |-----------------------------------------------------------------------------| r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.5919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8618 Z= 0.188 Angle : 0.554 6.478 11820 Z= 0.334 Chirality : 0.040 0.138 1510 Planarity : 0.003 0.039 1578 Dihedral : 7.129 59.225 1518 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.82 % Favored : 94.03 % 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 : 0.14 % 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: 0.52 (0.23), residues: 1408 helix: 1.93 (0.18), residues: 826 sheet: -0.75 (0.50), residues: 102 loop : -2.38 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 498 TYR 0.009 0.001 TYR A 612 PHE 0.017 0.002 PHE B 257 TRP 0.007 0.001 TRP B 718 HIS 0.005 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 8618) covalent geometry : angle 0.55429 (11820) hydrogen bonds : bond 0.03688 ( 655) hydrogen bonds : angle 3.87442 ( 1908) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 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 : 0.186 Fit side-chains revert: symmetry clash REVERT: B 255 MET cc_start: 0.8877 (tpt) cc_final: 0.8673 (tpp) REVERT: B 271 MET cc_start: 0.9727 (tpp) cc_final: 0.9483 (mmm) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.0909 time to fit residues: 3.1834 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 : 0.189 ------------------------------------------------------------------------------- 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: 8.9990 chunk 48 optimal weight: 8.9990 chunk 68 optimal weight: 0.4980 chunk 79 optimal weight: 30.0000 chunk 53 optimal weight: 5.9990 chunk 57 optimal weight: 9.9990 chunk 128 optimal weight: 0.0470 chunk 92 optimal weight: 0.7980 chunk 60 optimal weight: 0.0980 chunk 11 optimal weight: 20.0000 chunk 77 optimal weight: 9.9990 overall best weight: 1.4880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.037839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.032184 restraints weight = 68498.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.032913 restraints weight = 54817.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.033159 restraints weight = 41396.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.033546 restraints weight = 33189.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.033617 restraints weight = 28822.884| |-----------------------------------------------------------------------------| r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.6155 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= 0.108 Angle : 0.480 5.935 11820 Z= 0.283 Chirality : 0.039 0.126 1510 Planarity : 0.002 0.026 1578 Dihedral : 6.307 55.917 1518 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % 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 : 0.14 % 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: 0.73 (0.23), residues: 1408 helix: 1.96 (0.18), residues: 838 sheet: -0.59 (0.51), residues: 106 loop : -2.14 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 489 TYR 0.010 0.001 TYR B 389 PHE 0.010 0.001 PHE A 257 TRP 0.002 0.000 TRP B 718 HIS 0.002 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00191 ( 8618) covalent geometry : angle 0.48030 (11820) hydrogen bonds : bond 0.03322 ( 655) hydrogen bonds : angle 3.41973 ( 1908) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** 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 : 0.155 Fit side-chains REVERT: A 255 MET cc_start: 0.8872 (tpt) cc_final: 0.8578 (tpp) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0473 time to fit residues: 1.8219 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 : 0.159 ------------------------------------------------------------------------------- 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: 6.9990 chunk 126 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 chunk 86 optimal weight: 20.0000 chunk 54 optimal weight: 0.5980 chunk 28 optimal weight: 20.0000 chunk 96 optimal weight: 4.9990 chunk 116 optimal weight: 50.0000 chunk 37 optimal weight: 0.5980 chunk 120 optimal weight: 6.9990 chunk 66 optimal weight: 0.0980 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.038641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.032789 restraints weight = 69228.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.033414 restraints weight = 53619.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.033760 restraints weight = 41865.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.033962 restraints weight = 33728.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.034081 restraints weight = 31990.635| |-----------------------------------------------------------------------------| r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.6448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 8618 Z= 0.098 Angle : 0.457 4.718 11820 Z= 0.270 Chirality : 0.039 0.127 1510 Planarity : 0.002 0.025 1578 Dihedral : 5.972 55.138 1518 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.00 % 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: 0.77 (0.23), residues: 1408 helix: 1.96 (0.18), residues: 850 sheet: -0.58 (0.52), residues: 106 loop : -2.15 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 458 TYR 0.006 0.001 TYR B 612 PHE 0.011 0.001 PHE B 257 TRP 0.002 0.001 TRP B 718 HIS 0.001 0.000 HIS A 548 Details of bonding type rmsd covalent geometry : bond 0.00174 ( 8618) covalent geometry : angle 0.45738 (11820) hydrogen bonds : bond 0.03093 ( 655) hydrogen bonds : angle 3.25545 ( 1908) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 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 : 0.166 Fit side-chains revert: symmetry clash REVERT: A 255 MET cc_start: 0.8834 (tpt) cc_final: 0.8545 (tpp) REVERT: A 271 MET cc_start: 0.9688 (mmp) cc_final: 0.9404 (mmm) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0493 time to fit residues: 1.8327 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 : 0.157 ------------------------------------------------------------------------------- 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: 10.0000 chunk 19 optimal weight: 30.0000 chunk 128 optimal weight: 0.5980 chunk 54 optimal weight: 0.0870 chunk 45 optimal weight: 10.0000 chunk 82 optimal weight: 50.0000 chunk 4 optimal weight: 30.0000 chunk 26 optimal weight: 20.0000 chunk 60 optimal weight: 2.9990 overall best weight: 4.7368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.2958 r_free = 0.2958 target = 0.036061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.030435 restraints weight = 70021.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.030905 restraints weight = 57617.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.031160 restraints weight = 46652.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.031281 restraints weight = 38510.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.031380 restraints weight = 36466.972| |-----------------------------------------------------------------------------| r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.7180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8618 Z= 0.184 Angle : 0.550 7.995 11820 Z= 0.324 Chirality : 0.040 0.125 1510 Planarity : 0.003 0.032 1578 Dihedral : 6.898 59.183 1518 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Cbeta Deviations : 0.00 % 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: 0.55 (0.23), residues: 1408 helix: 1.75 (0.17), residues: 844 sheet: -1.10 (0.49), residues: 108 loop : -2.00 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 372 TYR 0.012 0.001 TYR A 612 PHE 0.017 0.002 PHE B 257 TRP 0.007 0.001 TRP A 718 HIS 0.004 0.002 HIS B 602 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 8618) covalent geometry : angle 0.54972 (11820) hydrogen bonds : bond 0.03423 ( 655) hydrogen bonds : angle 3.81109 ( 1908) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 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 : 0.169 Fit side-chains revert: symmetry clash REVERT: A 271 MET cc_start: 0.9785 (mmp) cc_final: 0.9533 (mmm) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0486 time to fit residues: 1.6277 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 : 0.114 ------------------------------------------------------------------------------- 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: 8.9990 chunk 91 optimal weight: 9.9990 chunk 128 optimal weight: 0.2980 chunk 96 optimal weight: 6.9990 chunk 68 optimal weight: 0.0050 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: 0.0040 overall best weight: 3.2610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.034346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.028021 restraints weight = 66903.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.028259 restraints weight = 60128.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.028479 restraints weight = 55077.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.028539 restraints weight = 45334.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.028575 restraints weight = 43648.771| |-----------------------------------------------------------------------------| r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.7391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8618 Z= 0.139 Angle : 0.501 7.500 11820 Z= 0.294 Chirality : 0.039 0.124 1510 Planarity : 0.002 0.021 1578 Dihedral : 6.413 58.305 1518 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Cbeta Deviations : 0.00 % 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: 0.84 (0.23), residues: 1408 helix: 2.13 (0.18), residues: 838 sheet: -1.10 (0.50), residues: 108 loop : -2.12 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 498 TYR 0.009 0.001 TYR B 612 PHE 0.014 0.002 PHE A 257 TRP 0.003 0.001 TRP B 718 HIS 0.002 0.001 HIS A 548 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 8618) covalent geometry : angle 0.50081 (11820) hydrogen bonds : bond 0.03213 ( 655) hydrogen bonds : angle 3.47003 ( 1908) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 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 : 0.157 Fit side-chains revert: symmetry clash REVERT: A 271 MET cc_start: 0.9802 (mmp) cc_final: 0.9568 (mmm) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0523 time to fit residues: 1.7521 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 : 0.157 ------------------------------------------------------------------------------- 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: 10.0000 chunk 39 optimal weight: 10.0000 chunk 108 optimal weight: 20.0000 chunk 88 optimal weight: 20.0000 chunk 51 optimal weight: 7.9990 chunk 89 optimal weight: 30.0000 chunk 98 optimal weight: 30.0000 chunk 68 optimal weight: 0.4980 chunk 128 optimal weight: 2.9990 chunk 84 optimal weight: 40.0000 overall best weight: 6.2992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 HIS ** 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 = 0.2876 r_free = 0.2876 target = 0.033455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.027597 restraints weight = 70348.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.027688 restraints weight = 63307.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.027848 restraints weight = 60917.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.028101 restraints weight = 51865.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.028179 restraints weight = 47573.216| |-----------------------------------------------------------------------------| r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.8251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8618 Z= 0.243 Angle : 0.627 8.508 11820 Z= 0.371 Chirality : 0.041 0.131 1510 Planarity : 0.004 0.038 1578 Dihedral : 7.629 56.892 1518 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % 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 : 0.00 % 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: -0.07 (0.22), residues: 1408 helix: 1.40 (0.17), residues: 842 sheet: -1.73 (0.49), residues: 106 loop : -2.45 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 489 TYR 0.015 0.002 TYR A 612 PHE 0.029 0.003 PHE B 604 TRP 0.007 0.001 TRP A 718 HIS 0.006 0.002 HIS B 602 Details of bonding type rmsd covalent geometry : bond 0.00444 ( 8618) covalent geometry : angle 0.62704 (11820) hydrogen bonds : bond 0.03953 ( 655) hydrogen bonds : angle 4.32589 ( 1908) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 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 : 0.153 Fit side-chains REVERT: A 271 MET cc_start: 0.9856 (mmp) cc_final: 0.9633 (mmm) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0371 time to fit residues: 1.3405 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 : 0.159 ------------------------------------------------------------------------------- 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: 0.0050 chunk 108 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 104 optimal weight: 8.9990 chunk 59 optimal weight: 0.0670 chunk 98 optimal weight: 30.0000 chunk 79 optimal weight: 30.0000 chunk 129 optimal weight: 0.0670 chunk 75 optimal weight: 2.9990 overall best weight: 0.3670 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.034386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.027961 restraints weight = 65355.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.028142 restraints weight = 55497.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.028351 restraints weight = 50836.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.028455 restraints weight = 44461.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.028510 restraints weight = 42790.767| |-----------------------------------------------------------------------------| r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.8052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8618 Z= 0.110 Angle : 0.541 9.307 11820 Z= 0.302 Chirality : 0.040 0.133 1510 Planarity : 0.002 0.022 1578 Dihedral : 6.322 58.126 1518 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % 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: 0.40 (0.22), residues: 1408 helix: 1.78 (0.17), residues: 854 sheet: -0.32 (0.61), residues: 74 loop : -2.59 (0.25), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 498 TYR 0.012 0.001 TYR A 389 PHE 0.016 0.001 PHE A 535 TRP 0.002 0.001 TRP B 718 HIS 0.001 0.000 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00203 ( 8618) covalent geometry : angle 0.54139 (11820) hydrogen bonds : bond 0.03393 ( 655) hydrogen bonds : angle 3.50999 ( 1908) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 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 : 0.162 Fit side-chains REVERT: A 271 MET cc_start: 0.9808 (mmp) cc_final: 0.9546 (mmm) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0317 time to fit residues: 1.2176 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 : 0.093 ------------------------------------------------------------------------------- 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: 30.0000 chunk 104 optimal weight: 7.9990 chunk 116 optimal weight: 40.0000 chunk 77 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 41 optimal weight: 30.0000 chunk 105 optimal weight: 0.9980 chunk 137 optimal weight: 10.0000 chunk 27 optimal weight: 30.0000 chunk 68 optimal weight: 0.1980 chunk 88 optimal weight: 40.0000 overall best weight: 5.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 602 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 = 0.2865 r_free = 0.2865 target = 0.033317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.027198 restraints weight = 68000.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.027485 restraints weight = 61135.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.027669 restraints weight = 54875.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.027745 restraints weight = 45768.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.027802 restraints weight = 44253.923| |-----------------------------------------------------------------------------| r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.8501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8618 Z= 0.218 Angle : 0.573 5.705 11820 Z= 0.344 Chirality : 0.040 0.124 1510 Planarity : 0.003 0.032 1578 Dihedral : 7.019 56.482 1518 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % 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 : 0.00 % 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: 0.23 (0.23), residues: 1408 helix: 1.73 (0.18), residues: 844 sheet: -1.74 (0.49), residues: 106 loop : -2.51 (0.26), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 458 TYR 0.014 0.001 TYR B 612 PHE 0.019 0.003 PHE A 493 TRP 0.007 0.001 TRP A 718 HIS 0.004 0.002 HIS B 602 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 8618) covalent geometry : angle 0.57322 (11820) hydrogen bonds : bond 0.03550 ( 655) hydrogen bonds : angle 4.00196 ( 1908) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 991.52 seconds wall clock time: 17 minutes 49.63 seconds (1069.63 seconds total)