Starting phenix.real_space_refine on Fri Aug 7 15:03:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/13dj_76991/08_2026/13dj_76991.cif Found real_map, /net/cci-nas-00/data/ceres_data/13dj_76991/08_2026/13dj_76991.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/13dj_76991/08_2026/13dj_76991.cif" } default_model = "/net/cci-nas-00/data/ceres_data/13dj_76991/08_2026/13dj_76991.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/13dj_76991/08_2026/13dj_76991.map" default_real_map = "/net/cci-nas-00/data/ceres_data/13dj_76991/08_2026/13dj_76991.map" } resolution = 3.17 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 ------------------------------------------------------------------------------- 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= 0.002 sd= 0.038 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: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 13995 2.51 5 N 3723 2.21 5 O 4182 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22005 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 915, 7335 Classifications: {'peptide': 915} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 51, 'TRANS': 858} Chain breaks: 1 Chain: "B" Number of atoms: 7335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 915, 7335 Classifications: {'peptide': 915} Link IDs: {'PCIS': 4, 'PTRANS': 51, 'TRANS': 859} Chain breaks: 1 Chain: "C" Number of atoms: 7335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 915, 7335 Classifications: {'peptide': 915} Link IDs: {'PCIS': 4, 'PTRANS': 51, 'TRANS': 859} Chain breaks: 1 Time building chain proxies: 4.78, per 1000 atoms: 0.22 Number of scatterers: 22005 At special positions: 0 Unit cell: (118.8, 116.6, 137.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 105 16.00 O 4182 8.00 N 3723 7.00 C 13995 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: 1.89 Conformation dependent library (CDL) restraints added in 1.3 seconds 5466 Ramachandran restraints generated. 2733 Oldfield, 0 Emsley, 2733 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5130 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 47 sheets defined 18.3% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 19 through 24 removed outlier: 3.568A pdb=" N TYR A 23 " --> pdb=" O ASP A 19 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 19 through 24' Processing helix chain 'A' and resid 25 through 35 Processing helix chain 'A' and resid 41 through 45 removed outlier: 3.765A pdb=" N PHE A 45 " --> pdb=" O ASN A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 99 Processing helix chain 'A' and resid 269 through 274 removed outlier: 3.876A pdb=" N THR A 273 " --> pdb=" O THR A 269 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA A 274 " --> pdb=" O THR A 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 269 through 274' Processing helix chain 'A' and resid 313 through 317 removed outlier: 4.030A pdb=" N GLY A 316 " --> pdb=" O GLU A 313 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN A 317 " --> pdb=" O LEU A 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 313 through 317' Processing helix chain 'A' and resid 331 through 334 Processing helix chain 'A' and resid 341 through 345 removed outlier: 3.900A pdb=" N MET A 345 " --> pdb=" O THR A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 377 removed outlier: 3.616A pdb=" N SER A 369 " --> pdb=" O ASN A 365 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR A 370 " --> pdb=" O THR A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 400 Processing helix chain 'A' and resid 463 through 477 removed outlier: 3.788A pdb=" N ASN A 467 " --> pdb=" O ASN A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 481 Processing helix chain 'A' and resid 482 through 486 Processing helix chain 'A' and resid 500 through 506 Processing helix chain 'A' and resid 510 through 514 Processing helix chain 'A' and resid 527 through 532 removed outlier: 3.969A pdb=" N ASN A 531 " --> pdb=" O TYR A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 551 removed outlier: 3.686A pdb=" N LEU A 550 " --> pdb=" O ARG A 546 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 592 Processing helix chain 'A' and resid 623 through 634 Processing helix chain 'A' and resid 714 through 716 No H-bonds generated for 'chain 'A' and resid 714 through 716' Processing helix chain 'A' and resid 762 through 775 Processing helix chain 'A' and resid 794 through 798 removed outlier: 3.708A pdb=" N PHE A 798 " --> pdb=" O PHE A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 822 Processing helix chain 'A' and resid 887 through 890 Processing helix chain 'A' and resid 891 through 897 removed outlier: 3.956A pdb=" N SER A 897 " --> pdb=" O LEU A 893 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 13 Processing helix chain 'B' and resid 19 through 24 removed outlier: 3.798A pdb=" N TYR B 23 " --> pdb=" O ASP B 19 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 19 through 24' Processing helix chain 'B' and resid 25 through 35 Processing helix chain 'B' and resid 97 through 99 No H-bonds generated for 'chain 'B' and resid 97 through 99' Processing helix chain 'B' and resid 331 through 334 Processing helix chain 'B' and resid 365 through 377 Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 463 through 477 removed outlier: 3.702A pdb=" N ASN B 467 " --> pdb=" O ASN B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 481 Processing helix chain 'B' and resid 482 through 486 Processing helix chain 'B' and resid 500 through 506 Processing helix chain 'B' and resid 510 through 514 Processing helix chain 'B' and resid 540 through 551 removed outlier: 3.688A pdb=" N LEU B 550 " --> pdb=" O ARG B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 592 removed outlier: 3.776A pdb=" N VAL B 592 " --> pdb=" O ASP B 588 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 588 through 592' Processing helix chain 'B' and resid 623 through 635 removed outlier: 3.601A pdb=" N ARG B 635 " --> pdb=" O GLU B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 710 Processing helix chain 'B' and resid 762 through 774 Processing helix chain 'B' and resid 794 through 798 removed outlier: 3.792A pdb=" N PHE B 798 " --> pdb=" O PHE B 795 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 822 removed outlier: 3.621A pdb=" N GLN B 822 " --> pdb=" O ILE B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 891 through 897 removed outlier: 3.720A pdb=" N ASN B 896 " --> pdb=" O LEU B 892 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER B 897 " --> pdb=" O LEU B 893 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 13 Processing helix chain 'C' and resid 25 through 35 Processing helix chain 'C' and resid 97 through 99 No H-bonds generated for 'chain 'C' and resid 97 through 99' Processing helix chain 'C' and resid 270 through 274 removed outlier: 3.507A pdb=" N ALA C 274 " --> pdb=" O THR C 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 270 through 274' Processing helix chain 'C' and resid 311 through 317 removed outlier: 3.575A pdb=" N MET C 315 " --> pdb=" O ARG C 312 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY C 316 " --> pdb=" O GLU C 313 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN C 317 " --> pdb=" O LEU C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 334 Processing helix chain 'C' and resid 366 through 378 Processing helix chain 'C' and resid 395 through 400 Processing helix chain 'C' and resid 463 through 477 removed outlier: 3.828A pdb=" N ASN C 467 " --> pdb=" O ASN C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 481 Processing helix chain 'C' and resid 482 through 486 Processing helix chain 'C' and resid 500 through 507 removed outlier: 3.590A pdb=" N ARG C 507 " --> pdb=" O TYR C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 514 Processing helix chain 'C' and resid 526 through 530 Processing helix chain 'C' and resid 540 through 551 removed outlier: 3.739A pdb=" N LEU C 550 " --> pdb=" O ARG C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 592 Processing helix chain 'C' and resid 600 through 605 removed outlier: 3.510A pdb=" N GLY C 605 " --> pdb=" O LEU C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 623 through 635 Processing helix chain 'C' and resid 705 through 710 Processing helix chain 'C' and resid 763 through 774 Processing helix chain 'C' and resid 785 through 789 Processing helix chain 'C' and resid 794 through 798 removed outlier: 3.727A pdb=" N PHE C 798 " --> pdb=" O PHE C 795 " (cutoff:3.500A) Processing helix chain 'C' and resid 818 through 822 removed outlier: 3.536A pdb=" N GLN C 822 " --> pdb=" O ILE C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 887 through 891 Processing helix chain 'C' and resid 892 through 897 removed outlier: 3.792A pdb=" N SER C 897 " --> pdb=" O LEU C 893 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 68 removed outlier: 6.968A pdb=" N ARG A 104 " --> pdb=" O ASP A 611 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ILE A 613 " --> pdb=" O ASP A 102 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASP A 102 " --> pdb=" O ILE A 613 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N LEU A 615 " --> pdb=" O TYR A 100 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N TYR A 100 " --> pdb=" O LEU A 615 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 88 Processing sheet with id=AA3, first strand: chain 'A' and resid 133 through 135 removed outlier: 3.563A pdb=" N TRP A 135 " --> pdb=" O HIS A 167 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N PHE A 169 " --> pdb=" O LEU A 224 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU A 224 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N GLN A 171 " --> pdb=" O ARG A 222 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ARG A 222 " --> pdb=" O GLN A 171 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ALA A 219 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N TYR A 287 " --> pdb=" O ALA A 219 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N GLY A 221 " --> pdb=" O TYR A 287 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N GLU A 289 " --> pdb=" O GLY A 221 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL A 223 " --> pdb=" O GLU A 289 " (cutoff:3.500A) removed outlier: 12.983A pdb=" N MET A 264 " --> pdb=" O PRO C 431 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N PHE A 266 " --> pdb=" O VAL C 429 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 133 through 135 removed outlier: 3.563A pdb=" N TRP A 135 " --> pdb=" O HIS A 167 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY A 170 " --> pdb=" O GLU C 451 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASN C 450 " --> pdb=" O LEU C 426 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU C 426 " --> pdb=" O ASN C 450 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 185 through 188 Processing sheet with id=AA6, first strand: chain 'A' and resid 237 through 238 Processing sheet with id=AA7, first strand: chain 'A' and resid 251 through 253 removed outlier: 6.657A pdb=" N VAL A 251 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N LEU A 258 " --> pdb=" O VAL A 251 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 298 through 302 removed outlier: 6.197A pdb=" N GLN A 318 " --> pdb=" O SER A 301 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 327 through 329 Processing sheet with id=AB1, first strand: chain 'A' and resid 401 through 402 Processing sheet with id=AB2, first strand: chain 'A' and resid 412 through 416 removed outlier: 3.952A pdb=" N ASN A 412 " --> pdb=" O ILE A 462 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASN B 412 " --> pdb=" O ILE B 462 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ASN C 412 " --> pdb=" O ILE C 462 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 133 through 136 removed outlier: 3.502A pdb=" N CYS B 133 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N GLY B 170 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 9.799A pdb=" N LEU B 224 " --> pdb=" O GLY B 170 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ALA B 172 " --> pdb=" O ARG B 222 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ARG B 222 " --> pdb=" O ALA B 172 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ALA B 219 " --> pdb=" O VAL B 285 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N TYR B 287 " --> pdb=" O ALA B 219 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N GLY B 221 " --> pdb=" O TYR B 287 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N GLU B 289 " --> pdb=" O GLY B 221 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL B 223 " --> pdb=" O GLU B 289 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N PHE B 266 " --> pdb=" O VAL A 429 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU A 426 " --> pdb=" O ASN A 450 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ASN A 450 " --> pdb=" O LEU A 426 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N LYS A 449 " --> pdb=" O VAL B 168 " (cutoff:3.500A) removed outlier: 9.181A pdb=" N GLY B 170 " --> pdb=" O LYS A 449 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLU A 451 " --> pdb=" O GLY B 170 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N ALA B 172 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ARG A 453 " --> pdb=" O ALA B 172 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N TYR B 174 " --> pdb=" O ARG A 453 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 641 through 644 removed outlier: 3.575A pdb=" N GLN A 641 " --> pdb=" O VAL A 928 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE A 923 " --> pdb=" O THR A 943 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR A 943 " --> pdb=" O PHE A 923 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 649 through 656 removed outlier: 3.517A pdb=" N LEU A 915 " --> pdb=" O LEU A 683 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA A 679 " --> pdb=" O LEU A 919 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLY A 677 " --> pdb=" O GLU A 921 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 662 through 670 removed outlier: 4.401A pdb=" N SER A 669 " --> pdb=" O HIS A 899 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N HIS A 899 " --> pdb=" O SER A 669 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ALA A 900 " --> pdb=" O PHE A 725 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N PHE A 725 " --> pdb=" O ALA A 900 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ASP A 902 " --> pdb=" O ILE A 723 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ILE A 723 " --> pdb=" O ASP A 902 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N THR A 904 " --> pdb=" O VAL A 721 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VAL A 721 " --> pdb=" O THR A 904 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLU A 906 " --> pdb=" O LYS A 719 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 662 through 670 removed outlier: 4.401A pdb=" N SER A 669 " --> pdb=" O HIS A 899 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N HIS A 899 " --> pdb=" O SER A 669 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ALA A 900 " --> pdb=" O PHE A 725 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N PHE A 725 " --> pdb=" O ALA A 900 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ASP A 902 " --> pdb=" O ILE A 723 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ILE A 723 " --> pdb=" O ASP A 902 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N THR A 904 " --> pdb=" O VAL A 721 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VAL A 721 " --> pdb=" O THR A 904 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLU A 906 " --> pdb=" O LYS A 719 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL A 721 " --> pdb=" O PHE A 743 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 799 through 806 Processing sheet with id=AB9, first strand: chain 'B' and resid 65 through 68 removed outlier: 3.563A pdb=" N ALA B 617 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ARG B 104 " --> pdb=" O ASP B 611 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ILE B 613 " --> pdb=" O ASP B 102 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ASP B 102 " --> pdb=" O ILE B 613 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N LEU B 615 " --> pdb=" O TYR B 100 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N TYR B 100 " --> pdb=" O LEU B 615 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY B 105 " --> pdb=" O PHE B 558 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 72 through 75 removed outlier: 3.760A pdb=" N ASP B 72 " --> pdb=" O ARG B 83 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 72 through 75 removed outlier: 3.760A pdb=" N ASP B 72 " --> pdb=" O ARG B 83 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 94 through 95 removed outlier: 3.593A pdb=" N LEU B 94 " --> pdb=" O LEU B 574 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 188 through 189 removed outlier: 3.696A pdb=" N THR B 192 " --> pdb=" O GLU B 189 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 237 through 238 Processing sheet with id=AC6, first strand: chain 'B' and resid 298 through 302 removed outlier: 6.199A pdb=" N GLN B 318 " --> pdb=" O SER B 301 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 327 through 329 Processing sheet with id=AC8, first strand: chain 'B' and resid 401 through 402 Processing sheet with id=AC9, first strand: chain 'B' and resid 439 through 441 removed outlier: 3.618A pdb=" N LEU B 426 " --> pdb=" O ASN B 450 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASN B 450 " --> pdb=" O LEU B 426 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLU B 451 " --> pdb=" O GLY C 170 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ALA C 172 " --> pdb=" O GLU B 451 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ARG B 453 " --> pdb=" O ALA C 172 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TRP C 135 " --> pdb=" O HIS C 167 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS C 133 " --> pdb=" O PHE C 169 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 439 through 441 removed outlier: 4.381A pdb=" N PHE C 266 " --> pdb=" O VAL B 429 " (cutoff:3.500A) removed outlier: 12.592A pdb=" N MET C 264 " --> pdb=" O PRO B 431 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N GLY C 221 " --> pdb=" O TYR C 287 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N GLU C 289 " --> pdb=" O GLY C 221 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL C 223 " --> pdb=" O GLU C 289 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ARG C 222 " --> pdb=" O GLN C 171 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N GLN C 171 " --> pdb=" O ARG C 222 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N LEU C 224 " --> pdb=" O PHE C 169 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N PHE C 169 " --> pdb=" O LEU C 224 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TRP C 135 " --> pdb=" O HIS C 167 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS C 133 " --> pdb=" O PHE C 169 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 641 through 644 removed outlier: 3.546A pdb=" N GLN B 641 " --> pdb=" O VAL B 928 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR B 943 " --> pdb=" O PHE B 923 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 649 through 656 removed outlier: 3.502A pdb=" N GLU B 921 " --> pdb=" O GLY B 677 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLY B 677 " --> pdb=" O GLU B 921 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE B 680 " --> pdb=" O TRP B 871 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TRP B 871 " --> pdb=" O PHE B 680 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 662 through 670 removed outlier: 3.507A pdb=" N VAL B 663 " --> pdb=" O PHE B 905 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N SER B 669 " --> pdb=" O HIS B 899 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N HIS B 899 " --> pdb=" O SER B 669 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS B 720 " --> pdb=" O GLU B 906 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 799 through 806 Processing sheet with id=AD6, first strand: chain 'C' and resid 65 through 68 removed outlier: 3.507A pdb=" N ALA C 617 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ARG C 104 " --> pdb=" O ASP C 611 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ILE C 613 " --> pdb=" O ASP C 102 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ASP C 102 " --> pdb=" O ILE C 613 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N LEU C 615 " --> pdb=" O TYR C 100 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N TYR C 100 " --> pdb=" O LEU C 615 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 79 through 88 removed outlier: 3.735A pdb=" N TYR C 581 " --> pdb=" O PHE C 84 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL C 347 " --> pdb=" O GLU C 582 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 94 through 95 removed outlier: 4.045A pdb=" N LEU C 94 " --> pdb=" O LEU C 574 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 185 through 188 removed outlier: 6.823A pdb=" N LYS C 194 " --> pdb=" O ILE C 186 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 237 through 238 Processing sheet with id=AE2, first strand: chain 'C' and resid 250 through 252 removed outlier: 3.760A pdb=" N VAL C 251 " --> pdb=" O GLU C 259 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU C 259 " --> pdb=" O VAL C 251 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 298 through 302 removed outlier: 6.386A pdb=" N GLN C 318 " --> pdb=" O SER C 301 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 327 through 329 Processing sheet with id=AE5, first strand: chain 'C' and resid 401 through 402 Processing sheet with id=AE6, first strand: chain 'C' and resid 641 through 644 removed outlier: 3.530A pdb=" N GLN C 641 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR C 943 " --> pdb=" O PHE C 923 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 649 through 656 removed outlier: 4.434A pdb=" N GLY C 677 " --> pdb=" O GLU C 921 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 662 through 670 removed outlier: 4.207A pdb=" N SER C 669 " --> pdb=" O HIS C 899 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N HIS C 899 " --> pdb=" O SER C 669 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS C 720 " --> pdb=" O GLU C 906 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 662 through 670 removed outlier: 4.207A pdb=" N SER C 669 " --> pdb=" O HIS C 899 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N HIS C 899 " --> pdb=" O SER C 669 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS C 720 " --> pdb=" O GLU C 906 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 755 through 756 removed outlier: 4.626A pdb=" N MET C 761 " --> pdb=" O VAL C 756 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 799 through 806 577 hydrogen bonds defined for protein. 1470 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: 4.63 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7206 1.34 - 1.46: 4979 1.46 - 1.58: 10225 1.58 - 1.69: 0 1.69 - 1.81: 189 Bond restraints: 22599 Sorted by residual: bond pdb=" CA SER C 353 " pdb=" CB SER C 353 " ideal model delta sigma weight residual 1.542 1.526 0.017 8.90e-03 1.26e+04 3.47e+00 bond pdb=" C GLY C 455 " pdb=" O GLY C 455 " ideal model delta sigma weight residual 1.237 1.229 0.008 7.00e-03 2.04e+04 1.26e+00 bond pdb=" C VAL A 71 " pdb=" O VAL A 71 " ideal model delta sigma weight residual 1.231 1.241 -0.010 1.02e-02 9.61e+03 9.03e-01 bond pdb=" C ILE C 705 " pdb=" O ILE C 705 " ideal model delta sigma weight residual 1.242 1.231 0.011 1.20e-02 6.94e+03 8.74e-01 bond pdb=" C ASN B 47 " pdb=" O ASN B 47 " ideal model delta sigma weight residual 1.239 1.250 -0.011 1.17e-02 7.31e+03 8.40e-01 ... (remaining 22594 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 29897 1.28 - 2.55: 677 2.55 - 3.83: 145 3.83 - 5.10: 11 5.10 - 6.38: 2 Bond angle restraints: 30732 Sorted by residual: angle pdb=" C ARG A 312 " pdb=" N GLU A 313 " pdb=" CA GLU A 313 " ideal model delta sigma weight residual 121.54 127.92 -6.38 1.91e+00 2.74e-01 1.12e+01 angle pdb=" N ILE C 186 " pdb=" CA ILE C 186 " pdb=" C ILE C 186 " ideal model delta sigma weight residual 112.43 109.36 3.07 9.20e-01 1.18e+00 1.11e+01 angle pdb=" C LYS B 194 " pdb=" N TYR B 195 " pdb=" CA TYR B 195 " ideal model delta sigma weight residual 121.54 127.25 -5.71 1.91e+00 2.74e-01 8.92e+00 angle pdb=" C SER C 353 " pdb=" CA SER C 353 " pdb=" CB SER C 353 " ideal model delta sigma weight residual 114.87 110.78 4.09 1.51e+00 4.39e-01 7.33e+00 angle pdb=" N GLY B 839 " pdb=" CA GLY B 839 " pdb=" C GLY B 839 " ideal model delta sigma weight residual 111.56 114.29 -2.73 1.01e+00 9.80e-01 7.30e+00 ... (remaining 30727 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.24: 12861 16.24 - 32.48: 438 32.48 - 48.72: 87 48.72 - 64.97: 25 64.97 - 81.21: 2 Dihedral angle restraints: 13413 sinusoidal: 5376 harmonic: 8037 Sorted by residual: dihedral pdb=" CA LYS B 194 " pdb=" C LYS B 194 " pdb=" N TYR B 195 " pdb=" CA TYR B 195 " ideal model delta harmonic sigma weight residual 180.00 150.02 29.98 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CA GLN C 354 " pdb=" C GLN C 354 " pdb=" N LEU C 355 " pdb=" CA LEU C 355 " ideal model delta harmonic sigma weight residual 180.00 153.98 26.02 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CA ALA C 352 " pdb=" C ALA C 352 " pdb=" N SER C 353 " pdb=" CA SER C 353 " ideal model delta harmonic sigma weight residual -180.00 -155.90 -24.10 0 5.00e+00 4.00e-02 2.32e+01 ... (remaining 13410 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1856 0.028 - 0.055: 859 0.055 - 0.083: 282 0.083 - 0.110: 181 0.110 - 0.138: 68 Chirality restraints: 3246 Sorted by residual: chirality pdb=" CA ILE A 667 " pdb=" N ILE A 667 " pdb=" C ILE A 667 " pdb=" CB ILE A 667 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.76e-01 chirality pdb=" CA VAL A 749 " pdb=" N VAL A 749 " pdb=" C VAL A 749 " pdb=" CB VAL A 749 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.71e-01 chirality pdb=" CA ILE C 179 " pdb=" N ILE C 179 " pdb=" C ILE C 179 " pdb=" CB ILE C 179 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.58e-01 ... (remaining 3243 not shown) Planarity restraints: 4047 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 410 " -0.022 5.00e-02 4.00e+02 3.40e-02 1.85e+00 pdb=" N PRO C 411 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO C 411 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 411 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 172 " -0.022 5.00e-02 4.00e+02 3.34e-02 1.79e+00 pdb=" N PRO A 173 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 173 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 173 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 943 " 0.022 5.00e-02 4.00e+02 3.27e-02 1.71e+00 pdb=" N PRO B 944 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 944 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 944 " 0.017 5.00e-02 4.00e+02 ... (remaining 4044 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 3195 2.76 - 3.30: 19087 3.30 - 3.83: 33736 3.83 - 4.37: 40475 4.37 - 4.90: 72565 Nonbonded interactions: 169058 Sorted by model distance: nonbonded pdb=" OG1 THR B 76 " pdb=" OG SER B 79 " model vdw 2.226 3.040 nonbonded pdb=" O ASN B 463 " pdb=" ND2 ASN B 467 " model vdw 2.247 3.120 nonbonded pdb=" O ASN C 599 " pdb=" OG SER C 702 " model vdw 2.250 3.040 nonbonded pdb=" OD2 ASP A 408 " pdb=" OH TYR C 234 " model vdw 2.261 3.040 nonbonded pdb=" O GLU A 36 " pdb=" OG1 THR A 37 " model vdw 2.268 3.040 ... (remaining 169053 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 21.600 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 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: 24.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6519 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 : 0.002 0.030 22599 Z= 0.108 Angle : 0.493 6.381 30732 Z= 0.295 Chirality : 0.042 0.138 3246 Planarity : 0.004 0.034 4047 Dihedral : 8.847 81.208 8283 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.62 % Favored : 96.34 % Rotamer: Outliers : 1.63 % Allowed : 3.80 % Favored : 94.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.15), residues: 2733 helix: 0.52 (0.31), residues: 333 sheet: 0.60 (0.24), residues: 504 loop : -1.34 (0.13), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 676 TYR 0.012 0.001 TYR B 195 PHE 0.007 0.001 PHE A 875 TRP 0.006 0.001 TRP B 678 HIS 0.003 0.001 HIS A 823 Details of bonding type rmsd/Z covalent geometry : bond 0.00188 / 0.11 (22599) covalent geometry : angle 0.49291 / 0.29 (30732) hydrogen bonds : bond 0.27365 / 17.84 ( 543) hydrogen bonds : angle 8.47518 / 5.84 ( 1470) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5466 Ramachandran restraints generated. 2733 Oldfield, 0 Emsley, 2733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5466 Ramachandran restraints generated. 2733 Oldfield, 0 Emsley, 2733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 611 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 THR cc_start: 0.7373 (m) cc_final: 0.7081 (p) REVERT: A 226 LYS cc_start: 0.7375 (pttt) cc_final: 0.7067 (ptmt) REVERT: A 252 LYS cc_start: 0.8013 (mttt) cc_final: 0.7668 (tttt) REVERT: A 261 GLN cc_start: 0.7780 (mt0) cc_final: 0.7280 (mm-40) REVERT: A 303 MET cc_start: 0.7033 (tpt) cc_final: 0.6777 (tpp) REVERT: A 317 GLN cc_start: 0.7702 (pt0) cc_final: 0.7494 (pt0) REVERT: A 337 MET cc_start: 0.7930 (mtp) cc_final: 0.7616 (mtp) REVERT: A 362 GLN cc_start: 0.8026 (mt0) cc_final: 0.7739 (mt0) REVERT: A 364 ARG cc_start: 0.7657 (ttm170) cc_final: 0.7362 (ttp-170) REVERT: A 402 GLU cc_start: 0.7746 (tt0) cc_final: 0.7240 (mt-10) REVERT: A 421 ILE cc_start: 0.7767 (pt) cc_final: 0.7463 (pt) REVERT: A 451 GLU cc_start: 0.6150 (mm-30) cc_final: 0.5461 (mm-30) REVERT: A 476 ASN cc_start: 0.7400 (m-40) cc_final: 0.6806 (m110) REVERT: A 484 LYS cc_start: 0.7524 (pttt) cc_final: 0.7264 (ptpp) REVERT: A 497 ASN cc_start: 0.6796 (t0) cc_final: 0.6111 (t0) REVERT: A 574 LEU cc_start: 0.7159 (mt) cc_final: 0.6909 (mt) REVERT: A 575 LEU cc_start: 0.7565 (mt) cc_final: 0.7364 (mp) REVERT: A 633 MET cc_start: 0.5651 (mtm) cc_final: 0.5296 (ttp) REVERT: A 636 ASN cc_start: 0.6217 (m-40) cc_final: 0.5681 (m110) REVERT: A 717 THR cc_start: 0.7399 (OUTLIER) cc_final: 0.6953 (p) REVERT: A 720 LYS cc_start: 0.7362 (ptpt) cc_final: 0.7006 (ptpp) REVERT: A 742 GLU cc_start: 0.6103 (OUTLIER) cc_final: 0.5434 (pp20) REVERT: A 785 GLU cc_start: 0.7279 (mm-30) cc_final: 0.7075 (mm-30) REVERT: A 801 MET cc_start: 0.7782 (mtm) cc_final: 0.7539 (mtt) REVERT: A 806 VAL cc_start: 0.7511 (m) cc_final: 0.7300 (p) REVERT: A 815 GLN cc_start: 0.7501 (mm-40) cc_final: 0.7214 (mm-40) REVERT: A 840 GLN cc_start: 0.6113 (pt0) cc_final: 0.5828 (pt0) REVERT: A 846 PHE cc_start: 0.7709 (t80) cc_final: 0.7261 (t80) REVERT: A 858 SER cc_start: 0.7483 (p) cc_final: 0.7089 (m) REVERT: A 928 VAL cc_start: 0.7234 (t) cc_final: 0.6877 (p) REVERT: A 936 ILE cc_start: 0.7970 (mt) cc_final: 0.7709 (mm) REVERT: B 104 ARG cc_start: 0.7402 (mtp180) cc_final: 0.6993 (mtm180) REVERT: B 137 GLU cc_start: 0.5159 (mt-10) cc_final: 0.4586 (mt-10) REVERT: B 174 TYR cc_start: 0.7294 (t80) cc_final: 0.7065 (t80) REVERT: B 303 MET cc_start: 0.7086 (tpt) cc_final: 0.6819 (tpp) REVERT: B 363 ASP cc_start: 0.7396 (m-30) cc_final: 0.7096 (m-30) REVERT: B 386 MET cc_start: 0.8023 (ttp) cc_final: 0.7774 (ttm) REVERT: B 402 GLU cc_start: 0.7707 (tt0) cc_final: 0.7408 (mt-10) REVERT: B 409 GLU cc_start: 0.7120 (mp0) cc_final: 0.6835 (mp0) REVERT: B 424 GLU cc_start: 0.6368 (mt-10) cc_final: 0.6043 (mt-10) REVERT: B 446 PHE cc_start: 0.5794 (OUTLIER) cc_final: 0.5020 (m-80) REVERT: B 451 GLU cc_start: 0.6167 (mm-30) cc_final: 0.5735 (mm-30) REVERT: B 461 GLU cc_start: 0.7078 (tt0) cc_final: 0.6817 (tt0) REVERT: B 463 ASN cc_start: 0.7368 (OUTLIER) cc_final: 0.6868 (t0) REVERT: B 484 LYS cc_start: 0.7533 (ptmt) cc_final: 0.7182 (ptpp) REVERT: B 488 SER cc_start: 0.7754 (m) cc_final: 0.7536 (p) REVERT: B 495 SER cc_start: 0.7870 (t) cc_final: 0.7635 (p) REVERT: B 508 VAL cc_start: 0.8043 (OUTLIER) cc_final: 0.7780 (m) REVERT: B 548 MET cc_start: 0.7324 (mtm) cc_final: 0.6997 (mtm) REVERT: B 591 MET cc_start: 0.6725 (mmm) cc_final: 0.6431 (mmm) REVERT: B 628 SER cc_start: 0.6023 (t) cc_final: 0.5776 (p) REVERT: B 636 ASN cc_start: 0.5709 (m-40) cc_final: 0.5049 (m110) REVERT: B 696 ASP cc_start: 0.7454 (t0) cc_final: 0.7241 (t0) REVERT: B 720 LYS cc_start: 0.7465 (ptpt) cc_final: 0.7147 (ptpp) REVERT: B 744 GLU cc_start: 0.7170 (mt-10) cc_final: 0.6843 (mt-10) REVERT: B 747 ARG cc_start: 0.7743 (mtt180) cc_final: 0.7288 (mtp85) REVERT: B 785 GLU cc_start: 0.6711 (mt-10) cc_final: 0.6395 (mt-10) REVERT: B 796 ARG cc_start: 0.7150 (tpp-160) cc_final: 0.6884 (tpt170) REVERT: B 807 ASP cc_start: 0.6879 (t0) cc_final: 0.6354 (t0) REVERT: B 816 GLN cc_start: 0.8052 (tt0) cc_final: 0.7703 (tt0) REVERT: B 846 PHE cc_start: 0.7894 (t80) cc_final: 0.7309 (t80) REVERT: B 853 LYS cc_start: 0.7879 (mttp) cc_final: 0.7630 (mttp) REVERT: B 859 ILE cc_start: 0.6386 (tp) cc_final: 0.6081 (pt) REVERT: B 870 LEU cc_start: 0.7279 (mp) cc_final: 0.7077 (mt) REVERT: B 928 VAL cc_start: 0.7606 (t) cc_final: 0.7219 (p) REVERT: B 937 GLU cc_start: 0.6954 (mt-10) cc_final: 0.6578 (mm-30) REVERT: C 22 GLU cc_start: 0.6300 (mt-10) cc_final: 0.6027 (mt-10) REVERT: C 59 ASP cc_start: 0.7159 (m-30) cc_final: 0.6928 (t0) REVERT: C 135 TRP cc_start: 0.6583 (p90) cc_final: 0.6223 (p90) REVERT: C 165 LYS cc_start: 0.5199 (mmtp) cc_final: 0.4912 (mmmm) REVERT: C 195 TYR cc_start: 0.6790 (m-80) cc_final: 0.6347 (m-80) REVERT: C 226 LYS cc_start: 0.7353 (pttt) cc_final: 0.6924 (ptmm) REVERT: C 252 LYS cc_start: 0.7289 (tppp) cc_final: 0.6983 (tppp) REVERT: C 264 MET cc_start: 0.7331 (mtm) cc_final: 0.6790 (mtm) REVERT: C 289 GLU cc_start: 0.7091 (pt0) cc_final: 0.6761 (pt0) REVERT: C 290 ASP cc_start: 0.6584 (t0) cc_final: 0.6165 (m-30) REVERT: C 294 GLU cc_start: 0.6934 (pt0) cc_final: 0.6646 (pt0) REVERT: C 297 ASP cc_start: 0.6631 (p0) cc_final: 0.6302 (p0) REVERT: C 303 MET cc_start: 0.7117 (tpt) cc_final: 0.6745 (tpp) REVERT: C 320 MET cc_start: 0.7005 (ttt) cc_final: 0.6742 (ttp) REVERT: C 342 THR cc_start: 0.7597 (p) cc_final: 0.7393 (m) REVERT: C 351 GLN cc_start: 0.7048 (OUTLIER) cc_final: 0.6531 (mp-120) REVERT: C 382 ARG cc_start: 0.7979 (mtp85) cc_final: 0.7484 (mtp180) REVERT: C 413 TYR cc_start: 0.7810 (m-80) cc_final: 0.7447 (m-80) REVERT: C 423 THR cc_start: 0.7472 (p) cc_final: 0.6967 (t) REVERT: C 424 GLU cc_start: 0.6679 (pt0) cc_final: 0.6352 (pt0) REVERT: C 451 GLU cc_start: 0.6690 (mm-30) cc_final: 0.6373 (mm-30) REVERT: C 461 GLU cc_start: 0.7246 (tt0) cc_final: 0.6819 (tt0) REVERT: C 484 LYS cc_start: 0.7761 (ptmt) cc_final: 0.7338 (pttt) REVERT: C 495 SER cc_start: 0.7942 (t) cc_final: 0.7740 (p) REVERT: C 508 VAL cc_start: 0.7596 (m) cc_final: 0.7305 (p) REVERT: C 515 ASP cc_start: 0.6757 (t0) cc_final: 0.6400 (t0) REVERT: C 539 ARG cc_start: 0.7737 (mtt180) cc_final: 0.7534 (mtt90) REVERT: C 575 LEU cc_start: 0.7647 (mt) cc_final: 0.7346 (mp) REVERT: C 676 ARG cc_start: 0.7216 (mtp180) cc_final: 0.6610 (mtm180) REVERT: C 719 LYS cc_start: 0.7401 (ttmt) cc_final: 0.7043 (ttmm) REVERT: C 735 ASP cc_start: 0.6292 (t0) cc_final: 0.5744 (t0) REVERT: C 744 GLU cc_start: 0.7465 (mt-10) cc_final: 0.7148 (mt-10) REVERT: C 774 TYR cc_start: 0.6670 (m-80) cc_final: 0.6123 (m-80) REVERT: C 791 MET cc_start: 0.7953 (ttt) cc_final: 0.7671 (ttp) REVERT: C 793 SER cc_start: 0.7905 (m) cc_final: 0.7326 (t) REVERT: C 807 ASP cc_start: 0.6517 (t0) cc_final: 0.6207 (t0) REVERT: C 815 GLN cc_start: 0.7234 (mm-40) cc_final: 0.7034 (mm-40) REVERT: C 817 VAL cc_start: 0.7223 (t) cc_final: 0.6591 (p) REVERT: C 836 MET cc_start: 0.7102 (ttp) cc_final: 0.6755 (ttm) REVERT: C 838 GLU cc_start: 0.7203 (pt0) cc_final: 0.6908 (pt0) REVERT: C 859 ILE cc_start: 0.6374 (tp) cc_final: 0.6052 (pt) REVERT: C 914 THR cc_start: 0.7190 (p) cc_final: 0.6947 (p) REVERT: C 921 GLU cc_start: 0.7436 (mm-30) cc_final: 0.7054 (mm-30) outliers start: 39 outliers final: 14 residues processed: 635 average time/residue: 0.1684 time to fit residues: 160.2841 Evaluate side-chains 545 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 525 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 742 GLU Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 435 GLN Chi-restraints excluded: chain B residue 446 PHE Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 463 ASN Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 351 GLN Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 567 PHE Chi-restraints excluded: chain C residue 925 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 8.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 54 HIS A 340 ASN A 351 GLN ** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 ASN A 538 HIS A 624 HIS A 890 GLN B 167 HIS B 178 ASN B 340 ASN ** B 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 ASN ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 641 GLN B 779 GLN B 825 ASN ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 GLN C 247 GLN C 318 GLN C 362 GLN C 536 ASN C 537 HIS C 636 ASN C 641 GLN C 659 ASN C 671 ASN C 769 GLN C 821 HIS C 825 ASN C 932 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.118397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.099279 restraints weight = 32652.581| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.12 r_work: 0.3046 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 22599 Z= 0.200 Angle : 0.567 13.574 30732 Z= 0.306 Chirality : 0.047 0.168 3246 Planarity : 0.005 0.041 4047 Dihedral : 5.832 79.178 3079 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.71 % Favored : 94.26 % Rotamer: Outliers : 2.42 % Allowed : 8.27 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.05 (0.15), residues: 2733 helix: 0.67 (0.31), residues: 315 sheet: 0.44 (0.22), residues: 576 loop : -1.42 (0.13), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 546 TYR 0.019 0.002 TYR B 80 PHE 0.014 0.002 PHE A 766 TRP 0.012 0.001 TRP C 439 HIS 0.008 0.001 HIS A 823 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.20 (22599) covalent geometry : angle 0.56718 / 0.31 (30732) hydrogen bonds : bond 0.05265 / 3.44 ( 543) hydrogen bonds : angle 5.65992 / 3.92 ( 1470) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5466 Ramachandran restraints generated. 2733 Oldfield, 0 Emsley, 2733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5466 Ramachandran restraints generated. 2733 Oldfield, 0 Emsley, 2733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 549 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ASN cc_start: 0.8025 (m110) cc_final: 0.7666 (m110) REVERT: A 192 THR cc_start: 0.8304 (m) cc_final: 0.8032 (p) REVERT: A 226 LYS cc_start: 0.8349 (pttt) cc_final: 0.8145 (ptmt) REVERT: A 228 THR cc_start: 0.8458 (m) cc_final: 0.8153 (t) REVERT: A 268 SER cc_start: 0.8146 (t) cc_final: 0.7872 (m) REVERT: A 311 SER cc_start: 0.8749 (p) cc_final: 0.8441 (p) REVERT: A 337 MET cc_start: 0.8738 (mtp) cc_final: 0.8460 (mtp) REVERT: A 362 GLN cc_start: 0.8355 (mt0) cc_final: 0.8062 (mt0) REVERT: A 408 ASP cc_start: 0.7327 (p0) cc_final: 0.6953 (p0) REVERT: A 413 TYR cc_start: 0.8688 (m-80) cc_final: 0.8207 (m-80) REVERT: A 451 GLU cc_start: 0.7471 (mm-30) cc_final: 0.6927 (mm-30) REVERT: A 476 ASN cc_start: 0.8656 (m-40) cc_final: 0.8290 (m110) REVERT: A 497 ASN cc_start: 0.8221 (t0) cc_final: 0.7915 (t0) REVERT: A 633 MET cc_start: 0.7260 (mtm) cc_final: 0.6668 (ttp) REVERT: A 636 ASN cc_start: 0.7553 (m-40) cc_final: 0.7127 (m110) REVERT: A 717 THR cc_start: 0.8709 (OUTLIER) cc_final: 0.8231 (p) REVERT: A 735 ASP cc_start: 0.7052 (t0) cc_final: 0.6487 (t0) REVERT: A 742 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6690 (pp20) REVERT: A 801 MET cc_start: 0.8365 (mtm) cc_final: 0.8165 (mtt) REVERT: A 815 GLN cc_start: 0.8252 (mm-40) cc_final: 0.7944 (mm-40) REVERT: A 858 SER cc_start: 0.8718 (p) cc_final: 0.8489 (m) REVERT: A 912 GLU cc_start: 0.7918 (pt0) cc_final: 0.7717 (pm20) REVERT: A 928 VAL cc_start: 0.8391 (t) cc_final: 0.7989 (p) REVERT: A 945 PHE cc_start: 0.8451 (m-80) cc_final: 0.8138 (m-10) REVERT: B 135 TRP cc_start: 0.7690 (p90) cc_final: 0.7225 (p-90) REVERT: B 137 GLU cc_start: 0.7345 (mt-10) cc_final: 0.6590 (mt-10) REVERT: B 290 ASP cc_start: 0.7669 (t0) cc_final: 0.7350 (t0) REVERT: B 363 ASP cc_start: 0.8025 (m-30) cc_final: 0.7789 (m-30) REVERT: B 380 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.8402 (tpt90) REVERT: B 423 THR cc_start: 0.7956 (p) cc_final: 0.7667 (p) REVERT: B 424 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7367 (mt-10) REVERT: B 446 PHE cc_start: 0.6364 (OUTLIER) cc_final: 0.5659 (m-80) REVERT: B 451 GLU cc_start: 0.7114 (mm-30) cc_final: 0.6860 (mm-30) REVERT: B 484 LYS cc_start: 0.8104 (ptmt) cc_final: 0.7888 (ptpp) REVERT: B 628 SER cc_start: 0.7573 (t) cc_final: 0.7343 (p) REVERT: B 636 ASN cc_start: 0.7383 (m-40) cc_final: 0.6808 (m110) REVERT: B 708 LEU cc_start: 0.8524 (mt) cc_final: 0.8312 (mp) REVERT: B 774 TYR cc_start: 0.8442 (m-80) cc_final: 0.8014 (m-80) REVERT: B 807 ASP cc_start: 0.7603 (t0) cc_final: 0.7396 (t0) REVERT: B 870 LEU cc_start: 0.8601 (mp) cc_final: 0.8386 (mt) REVERT: B 928 VAL cc_start: 0.8603 (t) cc_final: 0.8262 (p) REVERT: C 165 LYS cc_start: 0.7300 (mmtp) cc_final: 0.6938 (mmmm) REVERT: C 195 TYR cc_start: 0.7287 (m-80) cc_final: 0.7077 (m-80) REVERT: C 226 LYS cc_start: 0.8287 (pttt) cc_final: 0.7970 (ptmm) REVERT: C 252 LYS cc_start: 0.8142 (tppp) cc_final: 0.7584 (tppp) REVERT: C 264 MET cc_start: 0.8224 (mtm) cc_final: 0.7833 (mtm) REVERT: C 290 ASP cc_start: 0.7352 (t0) cc_final: 0.7037 (m-30) REVERT: C 303 MET cc_start: 0.8351 (tpt) cc_final: 0.8149 (tpp) REVERT: C 336 LEU cc_start: 0.8308 (mt) cc_final: 0.8106 (mt) REVERT: C 367 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.7188 (mt-10) REVERT: C 484 LYS cc_start: 0.8328 (ptmt) cc_final: 0.8092 (pttm) REVERT: C 575 LEU cc_start: 0.8552 (mt) cc_final: 0.8339 (mp) REVERT: C 676 ARG cc_start: 0.8391 (mtp180) cc_final: 0.8159 (mtm110) REVERT: C 719 LYS cc_start: 0.8724 (ttmt) cc_final: 0.8452 (ttmm) REVERT: C 735 ASP cc_start: 0.7094 (t0) cc_final: 0.6457 (t0) REVERT: C 744 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7998 (mt-10) REVERT: C 793 SER cc_start: 0.8883 (m) cc_final: 0.8327 (t) REVERT: C 807 ASP cc_start: 0.7289 (t0) cc_final: 0.7026 (t0) REVERT: C 815 GLN cc_start: 0.8142 (mm-40) cc_final: 0.7812 (mm-40) REVERT: C 817 VAL cc_start: 0.8468 (t) cc_final: 0.7677 (p) REVERT: C 926 VAL cc_start: 0.8037 (t) cc_final: 0.7627 (p) outliers start: 58 outliers final: 40 residues processed: 583 average time/residue: 0.1565 time to fit residues: 137.0421 Evaluate side-chains 569 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 524 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 742 GLU Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 887 ASP Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 91 ASN Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 435 GLN Chi-restraints excluded: chain B residue 446 PHE Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 351 GLN Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 367 GLU Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 556 VAL Chi-restraints excluded: chain C residue 567 PHE Chi-restraints excluded: chain C residue 636 ASN Chi-restraints excluded: chain C residue 749 VAL Chi-restraints excluded: chain C residue 786 SER Chi-restraints excluded: chain C residue 813 ASP Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 870 LEU Chi-restraints excluded: chain C residue 887 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 20 optimal weight: 2.9990 chunk 182 optimal weight: 2.9990 chunk 150 optimal weight: 0.9980 chunk 258 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 chunk 118 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 206 optimal weight: 0.9980 chunk 156 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 371 GLN A 471 ASN B 310 ASN ** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 ASN B 825 ASN ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 476 ASN C 636 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.118402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.099245 restraints weight = 32515.252| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.12 r_work: 0.3033 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 22599 Z= 0.153 Angle : 0.525 7.227 30732 Z= 0.284 Chirality : 0.045 0.161 3246 Planarity : 0.004 0.041 4047 Dihedral : 5.713 76.887 3071 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.72 % Favored : 95.24 % Rotamer: Outliers : 2.76 % Allowed : 9.77 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.04 (0.15), residues: 2733 helix: 0.67 (0.31), residues: 318 sheet: 0.45 (0.22), residues: 573 loop : -1.40 (0.13), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 635 TYR 0.018 0.001 TYR B 174 PHE 0.011 0.002 PHE B 558 TRP 0.010 0.001 TRP B 678 HIS 0.016 0.001 HIS A 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.15 (22599) covalent geometry : angle 0.52546 / 0.28 (30732) hydrogen bonds : bond 0.04339 / 2.83 ( 543) hydrogen bonds : angle 5.29464 / 3.66 ( 1470) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5466 Ramachandran restraints generated. 2733 Oldfield, 0 Emsley, 2733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5466 Ramachandran restraints generated. 2733 Oldfield, 0 Emsley, 2733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 512 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ASN cc_start: 0.8046 (m110) cc_final: 0.7661 (m110) REVERT: A 107 LEU cc_start: 0.8596 (tp) cc_final: 0.8367 (tp) REVERT: A 192 THR cc_start: 0.8282 (m) cc_final: 0.7999 (p) REVERT: A 228 THR cc_start: 0.8316 (m) cc_final: 0.7990 (t) REVERT: A 268 SER cc_start: 0.8076 (t) cc_final: 0.7801 (m) REVERT: A 298 THR cc_start: 0.8682 (OUTLIER) cc_final: 0.8388 (t) REVERT: A 362 GLN cc_start: 0.8345 (mt0) cc_final: 0.8056 (mt0) REVERT: A 413 TYR cc_start: 0.8692 (m-80) cc_final: 0.8179 (m-80) REVERT: A 451 GLU cc_start: 0.7503 (mm-30) cc_final: 0.6877 (mm-30) REVERT: A 476 ASN cc_start: 0.8623 (m-40) cc_final: 0.8227 (m110) REVERT: A 497 ASN cc_start: 0.8277 (t0) cc_final: 0.7798 (t0) REVERT: A 633 MET cc_start: 0.7262 (mtm) cc_final: 0.6710 (ttp) REVERT: A 636 ASN cc_start: 0.7480 (m-40) cc_final: 0.6960 (m110) REVERT: A 717 THR cc_start: 0.8655 (OUTLIER) cc_final: 0.8169 (p) REVERT: A 735 ASP cc_start: 0.7051 (t0) cc_final: 0.6465 (t0) REVERT: A 742 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.6676 (pp20) REVERT: A 801 MET cc_start: 0.8490 (mtm) cc_final: 0.8141 (mtt) REVERT: A 810 LYS cc_start: 0.8631 (mmtt) cc_final: 0.8417 (mmtp) REVERT: A 815 GLN cc_start: 0.8207 (mm-40) cc_final: 0.7769 (mm-40) REVERT: A 858 SER cc_start: 0.8595 (p) cc_final: 0.8384 (m) REVERT: A 912 GLU cc_start: 0.7918 (pt0) cc_final: 0.7674 (pm20) REVERT: A 928 VAL cc_start: 0.8342 (t) cc_final: 0.7962 (p) REVERT: A 945 PHE cc_start: 0.8385 (m-80) cc_final: 0.8088 (m-10) REVERT: B 93 VAL cc_start: 0.8221 (OUTLIER) cc_final: 0.7829 (p) REVERT: B 290 ASP cc_start: 0.7694 (t0) cc_final: 0.7391 (t0) REVERT: B 363 ASP cc_start: 0.8023 (m-30) cc_final: 0.7789 (m-30) REVERT: B 380 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.8326 (tpt90) REVERT: B 424 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7379 (mt-10) REVERT: B 446 PHE cc_start: 0.6307 (OUTLIER) cc_final: 0.5544 (m-80) REVERT: B 451 GLU cc_start: 0.7136 (mm-30) cc_final: 0.6870 (mm-30) REVERT: B 484 LYS cc_start: 0.8135 (ptmt) cc_final: 0.7912 (ptpp) REVERT: B 591 MET cc_start: 0.8092 (mmm) cc_final: 0.7704 (mmm) REVERT: B 628 SER cc_start: 0.7547 (t) cc_final: 0.7269 (p) REVERT: B 636 ASN cc_start: 0.7310 (m-40) cc_final: 0.6675 (m110) REVERT: B 774 TYR cc_start: 0.8366 (m-80) cc_final: 0.7891 (m-80) REVERT: B 870 LEU cc_start: 0.8540 (mp) cc_final: 0.8316 (mt) REVERT: B 903 MET cc_start: 0.8123 (mtp) cc_final: 0.7798 (mtm) REVERT: B 928 VAL cc_start: 0.8495 (t) cc_final: 0.8173 (p) REVERT: B 936 ILE cc_start: 0.8589 (mt) cc_final: 0.8346 (mm) REVERT: C 165 LYS cc_start: 0.7198 (mmtp) cc_final: 0.6840 (mmmm) REVERT: C 177 ILE cc_start: 0.7908 (mm) cc_final: 0.7657 (mt) REVERT: C 195 TYR cc_start: 0.7300 (m-80) cc_final: 0.7082 (m-80) REVERT: C 226 LYS cc_start: 0.8270 (pttt) cc_final: 0.7940 (ptmm) REVERT: C 252 LYS cc_start: 0.8135 (tppp) cc_final: 0.7539 (tppp) REVERT: C 264 MET cc_start: 0.8226 (mtm) cc_final: 0.7850 (mtm) REVERT: C 290 ASP cc_start: 0.7425 (t0) cc_final: 0.7058 (m-30) REVERT: C 303 MET cc_start: 0.8321 (tpt) cc_final: 0.8109 (tpp) REVERT: C 367 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.7143 (mt-10) REVERT: C 380 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.7679 (tpt-90) REVERT: C 409 GLU cc_start: 0.7779 (mp0) cc_final: 0.7549 (mp0) REVERT: C 439 TRP cc_start: 0.7979 (m100) cc_final: 0.7656 (m100) REVERT: C 484 LYS cc_start: 0.8318 (ptmt) cc_final: 0.8072 (pttm) REVERT: C 575 LEU cc_start: 0.8481 (mt) cc_final: 0.8260 (mp) REVERT: C 636 ASN cc_start: 0.7973 (t0) cc_final: 0.7660 (t0) REVERT: C 652 MET cc_start: 0.7983 (mmm) cc_final: 0.7718 (mmm) REVERT: C 676 ARG cc_start: 0.8362 (mtp180) cc_final: 0.8146 (mtm110) REVERT: C 719 LYS cc_start: 0.8666 (ttmt) cc_final: 0.8318 (ttmm) REVERT: C 735 ASP cc_start: 0.7105 (t0) cc_final: 0.6452 (t0) REVERT: C 793 SER cc_start: 0.8899 (m) cc_final: 0.8256 (t) REVERT: C 815 GLN cc_start: 0.8111 (mm-40) cc_final: 0.7714 (mm-40) REVERT: C 817 VAL cc_start: 0.8445 (t) cc_final: 0.7666 (p) REVERT: C 926 VAL cc_start: 0.8003 (t) cc_final: 0.7614 (p) outliers start: 66 outliers final: 44 residues processed: 549 average time/residue: 0.1673 time to fit residues: 137.4532 Evaluate side-chains 548 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 496 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 742 GLU Chi-restraints excluded: chain A residue 813 ASP Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 887 ASP Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 91 ASN Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 435 GLN Chi-restraints excluded: chain B residue 446 PHE Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 351 GLN Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 367 GLU Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 380 ARG Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 556 VAL Chi-restraints excluded: chain C residue 567 PHE Chi-restraints excluded: chain C residue 622 MET Chi-restraints excluded: chain C residue 749 VAL Chi-restraints excluded: chain C residue 813 ASP Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 870 LEU Chi-restraints excluded: chain C residue 887 ASP Chi-restraints excluded: chain C residue 939 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 126 optimal weight: 3.9990 chunk 256 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 198 optimal weight: 2.9990 chunk 186 optimal weight: 6.9990 chunk 50 optimal weight: 0.0170 chunk 79 optimal weight: 3.9990 chunk 246 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 221 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 overall best weight: 1.9424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 54 HIS A 471 ASN B 310 ASN B 317 GLN ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 362 GLN C 476 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.116938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.097929 restraints weight = 32379.001| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.10 r_work: 0.3018 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 22599 Z= 0.237 Angle : 0.591 10.076 30732 Z= 0.318 Chirality : 0.048 0.163 3246 Planarity : 0.005 0.056 4047 Dihedral : 5.888 76.266 3069 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.29 % Favored : 93.67 % Rotamer: Outliers : 3.43 % Allowed : 10.11 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.15), residues: 2733 helix: 0.28 (0.29), residues: 336 sheet: 0.36 (0.22), residues: 531 loop : -1.56 (0.13), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 46 TYR 0.023 0.002 TYR B 80 PHE 0.023 0.002 PHE A 846 TRP 0.014 0.002 TRP B 439 HIS 0.009 0.001 HIS A 823 Details of bonding type rmsd/Z covalent geometry : bond 0.00579 / 0.24 (22599) covalent geometry : angle 0.59089 / 0.32 (30732) hydrogen bonds : bond 0.04921 / 3.23 ( 543) hydrogen bonds : angle 5.24458 / 3.62 ( 1470) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5466 Ramachandran restraints generated. 2733 Oldfield, 0 Emsley, 2733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5466 Ramachandran restraints generated. 2733 Oldfield, 0 Emsley, 2733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 512 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ASN cc_start: 0.8057 (m110) cc_final: 0.7697 (m110) REVERT: A 107 LEU cc_start: 0.8588 (tp) cc_final: 0.8342 (tp) REVERT: A 228 THR cc_start: 0.8307 (m) cc_final: 0.7998 (t) REVERT: A 298 THR cc_start: 0.8689 (OUTLIER) cc_final: 0.8460 (t) REVERT: A 311 SER cc_start: 0.8723 (p) cc_final: 0.8363 (p) REVERT: A 313 GLU cc_start: 0.6201 (OUTLIER) cc_final: 0.5999 (pm20) REVERT: A 362 GLN cc_start: 0.8375 (mt0) cc_final: 0.8087 (mt0) REVERT: A 408 ASP cc_start: 0.7353 (p0) cc_final: 0.6983 (p0) REVERT: A 413 TYR cc_start: 0.8712 (m-80) cc_final: 0.8169 (m-80) REVERT: A 430 LYS cc_start: 0.7913 (pttt) cc_final: 0.7673 (pttm) REVERT: A 451 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7072 (mm-30) REVERT: A 476 ASN cc_start: 0.8684 (m-40) cc_final: 0.8310 (m110) REVERT: A 497 ASN cc_start: 0.8311 (t0) cc_final: 0.7920 (t0) REVERT: A 633 MET cc_start: 0.7444 (mtm) cc_final: 0.6644 (ttp) REVERT: A 636 ASN cc_start: 0.7655 (m-40) cc_final: 0.7158 (m110) REVERT: A 717 THR cc_start: 0.8662 (OUTLIER) cc_final: 0.8250 (p) REVERT: A 742 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.6727 (pp20) REVERT: A 801 MET cc_start: 0.8469 (mtm) cc_final: 0.8071 (mtt) REVERT: A 810 LYS cc_start: 0.8662 (mmtt) cc_final: 0.8438 (mmtp) REVERT: A 858 SER cc_start: 0.8686 (p) cc_final: 0.8436 (m) REVERT: A 912 GLU cc_start: 0.7969 (pt0) cc_final: 0.7733 (pm20) REVERT: A 928 VAL cc_start: 0.8400 (t) cc_final: 0.8035 (p) REVERT: A 937 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7764 (mm-30) REVERT: A 945 PHE cc_start: 0.8439 (m-80) cc_final: 0.8153 (m-10) REVERT: B 135 TRP cc_start: 0.7677 (p90) cc_final: 0.7232 (p-90) REVERT: B 290 ASP cc_start: 0.7708 (t0) cc_final: 0.7451 (t0) REVERT: B 310 ASN cc_start: 0.7674 (m110) cc_final: 0.7250 (t0) REVERT: B 380 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.8393 (tpt90) REVERT: B 409 GLU cc_start: 0.7660 (mp0) cc_final: 0.7457 (mp0) REVERT: B 424 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7383 (mt-10) REVERT: B 445 GLU cc_start: 0.6923 (tm-30) cc_final: 0.6671 (tm-30) REVERT: B 446 PHE cc_start: 0.6424 (OUTLIER) cc_final: 0.5713 (m-80) REVERT: B 591 MET cc_start: 0.8143 (mmm) cc_final: 0.7791 (mmm) REVERT: B 628 SER cc_start: 0.7713 (t) cc_final: 0.7445 (p) REVERT: B 636 ASN cc_start: 0.7521 (m-40) cc_final: 0.6872 (m110) REVERT: B 774 TYR cc_start: 0.8389 (m-80) cc_final: 0.7999 (m-80) REVERT: B 870 LEU cc_start: 0.8587 (mp) cc_final: 0.8385 (mt) REVERT: B 928 VAL cc_start: 0.8555 (t) cc_final: 0.8229 (p) REVERT: C 135 TRP cc_start: 0.7714 (p90) cc_final: 0.7436 (p90) REVERT: C 137 GLU cc_start: 0.7481 (mt-10) cc_final: 0.7256 (mt-10) REVERT: C 165 LYS cc_start: 0.7259 (mmtp) cc_final: 0.6983 (mmmm) REVERT: C 186 ILE cc_start: 0.7951 (pt) cc_final: 0.7620 (tt) REVERT: C 252 LYS cc_start: 0.8207 (tppp) cc_final: 0.7578 (tppp) REVERT: C 264 MET cc_start: 0.8244 (mtm) cc_final: 0.7912 (mtm) REVERT: C 290 ASP cc_start: 0.7425 (t0) cc_final: 0.7099 (m-30) REVERT: C 367 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7357 (mt-10) REVERT: C 380 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.8070 (tpt-90) REVERT: C 439 TRP cc_start: 0.8076 (m100) cc_final: 0.7742 (m100) REVERT: C 484 LYS cc_start: 0.8361 (ptmt) cc_final: 0.8095 (pttm) REVERT: C 636 ASN cc_start: 0.7998 (t0) cc_final: 0.7735 (t0) REVERT: C 719 LYS cc_start: 0.8704 (ttmt) cc_final: 0.8430 (ttmm) REVERT: C 735 ASP cc_start: 0.7188 (t0) cc_final: 0.6618 (t0) REVERT: C 793 SER cc_start: 0.8910 (m) cc_final: 0.8332 (t) REVERT: C 815 GLN cc_start: 0.8105 (mm-40) cc_final: 0.7694 (mm-40) REVERT: C 817 VAL cc_start: 0.8480 (t) cc_final: 0.7675 (p) REVERT: C 902 ASP cc_start: 0.7967 (m-30) cc_final: 0.7714 (m-30) REVERT: C 926 VAL cc_start: 0.8038 (t) cc_final: 0.7665 (p) outliers start: 82 outliers final: 60 residues processed: 559 average time/residue: 0.1520 time to fit residues: 127.2668 Evaluate side-chains 570 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 502 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 742 GLU Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 813 ASP Chi-restraints excluded: chain A residue 819 ILE Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 887 ASP Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 91 ASN Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 317 GLN Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 435 GLN Chi-restraints excluded: chain B residue 446 PHE Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 775 ASN Chi-restraints excluded: chain B residue 813 ASP Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 938 THR Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 367 GLU Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 380 ARG Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 556 VAL Chi-restraints excluded: chain C residue 567 PHE Chi-restraints excluded: chain C residue 749 VAL Chi-restraints excluded: chain C residue 813 ASP Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 836 MET Chi-restraints excluded: chain C residue 856 VAL Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 870 LEU Chi-restraints excluded: chain C residue 887 ASP Chi-restraints excluded: chain C residue 925 VAL Chi-restraints excluded: chain C residue 928 VAL Chi-restraints excluded: chain C residue 939 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 238 optimal weight: 2.9990 chunk 243 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 81 optimal weight: 0.0270 chunk 142 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 198 optimal weight: 0.0170 chunk 57 optimal weight: 2.9990 chunk 209 optimal weight: 0.0870 chunk 123 optimal weight: 6.9990 overall best weight: 0.4054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 54 HIS A 471 ASN B 365 ASN B 371 GLN C 91 ASN C 476 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.119732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.100538 restraints weight = 32229.473| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.12 r_work: 0.3070 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 22599 Z= 0.086 Angle : 0.483 7.694 30732 Z= 0.259 Chirality : 0.043 0.163 3246 Planarity : 0.004 0.054 4047 Dihedral : 5.286 77.350 3066 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.06 % Favored : 95.90 % Rotamer: Outliers : 2.55 % Allowed : 11.57 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.01 (0.15), residues: 2733 helix: 0.66 (0.30), residues: 336 sheet: 0.46 (0.21), residues: 576 loop : -1.39 (0.13), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 46 TYR 0.019 0.001 TYR C 787 PHE 0.022 0.001 PHE A 846 TRP 0.009 0.001 TRP A 469 HIS 0.003 0.001 HIS C 823 Details of bonding type rmsd/Z covalent geometry : bond 0.00191 / 0.09 (22599) covalent geometry : angle 0.48347 / 0.26 (30732) hydrogen bonds : bond 0.03211 / 2.08 ( 543) hydrogen bonds : angle 5.00282 / 3.46 ( 1470) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5466 Ramachandran restraints generated. 2733 Oldfield, 0 Emsley, 2733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5466 Ramachandran restraints generated. 2733 Oldfield, 0 Emsley, 2733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 505 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ASN cc_start: 0.8045 (m110) cc_final: 0.7686 (m110) REVERT: A 107 LEU cc_start: 0.8599 (tp) cc_final: 0.8363 (tp) REVERT: A 192 THR cc_start: 0.8280 (m) cc_final: 0.7961 (p) REVERT: A 298 THR cc_start: 0.8623 (OUTLIER) cc_final: 0.8415 (t) REVERT: A 362 GLN cc_start: 0.8410 (mt0) cc_final: 0.8122 (mt0) REVERT: A 408 ASP cc_start: 0.7284 (p0) cc_final: 0.6870 (p0) REVERT: A 413 TYR cc_start: 0.8629 (m-80) cc_final: 0.8183 (m-80) REVERT: A 451 GLU cc_start: 0.7524 (mm-30) cc_final: 0.6868 (mm-30) REVERT: A 476 ASN cc_start: 0.8592 (m-40) cc_final: 0.8170 (m110) REVERT: A 497 ASN cc_start: 0.8312 (t0) cc_final: 0.7900 (t0) REVERT: A 633 MET cc_start: 0.7160 (mtm) cc_final: 0.6648 (ttp) REVERT: A 636 ASN cc_start: 0.7535 (m-40) cc_final: 0.7023 (m110) REVERT: A 717 THR cc_start: 0.8531 (OUTLIER) cc_final: 0.8084 (p) REVERT: A 735 ASP cc_start: 0.7091 (t0) cc_final: 0.6499 (t0) REVERT: A 742 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.6687 (pp20) REVERT: A 801 MET cc_start: 0.8409 (mtm) cc_final: 0.8072 (mtt) REVERT: A 815 GLN cc_start: 0.8246 (mm-40) cc_final: 0.7954 (mm-40) REVERT: A 858 SER cc_start: 0.8470 (p) cc_final: 0.8253 (m) REVERT: A 912 GLU cc_start: 0.7847 (pt0) cc_final: 0.7637 (pm20) REVERT: A 928 VAL cc_start: 0.8298 (t) cc_final: 0.7927 (p) REVERT: A 937 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7680 (mm-30) REVERT: A 945 PHE cc_start: 0.8401 (m-80) cc_final: 0.8117 (m-10) REVERT: B 93 VAL cc_start: 0.8219 (OUTLIER) cc_final: 0.7851 (p) REVERT: B 135 TRP cc_start: 0.7515 (p90) cc_final: 0.7053 (p-90) REVERT: B 136 ASP cc_start: 0.7345 (m-30) cc_final: 0.7133 (m-30) REVERT: B 208 GLU cc_start: 0.6948 (pm20) cc_final: 0.6693 (pm20) REVERT: B 290 ASP cc_start: 0.7627 (t0) cc_final: 0.7381 (t0) REVERT: B 380 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.8332 (tpt90) REVERT: B 409 GLU cc_start: 0.7634 (mp0) cc_final: 0.7396 (mp0) REVERT: B 446 PHE cc_start: 0.6161 (OUTLIER) cc_final: 0.5532 (m-80) REVERT: B 484 LYS cc_start: 0.8093 (ptmt) cc_final: 0.7887 (ptpp) REVERT: B 591 MET cc_start: 0.8075 (mmm) cc_final: 0.7596 (mmm) REVERT: B 628 SER cc_start: 0.7660 (t) cc_final: 0.7338 (p) REVERT: B 636 ASN cc_start: 0.7413 (m-40) cc_final: 0.6705 (m110) REVERT: B 687 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8442 (pt0) REVERT: B 774 TYR cc_start: 0.8232 (m-80) cc_final: 0.8027 (m-80) REVERT: B 870 LEU cc_start: 0.8552 (mp) cc_final: 0.8319 (mt) REVERT: B 903 MET cc_start: 0.8098 (mtp) cc_final: 0.7675 (mtm) REVERT: B 928 VAL cc_start: 0.8414 (t) cc_final: 0.8091 (p) REVERT: C 165 LYS cc_start: 0.7227 (mmtp) cc_final: 0.6975 (mmmm) REVERT: C 252 LYS cc_start: 0.8172 (tppp) cc_final: 0.7547 (tppp) REVERT: C 264 MET cc_start: 0.8218 (mtm) cc_final: 0.7847 (mtm) REVERT: C 290 ASP cc_start: 0.7441 (t0) cc_final: 0.7112 (m-30) REVERT: C 367 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.7058 (mt-10) REVERT: C 439 TRP cc_start: 0.7913 (m100) cc_final: 0.7713 (m100) REVERT: C 484 LYS cc_start: 0.8289 (ptmt) cc_final: 0.8069 (pttm) REVERT: C 580 THR cc_start: 0.7817 (m) cc_final: 0.7539 (p) REVERT: C 636 ASN cc_start: 0.7907 (t0) cc_final: 0.7634 (t0) REVERT: C 670 ARG cc_start: 0.7954 (ttm-80) cc_final: 0.7664 (ptp-110) REVERT: C 676 ARG cc_start: 0.8370 (mtp180) cc_final: 0.8084 (mtm110) REVERT: C 690 SER cc_start: 0.7904 (t) cc_final: 0.7611 (p) REVERT: C 719 LYS cc_start: 0.8663 (ttmt) cc_final: 0.8309 (ttmm) REVERT: C 735 ASP cc_start: 0.7141 (t0) cc_final: 0.6622 (t0) REVERT: C 774 TYR cc_start: 0.8309 (m-80) cc_final: 0.7641 (m-80) REVERT: C 793 SER cc_start: 0.8896 (m) cc_final: 0.8271 (t) REVERT: C 817 VAL cc_start: 0.8469 (t) cc_final: 0.7706 (p) REVERT: C 926 VAL cc_start: 0.7946 (t) cc_final: 0.7596 (p) outliers start: 61 outliers final: 41 residues processed: 543 average time/residue: 0.1548 time to fit residues: 126.2347 Evaluate side-chains 544 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 495 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 742 GLU Chi-restraints excluded: chain A residue 813 ASP Chi-restraints excluded: chain A residue 819 ILE Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 887 ASP Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 435 GLN Chi-restraints excluded: chain B residue 446 PHE Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 775 ASN Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 74 GLU Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 367 GLU Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 556 VAL Chi-restraints excluded: chain C residue 567 PHE Chi-restraints excluded: chain C residue 749 VAL Chi-restraints excluded: chain C residue 786 SER Chi-restraints excluded: chain C residue 836 MET Chi-restraints excluded: chain C residue 887 ASP Chi-restraints excluded: chain C residue 906 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 167 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 119 optimal weight: 0.8980 chunk 131 optimal weight: 2.9990 chunk 256 optimal weight: 2.9990 chunk 211 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 356 ASN A 471 ASN B 310 ASN B 317 GLN B 365 ASN B 456 ASN B 775 ASN B 825 ASN C 265 GLN C 362 GLN C 450 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.116894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.097793 restraints weight = 32471.425| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.11 r_work: 0.3007 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 22599 Z= 0.237 Angle : 0.591 9.438 30732 Z= 0.317 Chirality : 0.048 0.165 3246 Planarity : 0.005 0.057 4047 Dihedral : 5.592 76.357 3064 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.44 % Favored : 93.52 % Rotamer: Outliers : 2.84 % Allowed : 11.61 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.26 (0.15), residues: 2733 helix: 0.33 (0.29), residues: 336 sheet: 0.33 (0.21), residues: 582 loop : -1.56 (0.13), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 46 TYR 0.021 0.002 TYR B 326 PHE 0.026 0.002 PHE A 846 TRP 0.012 0.002 TRP B 439 HIS 0.010 0.001 HIS A 823 Details of bonding type rmsd/Z covalent geometry : bond 0.00579 / 0.24 (22599) covalent geometry : angle 0.59089 / 0.32 (30732) hydrogen bonds : bond 0.04762 / 3.13 ( 543) hydrogen bonds : angle 5.12763 / 3.54 ( 1470) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5466 Ramachandran restraints generated. 2733 Oldfield, 0 Emsley, 2733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5466 Ramachandran restraints generated. 2733 Oldfield, 0 Emsley, 2733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 502 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLN cc_start: 0.5865 (OUTLIER) cc_final: 0.5440 (tp-100) REVERT: A 42 ASN cc_start: 0.8041 (m110) cc_final: 0.7673 (m110) REVERT: A 107 LEU cc_start: 0.8570 (tp) cc_final: 0.8323 (tp) REVERT: A 311 SER cc_start: 0.8722 (p) cc_final: 0.8413 (p) REVERT: A 362 GLN cc_start: 0.8367 (mt0) cc_final: 0.8062 (mt0) REVERT: A 413 TYR cc_start: 0.8683 (m-80) cc_final: 0.8126 (m-80) REVERT: A 451 GLU cc_start: 0.7610 (mm-30) cc_final: 0.6988 (mm-30) REVERT: A 476 ASN cc_start: 0.8682 (m-40) cc_final: 0.8303 (m110) REVERT: A 497 ASN cc_start: 0.8336 (t0) cc_final: 0.7914 (t0) REVERT: A 633 MET cc_start: 0.7272 (mtm) cc_final: 0.6506 (ttp) REVERT: A 636 ASN cc_start: 0.7579 (m-40) cc_final: 0.7022 (m110) REVERT: A 708 LEU cc_start: 0.8704 (mt) cc_final: 0.8453 (mp) REVERT: A 717 THR cc_start: 0.8554 (OUTLIER) cc_final: 0.8235 (p) REVERT: A 735 ASP cc_start: 0.7099 (t0) cc_final: 0.6502 (t0) REVERT: A 742 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.6748 (pp20) REVERT: A 801 MET cc_start: 0.8496 (mtm) cc_final: 0.8113 (mtt) REVERT: A 815 GLN cc_start: 0.8258 (mm-40) cc_final: 0.7969 (mm-40) REVERT: A 912 GLU cc_start: 0.8062 (pt0) cc_final: 0.7812 (pm20) REVERT: A 928 VAL cc_start: 0.8347 (t) cc_final: 0.7978 (p) REVERT: A 937 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7744 (mm-30) REVERT: A 945 PHE cc_start: 0.8401 (m-80) cc_final: 0.8125 (m-10) REVERT: B 135 TRP cc_start: 0.7657 (p90) cc_final: 0.7163 (p-90) REVERT: B 208 GLU cc_start: 0.7057 (pm20) cc_final: 0.6804 (pm20) REVERT: B 290 ASP cc_start: 0.7702 (t0) cc_final: 0.7458 (t0) REVERT: B 310 ASN cc_start: 0.7709 (m110) cc_final: 0.7239 (t0) REVERT: B 380 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.8376 (tpt90) REVERT: B 409 GLU cc_start: 0.7684 (mp0) cc_final: 0.7421 (mp0) REVERT: B 446 PHE cc_start: 0.6411 (OUTLIER) cc_final: 0.5485 (m-10) REVERT: B 484 LYS cc_start: 0.8122 (ptmt) cc_final: 0.7908 (ptpp) REVERT: B 591 MET cc_start: 0.8150 (mmm) cc_final: 0.7730 (mmm) REVERT: B 628 SER cc_start: 0.7670 (t) cc_final: 0.7388 (p) REVERT: B 636 ASN cc_start: 0.7478 (m-40) cc_final: 0.6790 (m110) REVERT: B 670 ARG cc_start: 0.8235 (ptp-110) cc_final: 0.8033 (ptp90) REVERT: B 687 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8466 (pt0) REVERT: B 774 TYR cc_start: 0.8346 (m-80) cc_final: 0.7940 (m-80) REVERT: B 807 ASP cc_start: 0.7664 (t0) cc_final: 0.7359 (t0) REVERT: B 903 MET cc_start: 0.8197 (mtp) cc_final: 0.7791 (mtm) REVERT: B 928 VAL cc_start: 0.8531 (t) cc_final: 0.8193 (p) REVERT: C 137 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7194 (mt-10) REVERT: C 165 LYS cc_start: 0.7205 (mmtp) cc_final: 0.6835 (mmmm) REVERT: C 186 ILE cc_start: 0.7941 (pt) cc_final: 0.7627 (tt) REVERT: C 252 LYS cc_start: 0.8174 (tppp) cc_final: 0.7499 (tppp) REVERT: C 264 MET cc_start: 0.8245 (mtm) cc_final: 0.7868 (mtm) REVERT: C 290 ASP cc_start: 0.7461 (t0) cc_final: 0.7114 (m-30) REVERT: C 315 MET cc_start: 0.6858 (tpp) cc_final: 0.5638 (mmt) REVERT: C 367 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7301 (mt-10) REVERT: C 439 TRP cc_start: 0.8032 (m100) cc_final: 0.7646 (m100) REVERT: C 484 LYS cc_start: 0.8362 (ptmt) cc_final: 0.8085 (pttm) REVERT: C 636 ASN cc_start: 0.7880 (t0) cc_final: 0.7614 (t0) REVERT: C 670 ARG cc_start: 0.7976 (ttm-80) cc_final: 0.7672 (ptp-110) REVERT: C 719 LYS cc_start: 0.8677 (ttmt) cc_final: 0.8317 (ttmm) REVERT: C 793 SER cc_start: 0.8897 (m) cc_final: 0.8261 (t) REVERT: C 817 VAL cc_start: 0.8433 (t) cc_final: 0.7623 (p) REVERT: C 902 ASP cc_start: 0.7936 (m-30) cc_final: 0.7720 (m-30) REVERT: C 926 VAL cc_start: 0.7992 (t) cc_final: 0.7638 (p) outliers start: 68 outliers final: 54 residues processed: 541 average time/residue: 0.1537 time to fit residues: 124.4233 Evaluate side-chains 558 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 497 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 742 GLU Chi-restraints excluded: chain A residue 813 ASP Chi-restraints excluded: chain A residue 819 ILE Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 887 ASP Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 317 GLN Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 435 GLN Chi-restraints excluded: chain B residue 446 PHE Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 938 THR Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 74 GLU Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 367 GLU Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 556 VAL Chi-restraints excluded: chain C residue 567 PHE Chi-restraints excluded: chain C residue 622 MET Chi-restraints excluded: chain C residue 662 ASN Chi-restraints excluded: chain C residue 749 VAL Chi-restraints excluded: chain C residue 775 ASN Chi-restraints excluded: chain C residue 836 MET Chi-restraints excluded: chain C residue 856 VAL Chi-restraints excluded: chain C residue 870 LEU Chi-restraints excluded: chain C residue 887 ASP Chi-restraints excluded: chain C residue 925 VAL Chi-restraints excluded: chain C residue 928 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 92 optimal weight: 7.9990 chunk 248 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 245 optimal weight: 7.9990 chunk 90 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 228 optimal weight: 0.8980 chunk 114 optimal weight: 0.7980 chunk 198 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 268 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 471 ASN B 317 GLN B 365 ASN B 825 ASN C 362 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.118404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.099312 restraints weight = 32359.702| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.12 r_work: 0.3055 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22599 Z= 0.127 Angle : 0.510 8.540 30732 Z= 0.274 Chirality : 0.044 0.158 3246 Planarity : 0.005 0.059 4047 Dihedral : 5.329 76.779 3064 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.65 % Favored : 95.32 % Rotamer: Outliers : 2.67 % Allowed : 12.11 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.11 (0.15), residues: 2733 helix: 0.53 (0.30), residues: 336 sheet: 0.40 (0.21), residues: 576 loop : -1.46 (0.13), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 46 TYR 0.014 0.001 TYR B 326 PHE 0.016 0.001 PHE A 846 TRP 0.023 0.001 TRP C 135 HIS 0.006 0.001 HIS C 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (22599) covalent geometry : angle 0.51046 / 0.27 (30732) hydrogen bonds : bond 0.03625 / 2.36 ( 543) hydrogen bonds : angle 4.96122 / 3.43 ( 1470) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5466 Ramachandran restraints generated. 2733 Oldfield, 0 Emsley, 2733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5466 Ramachandran restraints generated. 2733 Oldfield, 0 Emsley, 2733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 499 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLN cc_start: 0.5899 (OUTLIER) cc_final: 0.5444 (tp-100) REVERT: A 42 ASN cc_start: 0.8058 (m110) cc_final: 0.7699 (m110) REVERT: A 107 LEU cc_start: 0.8590 (tp) cc_final: 0.8345 (tp) REVERT: A 192 THR cc_start: 0.8273 (m) cc_final: 0.7955 (p) REVERT: A 362 GLN cc_start: 0.8355 (mt0) cc_final: 0.8055 (mt0) REVERT: A 413 TYR cc_start: 0.8649 (m-80) cc_final: 0.8165 (m-80) REVERT: A 451 GLU cc_start: 0.7559 (mm-30) cc_final: 0.6965 (mm-30) REVERT: A 476 ASN cc_start: 0.8645 (m-40) cc_final: 0.8265 (m110) REVERT: A 497 ASN cc_start: 0.8327 (t0) cc_final: 0.7939 (t0) REVERT: A 633 MET cc_start: 0.7227 (mtm) cc_final: 0.6600 (ttp) REVERT: A 636 ASN cc_start: 0.7563 (m-40) cc_final: 0.7052 (m110) REVERT: A 708 LEU cc_start: 0.8733 (mt) cc_final: 0.8493 (mp) REVERT: A 717 THR cc_start: 0.8545 (OUTLIER) cc_final: 0.8189 (p) REVERT: A 735 ASP cc_start: 0.7095 (t0) cc_final: 0.6507 (t0) REVERT: A 742 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.6837 (pp20) REVERT: A 801 MET cc_start: 0.8458 (mtm) cc_final: 0.8053 (mtt) REVERT: A 815 GLN cc_start: 0.8250 (mm-40) cc_final: 0.7950 (mm-40) REVERT: A 928 VAL cc_start: 0.8311 (t) cc_final: 0.7978 (p) REVERT: A 937 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7746 (mm-30) REVERT: A 945 PHE cc_start: 0.8403 (m-80) cc_final: 0.8132 (m-10) REVERT: B 135 TRP cc_start: 0.7563 (p90) cc_final: 0.7133 (p-90) REVERT: B 208 GLU cc_start: 0.7147 (pm20) cc_final: 0.6893 (pm20) REVERT: B 290 ASP cc_start: 0.7615 (t0) cc_final: 0.7386 (t0) REVERT: B 380 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.8317 (tpt90) REVERT: B 409 GLU cc_start: 0.7677 (mp0) cc_final: 0.7396 (mp0) REVERT: B 439 TRP cc_start: 0.7976 (m100) cc_final: 0.7750 (m100) REVERT: B 446 PHE cc_start: 0.6252 (OUTLIER) cc_final: 0.5259 (m-10) REVERT: B 484 LYS cc_start: 0.8121 (ptmt) cc_final: 0.7903 (ptpp) REVERT: B 591 MET cc_start: 0.8119 (mmm) cc_final: 0.7678 (mmm) REVERT: B 628 SER cc_start: 0.7729 (t) cc_final: 0.7421 (p) REVERT: B 636 ASN cc_start: 0.7413 (m-40) cc_final: 0.6735 (m110) REVERT: B 687 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8466 (pt0) REVERT: B 807 ASP cc_start: 0.7635 (t0) cc_final: 0.7349 (t0) REVERT: B 903 MET cc_start: 0.8193 (mtp) cc_final: 0.7868 (mtm) REVERT: B 928 VAL cc_start: 0.8454 (t) cc_final: 0.8108 (p) REVERT: C 137 GLU cc_start: 0.7510 (mt-10) cc_final: 0.7164 (mt-10) REVERT: C 165 LYS cc_start: 0.7174 (mmtp) cc_final: 0.6928 (mmmm) REVERT: C 252 LYS cc_start: 0.8178 (tppp) cc_final: 0.7526 (tppp) REVERT: C 264 MET cc_start: 0.8237 (mtm) cc_final: 0.7849 (mtm) REVERT: C 290 ASP cc_start: 0.7467 (t0) cc_final: 0.7133 (m-30) REVERT: C 315 MET cc_start: 0.6291 (tpp) cc_final: 0.5936 (mmm) REVERT: C 367 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.7145 (mt-10) REVERT: C 439 TRP cc_start: 0.7979 (m100) cc_final: 0.7689 (m100) REVERT: C 484 LYS cc_start: 0.8325 (ptmt) cc_final: 0.8080 (pttm) REVERT: C 515 ASP cc_start: 0.6934 (t0) cc_final: 0.6678 (m-30) REVERT: C 580 THR cc_start: 0.7878 (m) cc_final: 0.7591 (p) REVERT: C 636 ASN cc_start: 0.7938 (t0) cc_final: 0.7702 (t0) REVERT: C 670 ARG cc_start: 0.7984 (ttm-80) cc_final: 0.7715 (ptp-110) REVERT: C 676 ARG cc_start: 0.8481 (mtp180) cc_final: 0.8247 (mtm110) REVERT: C 690 SER cc_start: 0.7942 (t) cc_final: 0.7564 (p) REVERT: C 719 LYS cc_start: 0.8700 (ttmt) cc_final: 0.8448 (ttmm) REVERT: C 774 TYR cc_start: 0.8348 (m-80) cc_final: 0.7759 (m-80) REVERT: C 793 SER cc_start: 0.8895 (m) cc_final: 0.8331 (t) REVERT: C 817 VAL cc_start: 0.8475 (t) cc_final: 0.7686 (p) REVERT: C 902 ASP cc_start: 0.7970 (m-30) cc_final: 0.7766 (m-30) REVERT: C 926 VAL cc_start: 0.7978 (t) cc_final: 0.7625 (p) outliers start: 64 outliers final: 53 residues processed: 536 average time/residue: 0.1486 time to fit residues: 119.4340 Evaluate side-chains 556 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 496 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 742 GLU Chi-restraints excluded: chain A residue 813 ASP Chi-restraints excluded: chain A residue 819 ILE Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 887 ASP Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 317 GLN Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 435 GLN Chi-restraints excluded: chain B residue 446 PHE Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 938 THR Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 74 GLU Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 367 GLU Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 556 VAL Chi-restraints excluded: chain C residue 567 PHE Chi-restraints excluded: chain C residue 622 MET Chi-restraints excluded: chain C residue 749 VAL Chi-restraints excluded: chain C residue 786 SER Chi-restraints excluded: chain C residue 829 VAL Chi-restraints excluded: chain C residue 836 MET Chi-restraints excluded: chain C residue 856 VAL Chi-restraints excluded: chain C residue 870 LEU Chi-restraints excluded: chain C residue 887 ASP Chi-restraints excluded: chain C residue 906 GLU Chi-restraints excluded: chain C residue 925 VAL Chi-restraints excluded: chain C residue 928 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 41 optimal weight: 0.0370 chunk 88 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 243 optimal weight: 0.8980 chunk 125 optimal weight: 2.9990 chunk 245 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 218 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 197 optimal weight: 0.8980 chunk 46 optimal weight: 0.0670 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 14 HIS B 310 ASN B 317 GLN B 332 ASN B 365 ASN B 825 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.119822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.100635 restraints weight = 32258.172| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.12 r_work: 0.3043 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 22599 Z= 0.093 Angle : 0.486 8.071 30732 Z= 0.259 Chirality : 0.043 0.156 3246 Planarity : 0.004 0.059 4047 Dihedral : 5.115 77.088 3064 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.50 % Favored : 95.46 % Rotamer: Outliers : 2.42 % Allowed : 12.49 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.95 (0.15), residues: 2733 helix: 0.71 (0.30), residues: 336 sheet: 0.46 (0.22), residues: 576 loop : -1.33 (0.13), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 46 TYR 0.019 0.001 TYR C 787 PHE 0.025 0.001 PHE A 846 TRP 0.022 0.001 TRP C 135 HIS 0.004 0.001 HIS C 823 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.09 (22599) covalent geometry : angle 0.48640 / 0.26 (30732) hydrogen bonds : bond 0.03206 / 2.08 ( 543) hydrogen bonds : angle 4.83734 / 3.33 ( 1470) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5466 Ramachandran restraints generated. 2733 Oldfield, 0 Emsley, 2733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5466 Ramachandran restraints generated. 2733 Oldfield, 0 Emsley, 2733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 491 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLN cc_start: 0.5837 (OUTLIER) cc_final: 0.5473 (tp-100) REVERT: A 42 ASN cc_start: 0.8009 (m110) cc_final: 0.7668 (m110) REVERT: A 107 LEU cc_start: 0.8586 (tp) cc_final: 0.8346 (tp) REVERT: A 192 THR cc_start: 0.8271 (m) cc_final: 0.7952 (p) REVERT: A 261 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7974 (mm-40) REVERT: A 362 GLN cc_start: 0.8360 (mt0) cc_final: 0.8058 (mt0) REVERT: A 413 TYR cc_start: 0.8598 (m-80) cc_final: 0.8215 (m-80) REVERT: A 451 GLU cc_start: 0.7541 (mm-30) cc_final: 0.6844 (mm-30) REVERT: A 476 ASN cc_start: 0.8614 (m-40) cc_final: 0.8190 (m110) REVERT: A 497 ASN cc_start: 0.8344 (t0) cc_final: 0.7909 (t0) REVERT: A 633 MET cc_start: 0.7111 (mtm) cc_final: 0.6690 (ttp) REVERT: A 636 ASN cc_start: 0.7490 (m-40) cc_final: 0.6935 (m110) REVERT: A 708 LEU cc_start: 0.8641 (mt) cc_final: 0.8423 (mp) REVERT: A 717 THR cc_start: 0.8491 (OUTLIER) cc_final: 0.8063 (p) REVERT: A 735 ASP cc_start: 0.7053 (t0) cc_final: 0.6454 (t0) REVERT: A 742 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.6785 (pp20) REVERT: A 801 MET cc_start: 0.8434 (mtm) cc_final: 0.8061 (mtt) REVERT: A 815 GLN cc_start: 0.8225 (mm-40) cc_final: 0.7896 (mm-40) REVERT: A 858 SER cc_start: 0.8444 (p) cc_final: 0.8202 (m) REVERT: A 928 VAL cc_start: 0.8357 (t) cc_final: 0.8013 (p) REVERT: A 937 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7684 (mm-30) REVERT: A 939 VAL cc_start: 0.8672 (OUTLIER) cc_final: 0.8469 (t) REVERT: A 945 PHE cc_start: 0.8379 (m-80) cc_final: 0.8101 (m-10) REVERT: B 135 TRP cc_start: 0.7477 (p90) cc_final: 0.7035 (p-90) REVERT: B 208 GLU cc_start: 0.7159 (pm20) cc_final: 0.6888 (pm20) REVERT: B 290 ASP cc_start: 0.7649 (t0) cc_final: 0.7408 (t0) REVERT: B 310 ASN cc_start: 0.7506 (m110) cc_final: 0.6960 (t0) REVERT: B 409 GLU cc_start: 0.7708 (mp0) cc_final: 0.7412 (mp0) REVERT: B 439 TRP cc_start: 0.7905 (m100) cc_final: 0.7699 (m100) REVERT: B 445 GLU cc_start: 0.6805 (tm-30) cc_final: 0.6581 (tm-30) REVERT: B 446 PHE cc_start: 0.6004 (OUTLIER) cc_final: 0.5015 (m-10) REVERT: B 484 LYS cc_start: 0.8116 (ptmt) cc_final: 0.7894 (ptpp) REVERT: B 591 MET cc_start: 0.8076 (mmm) cc_final: 0.7591 (mmm) REVERT: B 628 SER cc_start: 0.7608 (t) cc_final: 0.7261 (p) REVERT: B 670 ARG cc_start: 0.8195 (ptp-110) cc_final: 0.7985 (ptp90) REVERT: B 774 TYR cc_start: 0.8234 (m-80) cc_final: 0.7470 (m-80) REVERT: B 807 ASP cc_start: 0.7658 (t0) cc_final: 0.7345 (t0) REVERT: B 903 MET cc_start: 0.8183 (mtp) cc_final: 0.7979 (mtm) REVERT: B 928 VAL cc_start: 0.8362 (t) cc_final: 0.8000 (p) REVERT: C 137 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7114 (mt-10) REVERT: C 165 LYS cc_start: 0.7126 (mmtp) cc_final: 0.6849 (mmmm) REVERT: C 252 LYS cc_start: 0.8148 (tppp) cc_final: 0.7483 (tppp) REVERT: C 264 MET cc_start: 0.8197 (mtm) cc_final: 0.7783 (mtm) REVERT: C 290 ASP cc_start: 0.7503 (t0) cc_final: 0.7145 (m-30) REVERT: C 367 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.7086 (mt-10) REVERT: C 439 TRP cc_start: 0.7864 (m100) cc_final: 0.7624 (m100) REVERT: C 484 LYS cc_start: 0.8307 (ptmt) cc_final: 0.8054 (pttm) REVERT: C 515 ASP cc_start: 0.6959 (t0) cc_final: 0.6680 (m-30) REVERT: C 579 TYR cc_start: 0.8182 (m-80) cc_final: 0.7778 (m-80) REVERT: C 670 ARG cc_start: 0.7898 (ttm-80) cc_final: 0.7618 (ptp-110) REVERT: C 676 ARG cc_start: 0.8399 (mtp180) cc_final: 0.8148 (mtm110) REVERT: C 690 SER cc_start: 0.7889 (t) cc_final: 0.7595 (p) REVERT: C 719 LYS cc_start: 0.8625 (ttmt) cc_final: 0.8402 (ttmm) REVERT: C 774 TYR cc_start: 0.8251 (m-80) cc_final: 0.6670 (m-80) REVERT: C 793 SER cc_start: 0.8917 (m) cc_final: 0.8373 (t) REVERT: C 817 VAL cc_start: 0.8423 (t) cc_final: 0.7662 (p) REVERT: C 926 VAL cc_start: 0.7926 (t) cc_final: 0.7582 (p) outliers start: 58 outliers final: 48 residues processed: 528 average time/residue: 0.1502 time to fit residues: 119.3303 Evaluate side-chains 538 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 483 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 742 GLU Chi-restraints excluded: chain A residue 813 ASP Chi-restraints excluded: chain A residue 819 ILE Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 887 ASP Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 317 GLN Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 435 GLN Chi-restraints excluded: chain B residue 446 PHE Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 938 THR Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 74 GLU Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 367 GLU Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 556 VAL Chi-restraints excluded: chain C residue 567 PHE Chi-restraints excluded: chain C residue 622 MET Chi-restraints excluded: chain C residue 749 VAL Chi-restraints excluded: chain C residue 813 ASP Chi-restraints excluded: chain C residue 829 VAL Chi-restraints excluded: chain C residue 836 MET Chi-restraints excluded: chain C residue 856 VAL Chi-restraints excluded: chain C residue 870 LEU Chi-restraints excluded: chain C residue 887 ASP Chi-restraints excluded: chain C residue 906 GLU Chi-restraints excluded: chain C residue 928 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 149 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 202 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 198 optimal weight: 2.9990 chunk 184 optimal weight: 2.9990 chunk 213 optimal weight: 8.9990 chunk 182 optimal weight: 6.9990 chunk 264 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 chunk 131 optimal weight: 0.0980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 14 HIS B 317 GLN B 825 ASN C 362 GLN ** C 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.118410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.099247 restraints weight = 32461.694| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.11 r_work: 0.3054 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22599 Z= 0.148 Angle : 0.521 9.802 30732 Z= 0.278 Chirality : 0.045 0.159 3246 Planarity : 0.005 0.060 4047 Dihedral : 5.211 76.441 3064 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.05 % Favored : 94.91 % Rotamer: Outliers : 2.59 % Allowed : 12.36 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.98 (0.15), residues: 2733 helix: 0.63 (0.30), residues: 336 sheet: 0.50 (0.22), residues: 573 loop : -1.37 (0.13), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 46 TYR 0.014 0.001 TYR A 326 PHE 0.027 0.002 PHE A 846 TRP 0.034 0.001 TRP C 135 HIS 0.007 0.001 HIS A 823 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (22599) covalent geometry : angle 0.52132 / 0.28 (30732) hydrogen bonds : bond 0.03789 / 2.49 ( 543) hydrogen bonds : angle 4.84172 / 3.33 ( 1470) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5466 Ramachandran restraints generated. 2733 Oldfield, 0 Emsley, 2733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5466 Ramachandran restraints generated. 2733 Oldfield, 0 Emsley, 2733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 486 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLN cc_start: 0.5884 (OUTLIER) cc_final: 0.5504 (tp-100) REVERT: A 42 ASN cc_start: 0.8042 (m110) cc_final: 0.7722 (m110) REVERT: A 107 LEU cc_start: 0.8605 (tp) cc_final: 0.8364 (tp) REVERT: A 192 THR cc_start: 0.8263 (m) cc_final: 0.7947 (p) REVERT: A 311 SER cc_start: 0.8676 (p) cc_final: 0.8388 (p) REVERT: A 362 GLN cc_start: 0.8384 (mt0) cc_final: 0.8075 (mt0) REVERT: A 413 TYR cc_start: 0.8644 (m-80) cc_final: 0.8176 (m-80) REVERT: A 451 GLU cc_start: 0.7545 (mm-30) cc_final: 0.6964 (mm-30) REVERT: A 476 ASN cc_start: 0.8647 (m-40) cc_final: 0.8254 (m110) REVERT: A 497 ASN cc_start: 0.8347 (t0) cc_final: 0.7966 (t0) REVERT: A 633 MET cc_start: 0.7254 (mtm) cc_final: 0.6784 (ttp) REVERT: A 636 ASN cc_start: 0.7585 (m-40) cc_final: 0.7065 (m110) REVERT: A 708 LEU cc_start: 0.8709 (mt) cc_final: 0.8500 (mp) REVERT: A 735 ASP cc_start: 0.7114 (t0) cc_final: 0.6526 (t0) REVERT: A 742 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.6818 (pp20) REVERT: A 801 MET cc_start: 0.8433 (mtm) cc_final: 0.8027 (mtt) REVERT: A 815 GLN cc_start: 0.8270 (mm-40) cc_final: 0.8027 (mm-40) REVERT: A 928 VAL cc_start: 0.8356 (t) cc_final: 0.8006 (p) REVERT: A 937 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7734 (mm-30) REVERT: A 939 VAL cc_start: 0.8742 (OUTLIER) cc_final: 0.8518 (t) REVERT: A 945 PHE cc_start: 0.8412 (m-80) cc_final: 0.8131 (m-10) REVERT: B 135 TRP cc_start: 0.7559 (p90) cc_final: 0.7111 (p-90) REVERT: B 208 GLU cc_start: 0.7207 (pm20) cc_final: 0.6958 (pm20) REVERT: B 290 ASP cc_start: 0.7620 (t0) cc_final: 0.7405 (t0) REVERT: B 310 ASN cc_start: 0.7614 (m110) cc_final: 0.7134 (t0) REVERT: B 409 GLU cc_start: 0.7653 (mp0) cc_final: 0.7364 (mp0) REVERT: B 439 TRP cc_start: 0.8042 (m100) cc_final: 0.7776 (m100) REVERT: B 446 PHE cc_start: 0.6139 (OUTLIER) cc_final: 0.5073 (m-10) REVERT: B 484 LYS cc_start: 0.8132 (ptmt) cc_final: 0.7918 (ptpp) REVERT: B 591 MET cc_start: 0.8108 (mmm) cc_final: 0.7638 (mmm) REVERT: B 628 SER cc_start: 0.7736 (t) cc_final: 0.7418 (p) REVERT: B 636 ASN cc_start: 0.7413 (m-40) cc_final: 0.6796 (m110) REVERT: B 687 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8468 (pt0) REVERT: B 690 SER cc_start: 0.7936 (t) cc_final: 0.7585 (p) REVERT: B 807 ASP cc_start: 0.7622 (t0) cc_final: 0.7340 (t0) REVERT: B 903 MET cc_start: 0.8194 (mtp) cc_final: 0.7965 (mtm) REVERT: B 928 VAL cc_start: 0.8445 (t) cc_final: 0.8109 (p) REVERT: C 135 TRP cc_start: 0.7392 (p90) cc_final: 0.7105 (p-90) REVERT: C 137 GLU cc_start: 0.7538 (mt-10) cc_final: 0.6473 (mt-10) REVERT: C 165 LYS cc_start: 0.7173 (mmtp) cc_final: 0.6967 (mmmm) REVERT: C 252 LYS cc_start: 0.8179 (tppp) cc_final: 0.7517 (tppp) REVERT: C 264 MET cc_start: 0.8248 (mtm) cc_final: 0.7853 (mtm) REVERT: C 290 ASP cc_start: 0.7472 (t0) cc_final: 0.7140 (m-30) REVERT: C 315 MET cc_start: 0.5965 (tpp) cc_final: 0.4638 (mmt) REVERT: C 367 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.7161 (mt-10) REVERT: C 439 TRP cc_start: 0.7970 (m100) cc_final: 0.7643 (m100) REVERT: C 484 LYS cc_start: 0.8320 (ptmt) cc_final: 0.8089 (pttm) REVERT: C 515 ASP cc_start: 0.6927 (t0) cc_final: 0.6667 (m-30) REVERT: C 579 TYR cc_start: 0.8221 (m-80) cc_final: 0.7905 (m-80) REVERT: C 636 ASN cc_start: 0.7926 (t0) cc_final: 0.7696 (t0) REVERT: C 670 ARG cc_start: 0.8016 (ttm-80) cc_final: 0.7748 (ptp-110) REVERT: C 676 ARG cc_start: 0.8470 (mtp180) cc_final: 0.8256 (mtm110) REVERT: C 719 LYS cc_start: 0.8693 (ttmt) cc_final: 0.8460 (ttmm) REVERT: C 793 SER cc_start: 0.8870 (m) cc_final: 0.8289 (t) REVERT: C 817 VAL cc_start: 0.8468 (t) cc_final: 0.7674 (p) REVERT: C 926 VAL cc_start: 0.7983 (t) cc_final: 0.7646 (p) outliers start: 62 outliers final: 52 residues processed: 520 average time/residue: 0.1438 time to fit residues: 113.4422 Evaluate side-chains 544 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 486 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 686 LYS Chi-restraints excluded: chain A residue 742 GLU Chi-restraints excluded: chain A residue 813 ASP Chi-restraints excluded: chain A residue 819 ILE Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 887 ASP Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 317 GLN Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 435 GLN Chi-restraints excluded: chain B residue 446 PHE Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 686 LYS Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 938 THR Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 74 GLU Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 367 GLU Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 556 VAL Chi-restraints excluded: chain C residue 567 PHE Chi-restraints excluded: chain C residue 622 MET Chi-restraints excluded: chain C residue 662 ASN Chi-restraints excluded: chain C residue 749 VAL Chi-restraints excluded: chain C residue 813 ASP Chi-restraints excluded: chain C residue 829 VAL Chi-restraints excluded: chain C residue 836 MET Chi-restraints excluded: chain C residue 856 VAL Chi-restraints excluded: chain C residue 870 LEU Chi-restraints excluded: chain C residue 887 ASP Chi-restraints excluded: chain C residue 906 GLU Chi-restraints excluded: chain C residue 925 VAL Chi-restraints excluded: chain C residue 928 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 124 optimal weight: 2.9990 chunk 66 optimal weight: 0.0670 chunk 156 optimal weight: 0.0170 chunk 101 optimal weight: 2.9990 chunk 249 optimal weight: 0.5980 chunk 168 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 202 optimal weight: 0.5980 chunk 165 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 14 HIS B 317 GLN B 365 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.119969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.100759 restraints weight = 32334.043| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.12 r_work: 0.3063 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 22599 Z= 0.087 Angle : 0.482 9.945 30732 Z= 0.255 Chirality : 0.043 0.157 3246 Planarity : 0.004 0.059 4047 Dihedral : 5.014 76.559 3063 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.13 % Favored : 95.83 % Rotamer: Outliers : 2.34 % Allowed : 12.82 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.82 (0.15), residues: 2733 helix: 0.81 (0.31), residues: 336 sheet: 0.52 (0.22), residues: 576 loop : -1.24 (0.13), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 46 TYR 0.014 0.001 TYR B 787 PHE 0.027 0.001 PHE A 846 TRP 0.024 0.001 TRP C 135 HIS 0.005 0.001 HIS C 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00199 / 0.09 (22599) covalent geometry : angle 0.48167 / 0.26 (30732) hydrogen bonds : bond 0.03003 / 1.95 ( 543) hydrogen bonds : angle 4.76396 / 3.28 ( 1470) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5466 Ramachandran restraints generated. 2733 Oldfield, 0 Emsley, 2733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5466 Ramachandran restraints generated. 2733 Oldfield, 0 Emsley, 2733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 488 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLN cc_start: 0.5709 (OUTLIER) cc_final: 0.5339 (tp-100) REVERT: A 42 ASN cc_start: 0.8026 (m110) cc_final: 0.7756 (m110) REVERT: A 107 LEU cc_start: 0.8564 (tp) cc_final: 0.8325 (tp) REVERT: A 192 THR cc_start: 0.8249 (m) cc_final: 0.7943 (p) REVERT: A 297 ASP cc_start: 0.7606 (p0) cc_final: 0.7348 (p0) REVERT: A 362 GLN cc_start: 0.8369 (mt0) cc_final: 0.8062 (mt0) REVERT: A 413 TYR cc_start: 0.8579 (m-80) cc_final: 0.8222 (m-80) REVERT: A 451 GLU cc_start: 0.7501 (mm-30) cc_final: 0.6906 (mm-30) REVERT: A 476 ASN cc_start: 0.8622 (m-40) cc_final: 0.8202 (m110) REVERT: A 497 ASN cc_start: 0.8354 (t0) cc_final: 0.7966 (t0) REVERT: A 633 MET cc_start: 0.7142 (mtm) cc_final: 0.6746 (ttp) REVERT: A 636 ASN cc_start: 0.7554 (m-40) cc_final: 0.7037 (m110) REVERT: A 735 ASP cc_start: 0.7077 (t0) cc_final: 0.6491 (t0) REVERT: A 742 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.6808 (pp20) REVERT: A 801 MET cc_start: 0.8393 (mtm) cc_final: 0.7999 (mtt) REVERT: A 815 GLN cc_start: 0.8252 (mm-40) cc_final: 0.8004 (mm-40) REVERT: A 928 VAL cc_start: 0.8389 (t) cc_final: 0.8049 (p) REVERT: A 937 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7681 (mm-30) REVERT: A 939 VAL cc_start: 0.8698 (OUTLIER) cc_final: 0.8466 (t) REVERT: A 945 PHE cc_start: 0.8399 (m-80) cc_final: 0.8121 (m-10) REVERT: B 135 TRP cc_start: 0.7466 (p90) cc_final: 0.7043 (p-90) REVERT: B 136 ASP cc_start: 0.7305 (m-30) cc_final: 0.7097 (m-30) REVERT: B 290 ASP cc_start: 0.7595 (t0) cc_final: 0.7357 (t0) REVERT: B 310 ASN cc_start: 0.7519 (m110) cc_final: 0.6989 (t0) REVERT: B 409 GLU cc_start: 0.7666 (mp0) cc_final: 0.7384 (mp0) REVERT: B 446 PHE cc_start: 0.5970 (OUTLIER) cc_final: 0.4999 (m-80) REVERT: B 484 LYS cc_start: 0.8123 (ptmt) cc_final: 0.7916 (ptpp) REVERT: B 628 SER cc_start: 0.7578 (t) cc_final: 0.7265 (p) REVERT: B 670 ARG cc_start: 0.8236 (ptp90) cc_final: 0.7940 (ptp90) REVERT: B 687 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8417 (pt0) REVERT: B 690 SER cc_start: 0.7908 (t) cc_final: 0.7564 (p) REVERT: B 774 TYR cc_start: 0.8235 (m-80) cc_final: 0.7469 (m-80) REVERT: B 782 TYR cc_start: 0.8712 (p90) cc_final: 0.8364 (p90) REVERT: B 807 ASP cc_start: 0.7589 (t0) cc_final: 0.7345 (t0) REVERT: B 903 MET cc_start: 0.8226 (mtp) cc_final: 0.7894 (mtm) REVERT: B 928 VAL cc_start: 0.8390 (t) cc_final: 0.8034 (p) REVERT: C 137 GLU cc_start: 0.7522 (mt-10) cc_final: 0.7141 (mt-10) REVERT: C 165 LYS cc_start: 0.7253 (mmtp) cc_final: 0.7005 (mmmm) REVERT: C 252 LYS cc_start: 0.8170 (tppp) cc_final: 0.7514 (tppp) REVERT: C 264 MET cc_start: 0.8233 (mtm) cc_final: 0.7798 (mtm) REVERT: C 290 ASP cc_start: 0.7470 (t0) cc_final: 0.7135 (m-30) REVERT: C 315 MET cc_start: 0.5875 (tpp) cc_final: 0.4735 (mmt) REVERT: C 367 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.7077 (mt-10) REVERT: C 439 TRP cc_start: 0.7866 (m100) cc_final: 0.7659 (m100) REVERT: C 484 LYS cc_start: 0.8301 (ptmt) cc_final: 0.8062 (pttm) REVERT: C 515 ASP cc_start: 0.6931 (t0) cc_final: 0.6661 (m-30) REVERT: C 579 TYR cc_start: 0.8141 (m-80) cc_final: 0.7898 (m-80) REVERT: C 670 ARG cc_start: 0.7968 (ttm-80) cc_final: 0.7760 (ptp-110) REVERT: C 690 SER cc_start: 0.7937 (t) cc_final: 0.7645 (p) REVERT: C 719 LYS cc_start: 0.8660 (ttmt) cc_final: 0.8453 (ttmm) REVERT: C 774 TYR cc_start: 0.8261 (m-80) cc_final: 0.6757 (m-80) REVERT: C 793 SER cc_start: 0.8922 (m) cc_final: 0.8395 (t) REVERT: C 817 VAL cc_start: 0.8471 (t) cc_final: 0.7708 (p) REVERT: C 926 VAL cc_start: 0.7934 (t) cc_final: 0.7588 (p) outliers start: 56 outliers final: 44 residues processed: 522 average time/residue: 0.1494 time to fit residues: 117.8900 Evaluate side-chains 531 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 481 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 686 LYS Chi-restraints excluded: chain A residue 742 GLU Chi-restraints excluded: chain A residue 813 ASP Chi-restraints excluded: chain A residue 819 ILE Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 887 ASP Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 317 GLN Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 435 GLN Chi-restraints excluded: chain B residue 446 PHE Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 74 GLU Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 367 GLU Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 556 VAL Chi-restraints excluded: chain C residue 567 PHE Chi-restraints excluded: chain C residue 622 MET Chi-restraints excluded: chain C residue 749 VAL Chi-restraints excluded: chain C residue 813 ASP Chi-restraints excluded: chain C residue 829 VAL Chi-restraints excluded: chain C residue 836 MET Chi-restraints excluded: chain C residue 856 VAL Chi-restraints excluded: chain C residue 870 LEU Chi-restraints excluded: chain C residue 887 ASP Chi-restraints excluded: chain C residue 906 GLU Chi-restraints excluded: chain C residue 928 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 1 optimal weight: 9.9990 chunk 39 optimal weight: 0.1980 chunk 186 optimal weight: 5.9990 chunk 249 optimal weight: 0.0980 chunk 187 optimal weight: 4.9990 chunk 135 optimal weight: 0.9990 chunk 203 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 232 optimal weight: 1.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 14 HIS B 317 GLN B 365 ASN B 825 ASN C 404 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.119977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.100809 restraints weight = 32442.232| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.11 r_work: 0.3080 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 22599 Z= 0.101 Angle : 0.492 10.017 30732 Z= 0.261 Chirality : 0.043 0.157 3246 Planarity : 0.004 0.057 4047 Dihedral : 5.020 76.824 3063 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.32 % Favored : 95.65 % Rotamer: Outliers : 2.26 % Allowed : 12.91 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.78 (0.15), residues: 2733 helix: 0.81 (0.30), residues: 336 sheet: 0.56 (0.22), residues: 576 loop : -1.21 (0.14), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 46 TYR 0.014 0.001 TYR A 787 PHE 0.027 0.001 PHE A 846 TRP 0.022 0.001 TRP C 135 HIS 0.005 0.001 HIS A 823 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.10 (22599) covalent geometry : angle 0.49175 / 0.26 (30732) hydrogen bonds : bond 0.03186 / 2.07 ( 543) hydrogen bonds : angle 4.71867 / 3.24 ( 1470) =============================================================================== Job complete usr+sys time: 4982.25 seconds wall clock time: 85 minutes 48.76 seconds (5148.76 seconds total)