Starting phenix.real_space_refine on Thu Feb 13 05:38:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t54_25694/02_2025/7t54_25694.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t54_25694/02_2025/7t54_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_25694/02_2025/7t54_25694.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t54_25694/02_2025/7t54_25694.map" model { file = "/net/cci-nas-00/data/ceres_data/7t54_25694/02_2025/7t54_25694.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t54_25694/02_2025/7t54_25694.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLN:plan1': 12, 'HIS:plan': 5, 'TYR:plan': 15, 'ASN:plan1': 22, 'TRP:plan': 2, 'ASP:plan': 33, 'PHE:plan': 22, 'GLU:plan': 19, 'ARG:plan': 12} 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: {'GLN:plan1': 12, 'HIS:plan': 5, 'TYR:plan': 15, 'ASN:plan1': 22, 'TRP:plan': 2, 'ASP:plan': 33, 'PHE:plan': 22, 'GLU:plan': 19, 'ARG:plan': 12} 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: 5.85, per 1000 atoms: 0.68 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: 2.51 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.11 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: 2.94 Time building geometry restraints manager: 2.82 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: 0.05 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: 2.350 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 23.970 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.900 ------------------------------------------------------------------------------- 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= 0.253 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.001 0.000 TRP A 718 HIS 0.003 0.001 HIS B 249 PHE 0.009 0.001 PHE B 270 TYR 0.022 0.001 TYR B 247 ARG 0.008 0.001 ARG A 498 *********************** 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 : 0.477 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: 0.1931 time to fit residues: 13.6517 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 : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 0.4980 chunk 106 optimal weight: 9.9990 chunk 58 optimal weight: 0.0170 chunk 36 optimal weight: 10.0000 chunk 71 optimal weight: 40.0000 chunk 56 optimal weight: 0.0370 chunk 109 optimal weight: 7.9990 chunk 42 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 chunk 127 optimal weight: 0.0670 overall best weight: 0.3236 ------------------------------------------------------------------------------- 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 B 679 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.039569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.032325 restraints weight = 59210.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.032734 restraints weight = 49292.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 16)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.032994 restraints weight = 42762.730| |-----------------------------------------------------------------------------| r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.4195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8618 Z= 0.172 Angle : 0.598 8.640 11820 Z= 0.354 Chirality : 0.042 0.154 1510 Planarity : 0.003 0.053 1578 Dihedral : 7.059 56.397 1518 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.43 % Allowed : 3.84 % Favored : 95.74 % 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 : 0.43 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.23), residues: 1408 helix: 2.43 (0.18), residues: 822 sheet: -1.09 (0.44), residues: 152 loop : -2.34 (0.25), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 718 HIS 0.003 0.001 HIS B 249 PHE 0.008 0.001 PHE A 361 TYR 0.010 0.001 TYR B 536 ARG 0.005 0.001 ARG A 458 *********************** 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 33 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 536 TYR cc_start: 0.8600 (m-10) cc_final: 0.8261 (m-80) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1718 time to fit residues: 7.7568 Evaluate side-chains 26 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 137 optimal weight: 10.0000 chunk 116 optimal weight: 40.0000 chunk 118 optimal weight: 0.9980 chunk 42 optimal weight: 7.9990 chunk 27 optimal weight: 30.0000 chunk 33 optimal weight: 10.0000 chunk 132 optimal weight: 10.0000 chunk 22 optimal weight: 0.5980 chunk 29 optimal weight: 40.0000 chunk 111 optimal weight: 20.0000 chunk 121 optimal weight: 0.0030 overall best weight: 3.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 679 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.036973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.030613 restraints weight = 62624.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.031037 restraints weight = 52706.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.031315 restraints weight = 45240.902| |-----------------------------------------------------------------------------| r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.5180 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= 0.213 Angle : 0.560 6.901 11820 Z= 0.343 Chirality : 0.040 0.151 1510 Planarity : 0.003 0.034 1578 Dihedral : 7.165 46.520 1518 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.54 % Favored : 94.32 % Rotamer: Outliers : 0.46 % Allowed : 3.65 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.23), residues: 1408 helix: 2.13 (0.18), residues: 836 sheet: -0.19 (0.53), residues: 102 loop : -2.39 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 718 HIS 0.011 0.002 HIS B 679 PHE 0.017 0.002 PHE B 257 TYR 0.011 0.001 TYR B 612 ARG 0.003 0.001 ARG A 559 *********************** 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 29 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 28 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 MET cc_start: 0.9687 (tpp) cc_final: 0.9459 (mmm) REVERT: A 598 MET cc_start: 0.8843 (tpp) cc_final: 0.8532 (tpt) outliers start: 1 outliers final: 0 residues processed: 29 average time/residue: 0.2158 time to fit residues: 8.1122 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 : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 54 optimal weight: 0.2980 chunk 64 optimal weight: 0.0030 chunk 115 optimal weight: 10.0000 chunk 41 optimal weight: 20.0000 chunk 15 optimal weight: 20.0000 chunk 28 optimal weight: 30.0000 chunk 78 optimal weight: 50.0000 chunk 56 optimal weight: 7.9990 chunk 135 optimal weight: 0.0970 chunk 17 optimal weight: 30.0000 chunk 72 optimal weight: 40.0000 overall best weight: 3.6794 ------------------------------------------------------------------------------- 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 = 0.3013 r_free = 0.3013 target = 0.038064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.032333 restraints weight = 68188.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.033074 restraints weight = 55994.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.033326 restraints weight = 42408.751| |-----------------------------------------------------------------------------| r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.5946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8618 Z= 0.197 Angle : 0.496 5.519 11820 Z= 0.303 Chirality : 0.040 0.157 1510 Planarity : 0.003 0.026 1578 Dihedral : 6.692 57.416 1518 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.23), residues: 1408 helix: 2.09 (0.18), residues: 838 sheet: -0.69 (0.53), residues: 94 loop : -2.27 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 718 HIS 0.003 0.001 HIS A 249 PHE 0.016 0.002 PHE B 257 TYR 0.008 0.001 TYR A 691 ARG 0.004 0.001 ARG B 559 *********************** 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 28 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.462 Fit side-chains REVERT: A 255 MET cc_start: 0.8927 (tpt) cc_final: 0.8677 (tpp) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.2291 time to fit residues: 8.1118 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 : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 14 optimal weight: 40.0000 chunk 91 optimal weight: 9.9990 chunk 78 optimal weight: 50.0000 chunk 59 optimal weight: 9.9990 chunk 101 optimal weight: 1.9990 chunk 27 optimal weight: 20.0000 chunk 100 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 29 optimal weight: 30.0000 chunk 85 optimal weight: 30.0000 chunk 63 optimal weight: 5.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 567 GLN ** A 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 652 ASN ** 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 = 0.2900 r_free = 0.2900 target = 0.034358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.028233 restraints weight = 67957.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.028696 restraints weight = 59182.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.028789 restraints weight = 53644.788| |-----------------------------------------------------------------------------| r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.7349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8618 Z= 0.317 Angle : 0.631 6.494 11820 Z= 0.376 Chirality : 0.041 0.135 1510 Planarity : 0.003 0.024 1578 Dihedral : 7.463 58.804 1518 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % 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 : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.22), residues: 1408 helix: 1.34 (0.17), residues: 836 sheet: -1.27 (0.48), residues: 106 loop : -2.33 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 718 HIS 0.007 0.002 HIS B 602 PHE 0.024 0.003 PHE B 493 TYR 0.009 0.001 TYR A 612 ARG 0.006 0.001 ARG A 458 *********************** 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 22 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.510 Fit side-chains REVERT: A 271 MET cc_start: 0.9751 (mmp) cc_final: 0.9413 (mmp) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.1168 time to fit residues: 4.1463 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 : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 87 optimal weight: 20.0000 chunk 46 optimal weight: 30.0000 chunk 124 optimal weight: 0.9990 chunk 127 optimal weight: 10.0000 chunk 102 optimal weight: 0.9980 chunk 62 optimal weight: 0.0170 chunk 120 optimal weight: 2.9990 chunk 89 optimal weight: 30.0000 chunk 27 optimal weight: 30.0000 chunk 35 optimal weight: 0.9990 chunk 76 optimal weight: 20.0000 overall best weight: 1.2024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 457 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 = 0.2911 r_free = 0.2911 target = 0.034874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.028468 restraints weight = 65436.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.028802 restraints weight = 57902.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.028945 restraints weight = 52972.125| |-----------------------------------------------------------------------------| r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.7204 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= 0.130 Angle : 0.480 5.595 11820 Z= 0.280 Chirality : 0.040 0.125 1510 Planarity : 0.002 0.025 1578 Dihedral : 6.327 56.701 1518 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % 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 : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.23), residues: 1408 helix: 2.00 (0.17), residues: 842 sheet: -1.01 (0.50), residues: 106 loop : -2.19 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 718 HIS 0.002 0.001 HIS A 679 PHE 0.014 0.001 PHE A 257 TYR 0.006 0.001 TYR B 612 ARG 0.002 0.001 ARG B 489 *********************** 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 22 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.484 Fit side-chains REVERT: A 255 MET cc_start: 0.8990 (tpt) cc_final: 0.8763 (tpp) REVERT: A 271 MET cc_start: 0.9746 (mmp) cc_final: 0.9478 (mmm) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0920 time to fit residues: 3.5033 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 : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 42 optimal weight: 0.0010 chunk 82 optimal weight: 30.0000 chunk 95 optimal weight: 4.9990 chunk 99 optimal weight: 50.0000 chunk 13 optimal weight: 0.0770 chunk 94 optimal weight: 0.6980 chunk 64 optimal weight: 0.4980 chunk 29 optimal weight: 50.0000 chunk 122 optimal weight: 5.9990 chunk 96 optimal weight: 20.0000 chunk 19 optimal weight: 30.0000 overall best weight: 1.2546 ------------------------------------------------------------------------------- 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 = 0.2926 r_free = 0.2926 target = 0.035232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.028572 restraints weight = 65320.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.028870 restraints weight = 58892.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.029108 restraints weight = 51819.015| |-----------------------------------------------------------------------------| r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.7399 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= 0.120 Angle : 0.447 4.569 11820 Z= 0.266 Chirality : 0.039 0.128 1510 Planarity : 0.002 0.022 1578 Dihedral : 6.076 57.976 1518 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.23), residues: 1408 helix: 2.08 (0.17), residues: 844 sheet: -1.18 (0.50), residues: 106 loop : -2.09 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 718 HIS 0.001 0.000 HIS B 679 PHE 0.013 0.001 PHE A 257 TYR 0.011 0.001 TYR A 389 ARG 0.002 0.000 ARG B 489 *********************** 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 23 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.564 Fit side-chains revert: symmetry clash REVERT: A 255 MET cc_start: 0.8918 (tpt) cc_final: 0.8668 (tpp) REVERT: A 271 MET cc_start: 0.9774 (mmp) cc_final: 0.9505 (mmm) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1007 time to fit residues: 3.9595 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 : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 113 optimal weight: 0.0470 chunk 6 optimal weight: 20.0000 chunk 8 optimal weight: 50.0000 chunk 107 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 chunk 48 optimal weight: 0.0970 chunk 68 optimal weight: 0.0020 chunk 109 optimal weight: 0.9980 chunk 45 optimal weight: 20.0000 chunk 23 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 overall best weight: 0.3684 ------------------------------------------------------------------------------- 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 = 0.2938 r_free = 0.2938 target = 0.035852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.029163 restraints weight = 62935.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.029572 restraints weight = 56279.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.029760 restraints weight = 50861.200| |-----------------------------------------------------------------------------| r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.7471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8618 Z= 0.120 Angle : 0.465 6.685 11820 Z= 0.267 Chirality : 0.039 0.129 1510 Planarity : 0.002 0.022 1578 Dihedral : 5.870 52.014 1518 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % 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 : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.23), residues: 1408 helix: 1.90 (0.17), residues: 846 sheet: -1.14 (0.51), residues: 106 loop : -1.89 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 718 HIS 0.001 0.000 HIS B 679 PHE 0.014 0.001 PHE B 604 TYR 0.010 0.001 TYR A 389 ARG 0.002 0.000 ARG B 489 *********************** 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 24 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: A 255 MET cc_start: 0.8908 (tpt) cc_final: 0.8639 (tpp) REVERT: A 271 MET cc_start: 0.9772 (mmp) cc_final: 0.9495 (mmm) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0824 time to fit residues: 3.4208 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 : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 139 optimal weight: 30.0000 chunk 87 optimal weight: 20.0000 chunk 93 optimal weight: 3.9990 chunk 110 optimal weight: 20.0000 chunk 36 optimal weight: 1.9990 chunk 66 optimal weight: 0.0070 chunk 75 optimal weight: 5.9990 chunk 18 optimal weight: 20.0000 chunk 42 optimal weight: 4.9990 chunk 71 optimal weight: 0.0030 chunk 6 optimal weight: 30.0000 overall best weight: 2.2014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.035284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.028771 restraints weight = 63926.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.028900 restraints weight = 58399.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.029107 restraints weight = 53953.109| |-----------------------------------------------------------------------------| r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.7644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8618 Z= 0.150 Angle : 0.497 7.461 11820 Z= 0.284 Chirality : 0.039 0.125 1510 Planarity : 0.002 0.021 1578 Dihedral : 6.167 59.211 1518 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.23), residues: 1408 helix: 1.99 (0.17), residues: 848 sheet: -1.34 (0.49), residues: 106 loop : -1.92 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 718 HIS 0.005 0.001 HIS A 602 PHE 0.014 0.001 PHE A 604 TYR 0.018 0.001 TYR A 225 ARG 0.003 0.001 ARG A 489 *********************** 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 : 0.469 Fit side-chains REVERT: A 255 MET cc_start: 0.8942 (tpt) cc_final: 0.8690 (tpp) REVERT: A 271 MET cc_start: 0.9791 (mmp) cc_final: 0.9550 (mmm) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0957 time to fit residues: 3.5048 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 : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 65 optimal weight: 4.9990 chunk 4 optimal weight: 0.0270 chunk 59 optimal weight: 2.9990 chunk 13 optimal weight: 0.0980 chunk 45 optimal weight: 8.9990 chunk 132 optimal weight: 0.3980 chunk 66 optimal weight: 2.9990 chunk 86 optimal weight: 20.0000 chunk 134 optimal weight: 20.0000 chunk 102 optimal weight: 2.9990 chunk 101 optimal weight: 0.0570 overall best weight: 0.7158 ------------------------------------------------------------------------------- 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 = 0.2944 r_free = 0.2944 target = 0.035791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.029155 restraints weight = 62852.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.029464 restraints weight = 57200.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.029662 restraints weight = 52633.306| |-----------------------------------------------------------------------------| r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.7731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8618 Z= 0.120 Angle : 0.484 7.067 11820 Z= 0.274 Chirality : 0.039 0.127 1510 Planarity : 0.002 0.022 1578 Dihedral : 5.929 55.007 1518 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.23), residues: 1408 helix: 2.06 (0.17), residues: 848 sheet: -1.38 (0.49), residues: 106 loop : -1.88 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 718 HIS 0.001 0.000 HIS A 679 PHE 0.009 0.001 PHE A 257 TYR 0.023 0.001 TYR B 225 ARG 0.003 0.000 ARG A 489 ********************** 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 23 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.518 Fit side-chains REVERT: A 255 MET cc_start: 0.8881 (tpt) cc_final: 0.8646 (tpp) REVERT: A 271 MET cc_start: 0.9790 (mmp) cc_final: 0.9533 (mmm) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.0933 time to fit residues: 3.6654 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 : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 68 optimal weight: 0.0030 chunk 46 optimal weight: 40.0000 chunk 87 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 136 optimal weight: 0.6980 chunk 69 optimal weight: 30.0000 chunk 111 optimal weight: 20.0000 chunk 40 optimal weight: 30.0000 chunk 74 optimal weight: 30.0000 chunk 98 optimal weight: 30.0000 overall best weight: 4.3396 ------------------------------------------------------------------------------- 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 = 0.2889 r_free = 0.2889 target = 0.034245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.027957 restraints weight = 68007.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.028173 restraints weight = 57891.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.028344 restraints weight = 52369.373| |-----------------------------------------------------------------------------| r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.8120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8618 Z= 0.214 Angle : 0.528 7.470 11820 Z= 0.312 Chirality : 0.039 0.129 1510 Planarity : 0.002 0.025 1578 Dihedral : 6.652 57.716 1518 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.23), residues: 1408 helix: 2.29 (0.17), residues: 844 sheet: -1.72 (0.47), residues: 108 loop : -2.30 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 718 HIS 0.003 0.001 HIS B 602 PHE 0.015 0.002 PHE A 257 TYR 0.013 0.001 TYR A 612 ARG 0.004 0.001 ARG A 489 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1752.15 seconds wall clock time: 32 minutes 12.13 seconds (1932.13 seconds total)