Starting phenix.real_space_refine on Tue Nov 18 12:24:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ygo_39258/11_2025/8ygo_39258.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ygo_39258/11_2025/8ygo_39258.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ygo_39258/11_2025/8ygo_39258.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ygo_39258/11_2025/8ygo_39258.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ygo_39258/11_2025/8ygo_39258.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ygo_39258/11_2025/8ygo_39258.map" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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 55 5.16 5 C 9170 2.51 5 N 2283 2.21 5 O 2700 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14208 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 703, 5890 Classifications: {'peptide': 703} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 693} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 5930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 707, 5930 Classifications: {'peptide': 707} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 697} Chain: "C" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1190 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 1 Chain: "D" Number of atoms: 1198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1198 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 1 Time building chain proxies: 3.54, per 1000 atoms: 0.25 Number of scatterers: 14208 At special positions: 0 Unit cell: (117.86, 113.71, 112.05, 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 55 16.00 O 2700 8.00 N 2283 7.00 C 9170 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: 1.24 Conformation dependent library (CDL) restraints added in 665.4 milliseconds 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3262 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 8 sheets defined 62.3% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 304 through 315 removed outlier: 3.533A pdb=" N VAL A 308 " --> pdb=" O LYS A 304 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N TYR A 311 " --> pdb=" O GLU A 307 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE A 312 " --> pdb=" O VAL A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 321 removed outlier: 3.975A pdb=" N ALA A 321 " --> pdb=" O PRO A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 328 No H-bonds generated for 'chain 'A' and resid 326 through 328' Processing helix chain 'A' and resid 329 through 334 removed outlier: 4.145A pdb=" N VAL A 333 " --> pdb=" O ASP A 329 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 329 through 334' Processing helix chain 'A' and resid 355 through 366 removed outlier: 4.202A pdb=" N PHE A 360 " --> pdb=" O TYR A 356 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE A 361 " --> pdb=" O MET A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 372 removed outlier: 4.186A pdb=" N SER A 371 " --> pdb=" O CYS A 367 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS A 372 " --> pdb=" O ASP A 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 367 through 372' Processing helix chain 'A' and resid 374 through 392 Processing helix chain 'A' and resid 411 through 416 removed outlier: 3.870A pdb=" N HIS A 415 " --> pdb=" O SER A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 426 removed outlier: 3.594A pdb=" N GLU A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 445 Processing helix chain 'A' and resid 447 through 462 removed outlier: 3.722A pdb=" N SER A 451 " --> pdb=" O ARG A 447 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N TYR A 452 " --> pdb=" O TRP A 448 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP A 453 " --> pdb=" O GLU A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 500 removed outlier: 4.401A pdb=" N TYR A 471 " --> pdb=" O ASN A 467 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N LEU A 497 " --> pdb=" O ASN A 493 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N LEU A 498 " --> pdb=" O GLY A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 520 Processing helix chain 'A' and resid 532 through 539 removed outlier: 3.734A pdb=" N TYR A 539 " --> pdb=" O PHE A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 546 removed outlier: 4.733A pdb=" N PHE A 544 " --> pdb=" O ILE A 541 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 545 " --> pdb=" O LEU A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 572 removed outlier: 3.563A pdb=" N TYR A 552 " --> pdb=" O ASN A 548 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS A 557 " --> pdb=" O ASP A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 598 removed outlier: 3.888A pdb=" N VAL A 583 " --> pdb=" O SER A 579 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL A 584 " --> pdb=" O SER A 580 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN A 598 " --> pdb=" O PHE A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 604 removed outlier: 3.938A pdb=" N VAL A 603 " --> pdb=" O LEU A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 628 removed outlier: 3.739A pdb=" N THR A 628 " --> pdb=" O GLU A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 639 removed outlier: 3.646A pdb=" N PHE A 638 " --> pdb=" O LEU A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 659 Processing helix chain 'A' and resid 660 through 670 Processing helix chain 'A' and resid 680 through 701 removed outlier: 3.593A pdb=" N ILE A 684 " --> pdb=" O GLU A 680 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA A 701 " --> pdb=" O LYS A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 723 removed outlier: 3.594A pdb=" N GLN A 711 " --> pdb=" O VAL A 707 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N SER A 714 " --> pdb=" O THR A 710 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N GLU A 715 " --> pdb=" O GLN A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 726 No H-bonds generated for 'chain 'A' and resid 724 through 726' Processing helix chain 'A' and resid 729 through 742 Processing helix chain 'A' and resid 750 through 765 removed outlier: 4.431A pdb=" N CYS A 764 " --> pdb=" O ARG A 760 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASN A 765 " --> pdb=" O LEU A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 786 removed outlier: 3.560A pdb=" N ILE A 772 " --> pdb=" O PRO A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 812 removed outlier: 3.904A pdb=" N ASP A 803 " --> pdb=" O LEU A 799 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N TYR A 804 " --> pdb=" O TYR A 800 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N PHE A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 826 removed outlier: 3.552A pdb=" N CYS A 826 " --> pdb=" O GLU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 840 removed outlier: 3.947A pdb=" N LYS A 840 " --> pdb=" O ASP A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 845 Processing helix chain 'A' and resid 846 through 855 removed outlier: 3.958A pdb=" N SER A 855 " --> pdb=" O SER A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 870 Processing helix chain 'A' and resid 878 through 903 Processing helix chain 'A' and resid 914 through 922 Processing helix chain 'A' and resid 929 through 934 removed outlier: 3.929A pdb=" N GLU A 932 " --> pdb=" O LYS A 929 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE A 934 " --> pdb=" O GLU A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 945 Processing helix chain 'A' and resid 950 through 954 Processing helix chain 'A' and resid 957 through 962 removed outlier: 3.633A pdb=" N LYS A 960 " --> pdb=" O SER A 957 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR A 962 " --> pdb=" O LEU A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 970 Processing helix chain 'A' and resid 973 through 976 removed outlier: 3.538A pdb=" N MET A 976 " --> pdb=" O ASN A 973 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 973 through 976' Processing helix chain 'A' and resid 977 through 991 removed outlier: 3.537A pdb=" N ILE A 981 " --> pdb=" O LYS A 977 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLU A 982 " --> pdb=" O HIS A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1003 removed outlier: 3.730A pdb=" N LEU A 997 " --> pdb=" O ASP A 993 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR A1003 " --> pdb=" O ILE A 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 317 Processing helix chain 'B' and resid 318 through 321 removed outlier: 4.078A pdb=" N ALA B 321 " --> pdb=" O PRO B 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 318 through 321' Processing helix chain 'B' and resid 329 through 334 removed outlier: 3.997A pdb=" N VAL B 333 " --> pdb=" O ASP B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 365 Processing helix chain 'B' and resid 366 through 371 removed outlier: 3.668A pdb=" N SER B 371 " --> pdb=" O CYS B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 392 Processing helix chain 'B' and resid 417 through 427 Processing helix chain 'B' and resid 431 through 445 Processing helix chain 'B' and resid 447 through 462 removed outlier: 3.680A pdb=" N TYR B 452 " --> pdb=" O TRP B 448 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP B 453 " --> pdb=" O GLU B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 466 Processing helix chain 'B' and resid 468 through 501 removed outlier: 3.554A pdb=" N TYR B 472 " --> pdb=" O GLY B 468 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N LEU B 497 " --> pdb=" O ASN B 493 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N LEU B 498 " --> pdb=" O GLY B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 519 removed outlier: 4.012A pdb=" N MET B 519 " --> pdb=" O ILE B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 530 removed outlier: 4.686A pdb=" N ASN B 529 " --> pdb=" O ASP B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 539 Processing helix chain 'B' and resid 540 through 544 removed outlier: 4.141A pdb=" N PHE B 544 " --> pdb=" O ILE B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 551 Processing helix chain 'B' and resid 552 through 570 Processing helix chain 'B' and resid 581 through 598 removed outlier: 3.622A pdb=" N ASN B 598 " --> pdb=" O PHE B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 628 removed outlier: 3.573A pdb=" N HIS B 609 " --> pdb=" O PHE B 605 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR B 628 " --> pdb=" O GLU B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 658 Processing helix chain 'B' and resid 660 through 671 Processing helix chain 'B' and resid 672 through 676 Processing helix chain 'B' and resid 680 through 701 removed outlier: 3.652A pdb=" N ILE B 684 " --> pdb=" O GLU B 680 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA B 701 " --> pdb=" O LYS B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 723 removed outlier: 3.782A pdb=" N GLN B 711 " --> pdb=" O VAL B 707 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE B 713 " --> pdb=" O TYR B 709 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N SER B 714 " --> pdb=" O THR B 710 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLU B 715 " --> pdb=" O GLN B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 726 No H-bonds generated for 'chain 'B' and resid 724 through 726' Processing helix chain 'B' and resid 729 through 742 removed outlier: 3.572A pdb=" N LEU B 733 " --> pdb=" O SER B 729 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 762 removed outlier: 3.749A pdb=" N ARG B 754 " --> pdb=" O ASP B 750 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N TYR B 755 " --> pdb=" O ILE B 751 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL B 756 " --> pdb=" O GLY B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 786 Processing helix chain 'B' and resid 800 through 812 removed outlier: 3.943A pdb=" N TYR B 804 " --> pdb=" O TYR B 800 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY B 805 " --> pdb=" O SER B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 827 Processing helix chain 'B' and resid 833 through 841 removed outlier: 4.454A pdb=" N PHE B 837 " --> pdb=" O LYS B 833 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU B 841 " --> pdb=" O PHE B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 846 through 856 Processing helix chain 'B' and resid 861 through 871 removed outlier: 3.646A pdb=" N LEU B 865 " --> pdb=" O ASN B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 878 through 903 removed outlier: 3.720A pdb=" N GLU B 882 " --> pdb=" O THR B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 911 through 922 removed outlier: 3.657A pdb=" N THR B 915 " --> pdb=" O ASP B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 928 through 934 removed outlier: 3.526A pdb=" N GLU B 931 " --> pdb=" O SER B 928 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE B 934 " --> pdb=" O GLU B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 937 through 945 Processing helix chain 'B' and resid 946 through 949 removed outlier: 3.692A pdb=" N PHE B 949 " --> pdb=" O PRO B 946 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 946 through 949' Processing helix chain 'B' and resid 950 through 954 removed outlier: 3.517A pdb=" N LYS B 953 " --> pdb=" O ASP B 950 " (cutoff:3.500A) Processing helix chain 'B' and resid 955 through 962 removed outlier: 3.558A pdb=" N TYR B 962 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 973 Processing helix chain 'B' and resid 976 through 991 removed outlier: 3.819A pdb=" N ASN B 990 " --> pdb=" O GLU B 986 " (cutoff:3.500A) Processing helix chain 'B' and resid 993 through 1003 removed outlier: 3.545A pdb=" N LEU B 997 " --> pdb=" O ASP B 993 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR B1003 " --> pdb=" O ILE B 999 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 78 removed outlier: 4.015A pdb=" N MET C 75 " --> pdb=" O GLU C 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 43 removed outlier: 4.393A pdb=" N ARG D 42 " --> pdb=" O GLU D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 78 Processing sheet with id=AA1, first strand: chain 'A' and resid 338 through 340 Processing sheet with id=AA2, first strand: chain 'A' and resid 404 through 405 removed outlier: 3.861A pdb=" N THR A 405 " --> pdb=" O VAL C 4 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL C 4 " --> pdb=" O THR A 405 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 574 through 575 removed outlier: 4.112A pdb=" N SER C 31 " --> pdb=" O THR C 62 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N THR C 62 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA C 35 " --> pdb=" O GLU C 58 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU C 58 " --> pdb=" O ALA C 35 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ILE C 59 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE C 220 " --> pdb=" O LEU C 61 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 904 through 907 Processing sheet with id=AA5, first strand: chain 'B' and resid 338 through 340 Processing sheet with id=AA6, first strand: chain 'B' and resid 574 through 575 removed outlier: 3.689A pdb=" N SER D 31 " --> pdb=" O THR D 62 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR D 62 " --> pdb=" O SER D 31 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER D 33 " --> pdb=" O ASN D 60 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA D 35 " --> pdb=" O GLU D 58 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 11 through 14 removed outlier: 3.687A pdb=" N VAL C 11 " --> pdb=" O THR C 24 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 173 through 180 693 hydrogen bonds defined for protein. 1977 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.25 Time building geometry restraints manager: 1.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3928 1.33 - 1.45: 2650 1.45 - 1.57: 7847 1.57 - 1.69: 0 1.69 - 1.81: 94 Bond restraints: 14519 Sorted by residual: bond pdb=" C MET B 531 " pdb=" N PRO B 532 " ideal model delta sigma weight residual 1.334 1.393 -0.059 2.34e-02 1.83e+03 6.32e+00 bond pdb=" CG ARG B 517 " pdb=" CD ARG B 517 " ideal model delta sigma weight residual 1.520 1.560 -0.040 3.00e-02 1.11e+03 1.81e+00 bond pdb=" CB PRO D 49 " pdb=" CG PRO D 49 " ideal model delta sigma weight residual 1.492 1.555 -0.063 5.00e-02 4.00e+02 1.57e+00 bond pdb=" CB ASN A 863 " pdb=" CG ASN A 863 " ideal model delta sigma weight residual 1.516 1.544 -0.028 2.50e-02 1.60e+03 1.29e+00 bond pdb=" CA PHE D 67 " pdb=" CB PHE D 67 " ideal model delta sigma weight residual 1.527 1.545 -0.018 1.61e-02 3.86e+03 1.26e+00 ... (remaining 14514 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.15: 19385 3.15 - 6.30: 129 6.30 - 9.46: 10 9.46 - 12.61: 4 12.61 - 15.76: 2 Bond angle restraints: 19530 Sorted by residual: angle pdb=" C GLN B 905 " pdb=" N THR B 906 " pdb=" CA THR B 906 " ideal model delta sigma weight residual 121.54 131.44 -9.90 1.91e+00 2.74e-01 2.69e+01 angle pdb=" N PHE D 23 " pdb=" CA PHE D 23 " pdb=" C PHE D 23 " ideal model delta sigma weight residual 107.73 113.85 -6.12 1.34e+00 5.57e-01 2.08e+01 angle pdb=" CA LEU C 53 " pdb=" CB LEU C 53 " pdb=" CG LEU C 53 " ideal model delta sigma weight residual 116.30 132.06 -15.76 3.50e+00 8.16e-02 2.03e+01 angle pdb=" CA LEU C 50 " pdb=" CB LEU C 50 " pdb=" CG LEU C 50 " ideal model delta sigma weight residual 116.30 131.78 -15.48 3.50e+00 8.16e-02 1.96e+01 angle pdb=" N GLY A 635 " pdb=" CA GLY A 635 " pdb=" C GLY A 635 " ideal model delta sigma weight residual 112.50 117.29 -4.79 1.16e+00 7.43e-01 1.71e+01 ... (remaining 19525 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.05: 7199 18.05 - 36.10: 1108 36.10 - 54.15: 313 54.15 - 72.20: 44 72.20 - 90.24: 19 Dihedral angle restraints: 8683 sinusoidal: 3614 harmonic: 5069 Sorted by residual: dihedral pdb=" CA LYS D 64 " pdb=" C LYS D 64 " pdb=" N ASN D 65 " pdb=" CA ASN D 65 " ideal model delta harmonic sigma weight residual 180.00 146.67 33.33 0 5.00e+00 4.00e-02 4.44e+01 dihedral pdb=" CA SER B 908 " pdb=" C SER B 908 " pdb=" N SER B 909 " pdb=" CA SER B 909 " ideal model delta harmonic sigma weight residual 180.00 148.02 31.98 0 5.00e+00 4.00e-02 4.09e+01 dihedral pdb=" CA MET C 231 " pdb=" C MET C 231 " pdb=" N ALA C 232 " pdb=" CA ALA C 232 " ideal model delta harmonic sigma weight residual -180.00 -157.48 -22.52 0 5.00e+00 4.00e-02 2.03e+01 ... (remaining 8680 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1478 0.043 - 0.085: 474 0.085 - 0.128: 105 0.128 - 0.170: 10 0.170 - 0.213: 3 Chirality restraints: 2070 Sorted by residual: chirality pdb=" CG LEU D 50 " pdb=" CB LEU D 50 " pdb=" CD1 LEU D 50 " pdb=" CD2 LEU D 50 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA PRO B 532 " pdb=" N PRO B 532 " pdb=" C PRO B 532 " pdb=" CB PRO B 532 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA PHE D 67 " pdb=" N PHE D 67 " pdb=" C PHE D 67 " pdb=" CB PHE D 67 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.33e-01 ... (remaining 2067 not shown) Planarity restraints: 2504 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 448 " 0.014 2.00e-02 2.50e+03 1.60e-02 6.41e+00 pdb=" CG TRP B 448 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP B 448 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP B 448 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP B 448 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 448 " -0.011 2.00e-02 2.50e+03 pdb=" CE3 TRP B 448 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 448 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 448 " 0.013 2.00e-02 2.50e+03 pdb=" CH2 TRP B 448 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET B 531 " 0.039 5.00e-02 4.00e+02 6.02e-02 5.80e+00 pdb=" N PRO B 532 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 532 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 532 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 748 " -0.011 2.00e-02 2.50e+03 2.11e-02 4.45e+00 pdb=" C ASP A 748 " 0.037 2.00e-02 2.50e+03 pdb=" O ASP A 748 " -0.014 2.00e-02 2.50e+03 pdb=" N LEU A 749 " -0.012 2.00e-02 2.50e+03 ... (remaining 2501 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 252 2.67 - 3.23: 13810 3.23 - 3.79: 21455 3.79 - 4.34: 27131 4.34 - 4.90: 44447 Nonbonded interactions: 107095 Sorted by model distance: nonbonded pdb=" OH TYR B 414 " pdb=" OD1 ASN B 654 " model vdw 2.118 3.040 nonbonded pdb=" O GLU A 516 " pdb=" OG1 THR A 520 " model vdw 2.133 3.040 nonbonded pdb=" OH TYR A 414 " pdb=" OD1 ASN A 654 " model vdw 2.207 3.040 nonbonded pdb=" OD1 ASN A 563 " pdb=" ND2 ASN B 614 " model vdw 2.209 3.120 nonbonded pdb=" N GLU A 746 " pdb=" OE1 GLU A 746 " model vdw 2.221 3.120 ... (remaining 107090 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 303 through 632 or (resid 633 and (name N or name CA or na \ me C or name O or name CB )) or resid 634 through 1005)) } ncs_group { reference = chain 'C' selection = (chain 'D' and resid 2 through 240) } 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: 2.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.110 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6542 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 14519 Z= 0.176 Angle : 0.710 15.760 19530 Z= 0.382 Chirality : 0.043 0.213 2070 Planarity : 0.004 0.060 2504 Dihedral : 18.575 90.245 5421 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.59 % Allowed : 6.89 % Favored : 92.53 % Rotamer: Outliers : 0.45 % Allowed : 30.26 % Favored : 69.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.29 (0.21), residues: 1699 helix: 1.27 (0.18), residues: 914 sheet: -1.27 (0.51), residues: 113 loop : -2.15 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 517 TYR 0.034 0.002 TYR A 324 PHE 0.025 0.002 PHE A 921 TRP 0.038 0.003 TRP B 448 HIS 0.003 0.001 HIS B 606 Details of bonding type rmsd covalent geometry : bond 0.00390 (14519) covalent geometry : angle 0.71036 (19530) hydrogen bonds : bond 0.18738 ( 693) hydrogen bonds : angle 5.72210 ( 1977) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 316 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 MET cc_start: 0.4164 (tpt) cc_final: 0.3079 (tpt) REVERT: A 361 PHE cc_start: 0.6560 (m-10) cc_final: 0.6236 (m-80) REVERT: A 395 CYS cc_start: 0.6878 (m) cc_final: 0.6580 (m) REVERT: A 423 LYS cc_start: 0.8439 (mttt) cc_final: 0.8193 (mttt) REVERT: A 442 LEU cc_start: 0.7823 (mt) cc_final: 0.7346 (mp) REVERT: A 554 ASP cc_start: 0.7838 (m-30) cc_final: 0.7537 (m-30) REVERT: A 777 ASP cc_start: 0.6750 (m-30) cc_final: 0.6403 (m-30) REVERT: A 813 LYS cc_start: 0.8452 (mmtp) cc_final: 0.8231 (mttm) REVERT: A 923 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7510 (mp0) REVERT: B 394 ILE cc_start: 0.8588 (mm) cc_final: 0.8274 (mt) REVERT: B 438 LYS cc_start: 0.8085 (mtpt) cc_final: 0.7866 (mtpp) REVERT: B 480 ARG cc_start: 0.6267 (mmt180) cc_final: 0.4607 (mmt180) REVERT: B 486 THR cc_start: 0.7510 (m) cc_final: 0.7263 (t) REVERT: B 680 GLU cc_start: 0.7988 (pm20) cc_final: 0.7763 (pm20) REVERT: B 722 PHE cc_start: 0.8562 (OUTLIER) cc_final: 0.7961 (t80) REVERT: B 793 GLU cc_start: 0.6662 (mp0) cc_final: 0.6433 (mp0) REVERT: B 948 ASN cc_start: 0.6531 (t0) cc_final: 0.6280 (t0) REVERT: B 963 ASN cc_start: 0.6843 (t0) cc_final: 0.6624 (t0) outliers start: 7 outliers final: 5 residues processed: 319 average time/residue: 0.1284 time to fit residues: 59.0529 Evaluate side-chains 302 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 296 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 782 GLN Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 797 ASN Chi-restraints excluded: chain D residue 62 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 50.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 HIS A 351 ASN A 477 ASN A 483 GLN ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 961 ASN ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 351 ASN ** B 867 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.186067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.159655 restraints weight = 21126.127| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 2.98 r_work: 0.3854 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14519 Z= 0.154 Angle : 0.641 13.569 19530 Z= 0.340 Chirality : 0.042 0.228 2070 Planarity : 0.004 0.055 2504 Dihedral : 5.323 55.272 1889 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.83 % Favored : 92.64 % Rotamer: Outliers : 3.59 % Allowed : 27.31 % Favored : 69.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.18 (0.21), residues: 1699 helix: 1.25 (0.17), residues: 923 sheet: -1.47 (0.46), residues: 126 loop : -1.90 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 517 TYR 0.019 0.002 TYR A 324 PHE 0.042 0.002 PHE A 544 TRP 0.021 0.002 TRP B 919 HIS 0.006 0.001 HIS B 786 Details of bonding type rmsd covalent geometry : bond 0.00339 (14519) covalent geometry : angle 0.64084 (19530) hydrogen bonds : bond 0.05345 ( 693) hydrogen bonds : angle 4.47559 ( 1977) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 297 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 TYR cc_start: 0.8153 (t80) cc_final: 0.7772 (t80) REVERT: A 357 MET cc_start: 0.4610 (tpt) cc_final: 0.4331 (tpt) REVERT: A 396 MET cc_start: 0.7643 (OUTLIER) cc_final: 0.7167 (ttp) REVERT: A 423 LYS cc_start: 0.8449 (mttt) cc_final: 0.8246 (mttt) REVERT: A 445 LEU cc_start: 0.7442 (tp) cc_final: 0.7083 (tt) REVERT: A 548 ASN cc_start: 0.4597 (OUTLIER) cc_final: 0.4094 (p0) REVERT: A 554 ASP cc_start: 0.7841 (m-30) cc_final: 0.7408 (m-30) REVERT: A 685 GLU cc_start: 0.7346 (tp30) cc_final: 0.7072 (tp30) REVERT: A 777 ASP cc_start: 0.7566 (OUTLIER) cc_final: 0.7290 (m-30) REVERT: A 831 LYS cc_start: 0.6346 (mtmm) cc_final: 0.6106 (mtmm) REVERT: A 913 MET cc_start: 0.7551 (mmm) cc_final: 0.6709 (tpp) REVERT: A 923 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7801 (mp0) REVERT: B 394 ILE cc_start: 0.8563 (mm) cc_final: 0.8334 (mt) REVERT: B 438 LYS cc_start: 0.8294 (mtpt) cc_final: 0.8044 (mtpp) REVERT: B 486 THR cc_start: 0.7643 (m) cc_final: 0.7398 (t) REVERT: B 570 SER cc_start: 0.8438 (m) cc_final: 0.8130 (t) REVERT: B 722 PHE cc_start: 0.8651 (OUTLIER) cc_final: 0.8171 (t80) REVERT: B 948 ASN cc_start: 0.6829 (t0) cc_final: 0.6583 (t0) REVERT: B 976 MET cc_start: 0.7114 (pmm) cc_final: 0.6913 (pmm) REVERT: B 981 ILE cc_start: 0.7437 (OUTLIER) cc_final: 0.7168 (mp) REVERT: D 34 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.8000 (mm-40) REVERT: D 50 LEU cc_start: 0.4606 (OUTLIER) cc_final: 0.4400 (pp) REVERT: D 51 TYR cc_start: 0.6512 (OUTLIER) cc_final: 0.6237 (m-80) REVERT: D 172 GLU cc_start: 0.7621 (pm20) cc_final: 0.7163 (pm20) outliers start: 56 outliers final: 26 residues processed: 332 average time/residue: 0.1267 time to fit residues: 60.9919 Evaluate side-chains 323 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 289 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 548 ASN Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 777 ASP Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 377 GLN Chi-restraints excluded: chain B residue 408 GLU Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 444 CYS Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 797 ASN Chi-restraints excluded: chain B residue 802 ARG Chi-restraints excluded: chain B residue 859 VAL Chi-restraints excluded: chain B residue 981 ILE Chi-restraints excluded: chain C residue 77 GLN Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 34 GLN Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 219 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 97 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 108 optimal weight: 0.0870 chunk 83 optimal weight: 0.6980 chunk 148 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 ASN A 765 ASN ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 867 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.186018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.159155 restraints weight = 21121.434| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 3.06 r_work: 0.3842 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14519 Z= 0.136 Angle : 0.589 10.804 19530 Z= 0.315 Chirality : 0.041 0.209 2070 Planarity : 0.003 0.055 2504 Dihedral : 4.821 47.007 1881 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.47 % Allowed : 7.30 % Favored : 92.23 % Rotamer: Outliers : 4.42 % Allowed : 26.73 % Favored : 68.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.21), residues: 1699 helix: 1.34 (0.18), residues: 932 sheet: -1.37 (0.47), residues: 126 loop : -1.91 (0.23), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 517 TYR 0.015 0.001 TYR A 649 PHE 0.033 0.001 PHE A 544 TRP 0.017 0.001 TRP B 919 HIS 0.003 0.001 HIS B 786 Details of bonding type rmsd covalent geometry : bond 0.00297 (14519) covalent geometry : angle 0.58873 (19530) hydrogen bonds : bond 0.04801 ( 693) hydrogen bonds : angle 4.29388 ( 1977) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 302 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 MET cc_start: 0.4594 (tpt) cc_final: 0.4292 (tpt) REVERT: A 395 CYS cc_start: 0.7427 (m) cc_final: 0.7191 (m) REVERT: A 396 MET cc_start: 0.7672 (OUTLIER) cc_final: 0.7237 (ttp) REVERT: A 423 LYS cc_start: 0.8408 (mttt) cc_final: 0.8208 (mttt) REVERT: A 442 LEU cc_start: 0.7773 (mt) cc_final: 0.7489 (mp) REVERT: A 445 LEU cc_start: 0.7483 (tp) cc_final: 0.7171 (tt) REVERT: A 548 ASN cc_start: 0.4406 (OUTLIER) cc_final: 0.3905 (p0) REVERT: A 551 LEU cc_start: 0.6005 (OUTLIER) cc_final: 0.5765 (mt) REVERT: A 554 ASP cc_start: 0.7859 (m-30) cc_final: 0.7323 (m-30) REVERT: A 685 GLU cc_start: 0.7352 (tp30) cc_final: 0.7099 (tp30) REVERT: A 777 ASP cc_start: 0.7593 (m-30) cc_final: 0.7306 (m-30) REVERT: A 840 LYS cc_start: 0.7077 (OUTLIER) cc_final: 0.6469 (ptpt) REVERT: A 913 MET cc_start: 0.7622 (mmm) cc_final: 0.7331 (tpp) REVERT: A 923 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7751 (mp0) REVERT: B 315 LYS cc_start: 0.8070 (mmtm) cc_final: 0.7411 (mmmt) REVERT: B 357 MET cc_start: 0.7168 (mmm) cc_final: 0.6898 (mmm) REVERT: B 438 LYS cc_start: 0.8275 (mtpt) cc_final: 0.8054 (mtpp) REVERT: B 480 ARG cc_start: 0.7015 (mmt180) cc_final: 0.4970 (mmt180) REVERT: B 486 THR cc_start: 0.7765 (m) cc_final: 0.7544 (t) REVERT: B 517 ARG cc_start: 0.7951 (mtm110) cc_final: 0.7687 (ttm-80) REVERT: B 570 SER cc_start: 0.8428 (m) cc_final: 0.8143 (t) REVERT: B 722 PHE cc_start: 0.8624 (OUTLIER) cc_final: 0.8041 (t80) REVERT: B 802 ARG cc_start: 0.3505 (OUTLIER) cc_final: 0.3138 (ptp90) REVERT: B 948 ASN cc_start: 0.6922 (t0) cc_final: 0.6663 (t0) REVERT: B 981 ILE cc_start: 0.7416 (OUTLIER) cc_final: 0.7149 (mp) REVERT: C 77 GLN cc_start: 0.4932 (OUTLIER) cc_final: 0.4594 (tp-100) REVERT: D 34 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.7978 (mm-40) REVERT: D 50 LEU cc_start: 0.4543 (OUTLIER) cc_final: 0.4332 (pp) REVERT: D 51 TYR cc_start: 0.6355 (OUTLIER) cc_final: 0.5973 (m-80) REVERT: D 172 GLU cc_start: 0.7737 (pm20) cc_final: 0.7265 (pm20) outliers start: 69 outliers final: 33 residues processed: 344 average time/residue: 0.1254 time to fit residues: 62.3882 Evaluate side-chains 344 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 300 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 548 ASN Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 782 GLN Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 377 GLN Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 444 CYS Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 685 GLU Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 797 ASN Chi-restraints excluded: chain B residue 802 ARG Chi-restraints excluded: chain B residue 859 VAL Chi-restraints excluded: chain B residue 913 MET Chi-restraints excluded: chain B residue 981 ILE Chi-restraints excluded: chain C residue 77 GLN Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 34 GLN Chi-restraints excluded: chain D residue 48 LYS Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 219 LYS Chi-restraints excluded: chain D residue 226 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 26 optimal weight: 0.2980 chunk 13 optimal weight: 2.9990 chunk 140 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 149 optimal weight: 50.0000 chunk 154 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 167 optimal weight: 0.1980 chunk 127 optimal weight: 0.3980 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 ASN A 797 ASN ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.186119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.159242 restraints weight = 21146.820| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 3.07 r_work: 0.3847 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 14519 Z= 0.125 Angle : 0.570 12.983 19530 Z= 0.302 Chirality : 0.041 0.242 2070 Planarity : 0.003 0.050 2504 Dihedral : 4.840 55.984 1881 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.41 % Allowed : 7.06 % Favored : 92.53 % Rotamer: Outliers : 5.06 % Allowed : 26.54 % Favored : 68.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.03 (0.21), residues: 1699 helix: 1.45 (0.18), residues: 937 sheet: -1.30 (0.48), residues: 126 loop : -1.95 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 517 TYR 0.013 0.001 TYR A 649 PHE 0.026 0.001 PHE A 544 TRP 0.018 0.001 TRP B 919 HIS 0.003 0.001 HIS B 881 Details of bonding type rmsd covalent geometry : bond 0.00275 (14519) covalent geometry : angle 0.57008 (19530) hydrogen bonds : bond 0.04280 ( 693) hydrogen bonds : angle 4.12300 ( 1977) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 302 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 ARG cc_start: 0.8064 (ptp90) cc_final: 0.7826 (ptp-170) REVERT: A 345 THR cc_start: 0.5885 (OUTLIER) cc_final: 0.4959 (p) REVERT: A 357 MET cc_start: 0.4458 (tpt) cc_final: 0.4125 (tpt) REVERT: A 396 MET cc_start: 0.7654 (OUTLIER) cc_final: 0.7299 (ttp) REVERT: A 423 LYS cc_start: 0.8440 (mttt) cc_final: 0.8159 (mttt) REVERT: A 442 LEU cc_start: 0.7839 (mt) cc_final: 0.7512 (mp) REVERT: A 445 LEU cc_start: 0.7523 (tp) cc_final: 0.7228 (tt) REVERT: A 548 ASN cc_start: 0.4374 (OUTLIER) cc_final: 0.3912 (p0) REVERT: A 685 GLU cc_start: 0.7319 (tp30) cc_final: 0.7083 (tp30) REVERT: A 777 ASP cc_start: 0.7579 (m-30) cc_final: 0.7291 (m-30) REVERT: A 840 LYS cc_start: 0.6965 (OUTLIER) cc_final: 0.6322 (ptpt) REVERT: A 923 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7709 (mp0) REVERT: A 976 MET cc_start: 0.7629 (mtm) cc_final: 0.7330 (ptt) REVERT: B 391 ASN cc_start: 0.6183 (m-40) cc_final: 0.5936 (m-40) REVERT: B 436 TYR cc_start: 0.6866 (t80) cc_final: 0.6574 (t80) REVERT: B 480 ARG cc_start: 0.7231 (mmt180) cc_final: 0.5181 (mmt180) REVERT: B 487 GLN cc_start: 0.7901 (mt0) cc_final: 0.7619 (mt0) REVERT: B 570 SER cc_start: 0.8389 (m) cc_final: 0.8135 (t) REVERT: B 697 LYS cc_start: 0.8135 (tppp) cc_final: 0.7749 (tppp) REVERT: B 722 PHE cc_start: 0.8583 (OUTLIER) cc_final: 0.7918 (t80) REVERT: B 948 ASN cc_start: 0.6965 (t0) cc_final: 0.6685 (t0) REVERT: B 981 ILE cc_start: 0.7430 (OUTLIER) cc_final: 0.7164 (mp) REVERT: B 982 GLU cc_start: 0.8161 (pt0) cc_final: 0.7873 (pt0) REVERT: C 77 GLN cc_start: 0.4896 (OUTLIER) cc_final: 0.4575 (tp-100) REVERT: D 34 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.8004 (mm-40) REVERT: D 50 LEU cc_start: 0.4536 (OUTLIER) cc_final: 0.4203 (pp) REVERT: D 51 TYR cc_start: 0.6218 (OUTLIER) cc_final: 0.5656 (m-10) REVERT: D 172 GLU cc_start: 0.7736 (pm20) cc_final: 0.7278 (pm20) outliers start: 79 outliers final: 41 residues processed: 352 average time/residue: 0.1278 time to fit residues: 64.7872 Evaluate side-chains 345 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 294 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 548 ASN Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 782 GLN Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 377 GLN Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 444 CYS Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 685 GLU Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 797 ASN Chi-restraints excluded: chain B residue 831 LYS Chi-restraints excluded: chain B residue 859 VAL Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 878 THR Chi-restraints excluded: chain B residue 906 THR Chi-restraints excluded: chain B residue 913 MET Chi-restraints excluded: chain B residue 981 ILE Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 77 GLN Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 34 GLN Chi-restraints excluded: chain D residue 48 LYS Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 219 LYS Chi-restraints excluded: chain D residue 226 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 148 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 119 optimal weight: 0.0020 chunk 31 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 142 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 48 optimal weight: 7.9990 chunk 65 optimal weight: 0.0370 overall best weight: 0.5068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 ASN A 797 ASN ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 905 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.186862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.160565 restraints weight = 21153.501| |-----------------------------------------------------------------------------| r_work (start): 0.4009 rms_B_bonded: 2.90 r_work: 0.3872 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6835 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14519 Z= 0.120 Angle : 0.564 10.389 19530 Z= 0.300 Chirality : 0.041 0.204 2070 Planarity : 0.003 0.050 2504 Dihedral : 4.785 54.634 1881 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.42 % Favored : 92.23 % Rotamer: Outliers : 4.55 % Allowed : 28.21 % Favored : 67.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.13 (0.21), residues: 1699 helix: 1.55 (0.18), residues: 932 sheet: -1.27 (0.48), residues: 126 loop : -1.90 (0.23), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 517 TYR 0.022 0.001 TYR D 192 PHE 0.025 0.001 PHE D 67 TRP 0.020 0.001 TRP B 919 HIS 0.003 0.001 HIS B 881 Details of bonding type rmsd covalent geometry : bond 0.00259 (14519) covalent geometry : angle 0.56370 (19530) hydrogen bonds : bond 0.04192 ( 693) hydrogen bonds : angle 4.08922 ( 1977) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 302 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 LYS cc_start: 0.7770 (mmmm) cc_final: 0.7541 (mmmm) REVERT: A 357 MET cc_start: 0.4409 (tpt) cc_final: 0.4069 (tpt) REVERT: A 396 MET cc_start: 0.7598 (OUTLIER) cc_final: 0.7220 (ttp) REVERT: A 423 LYS cc_start: 0.8417 (mttt) cc_final: 0.8163 (mttt) REVERT: A 442 LEU cc_start: 0.7941 (mt) cc_final: 0.7645 (mp) REVERT: A 445 LEU cc_start: 0.7523 (tp) cc_final: 0.7229 (tt) REVERT: A 548 ASN cc_start: 0.4339 (OUTLIER) cc_final: 0.3856 (p0) REVERT: A 553 ASP cc_start: 0.7803 (t0) cc_final: 0.7509 (t0) REVERT: A 685 GLU cc_start: 0.7295 (tp30) cc_final: 0.7074 (tp30) REVERT: A 777 ASP cc_start: 0.7528 (m-30) cc_final: 0.7193 (m-30) REVERT: A 923 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7686 (mp0) REVERT: A 945 ASP cc_start: 0.8202 (m-30) cc_final: 0.7963 (m-30) REVERT: A 976 MET cc_start: 0.7597 (mtm) cc_final: 0.7382 (ptt) REVERT: B 391 ASN cc_start: 0.6103 (m-40) cc_final: 0.5859 (m-40) REVERT: B 436 TYR cc_start: 0.6825 (t80) cc_final: 0.6502 (t80) REVERT: B 570 SER cc_start: 0.8385 (m) cc_final: 0.8137 (t) REVERT: B 674 ASP cc_start: 0.8263 (t0) cc_final: 0.8046 (t0) REVERT: B 697 LYS cc_start: 0.8115 (tppp) cc_final: 0.7703 (tppp) REVERT: B 722 PHE cc_start: 0.8588 (OUTLIER) cc_final: 0.7927 (t80) REVERT: B 818 LYS cc_start: 0.6987 (mmmt) cc_final: 0.5855 (mmmm) REVERT: B 822 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7687 (mp0) REVERT: B 948 ASN cc_start: 0.6969 (t0) cc_final: 0.6685 (t0) REVERT: B 981 ILE cc_start: 0.7409 (OUTLIER) cc_final: 0.7153 (mp) REVERT: C 67 PHE cc_start: 0.6025 (t80) cc_final: 0.5771 (t80) REVERT: C 77 GLN cc_start: 0.4886 (OUTLIER) cc_final: 0.4530 (tp-100) REVERT: D 34 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.8052 (mm-40) REVERT: D 50 LEU cc_start: 0.4393 (OUTLIER) cc_final: 0.4035 (pp) REVERT: D 51 TYR cc_start: 0.6191 (OUTLIER) cc_final: 0.5661 (m-10) REVERT: D 172 GLU cc_start: 0.7737 (pm20) cc_final: 0.7290 (pm20) REVERT: D 174 GLU cc_start: 0.7424 (tm-30) cc_final: 0.7222 (tm-30) outliers start: 71 outliers final: 44 residues processed: 347 average time/residue: 0.1240 time to fit residues: 62.5407 Evaluate side-chains 351 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 298 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 548 ASN Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 782 GLN Chi-restraints excluded: chain A residue 808 ILE Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 377 GLN Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 444 CYS Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 685 GLU Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 797 ASN Chi-restraints excluded: chain B residue 822 GLU Chi-restraints excluded: chain B residue 831 LYS Chi-restraints excluded: chain B residue 859 VAL Chi-restraints excluded: chain B residue 878 THR Chi-restraints excluded: chain B residue 902 LYS Chi-restraints excluded: chain B residue 913 MET Chi-restraints excluded: chain B residue 981 ILE Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 77 GLN Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 34 GLN Chi-restraints excluded: chain D residue 48 LYS Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 219 LYS Chi-restraints excluded: chain D residue 226 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 88 optimal weight: 0.9980 chunk 80 optimal weight: 0.0030 chunk 150 optimal weight: 0.0060 chunk 28 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 128 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 overall best weight: 0.8008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 ASN A 797 ASN ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.185321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.158910 restraints weight = 21042.029| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 2.91 r_work: 0.3851 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6873 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14519 Z= 0.136 Angle : 0.575 9.697 19530 Z= 0.304 Chirality : 0.041 0.211 2070 Planarity : 0.003 0.049 2504 Dihedral : 4.764 51.692 1881 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.41 % Allowed : 7.06 % Favored : 92.53 % Rotamer: Outliers : 4.94 % Allowed : 27.88 % Favored : 67.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.09 (0.21), residues: 1699 helix: 1.48 (0.18), residues: 940 sheet: -1.16 (0.48), residues: 125 loop : -1.93 (0.23), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 517 TYR 0.019 0.001 TYR D 192 PHE 0.024 0.001 PHE D 67 TRP 0.016 0.001 TRP B 919 HIS 0.003 0.001 HIS B 881 Details of bonding type rmsd covalent geometry : bond 0.00304 (14519) covalent geometry : angle 0.57502 (19530) hydrogen bonds : bond 0.04440 ( 693) hydrogen bonds : angle 4.07162 ( 1977) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 299 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 THR cc_start: 0.5828 (OUTLIER) cc_final: 0.4916 (p) REVERT: A 350 LYS cc_start: 0.7798 (mmmm) cc_final: 0.7541 (mmmm) REVERT: A 423 LYS cc_start: 0.8437 (mttt) cc_final: 0.8157 (mttt) REVERT: A 442 LEU cc_start: 0.7943 (mt) cc_final: 0.7651 (mp) REVERT: A 445 LEU cc_start: 0.7489 (tp) cc_final: 0.7195 (tt) REVERT: A 548 ASN cc_start: 0.4538 (OUTLIER) cc_final: 0.3963 (p0) REVERT: A 553 ASP cc_start: 0.7856 (t0) cc_final: 0.7565 (t0) REVERT: A 593 ARG cc_start: 0.5986 (ttt90) cc_final: 0.3281 (ttt90) REVERT: A 685 GLU cc_start: 0.7305 (tp30) cc_final: 0.7083 (tp30) REVERT: A 777 ASP cc_start: 0.7495 (m-30) cc_final: 0.7168 (m-30) REVERT: A 840 LYS cc_start: 0.7004 (OUTLIER) cc_final: 0.6258 (ptpt) REVERT: A 921 PHE cc_start: 0.7766 (t80) cc_final: 0.7480 (t80) REVERT: A 923 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7706 (mp0) REVERT: A 945 ASP cc_start: 0.8206 (m-30) cc_final: 0.7961 (m-30) REVERT: A 976 MET cc_start: 0.7613 (mtm) cc_final: 0.7409 (ptt) REVERT: B 306 ASP cc_start: 0.6407 (OUTLIER) cc_final: 0.6089 (p0) REVERT: B 436 TYR cc_start: 0.6881 (t80) cc_final: 0.6551 (t80) REVERT: B 517 ARG cc_start: 0.7979 (mtm110) cc_final: 0.7673 (ttm-80) REVERT: B 570 SER cc_start: 0.8436 (m) cc_final: 0.8193 (t) REVERT: B 674 ASP cc_start: 0.8269 (t0) cc_final: 0.8026 (t0) REVERT: B 697 LYS cc_start: 0.8141 (tppp) cc_final: 0.7738 (tppp) REVERT: B 818 LYS cc_start: 0.7052 (mmmt) cc_final: 0.5887 (mmmm) REVERT: B 822 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7680 (mp0) REVERT: B 948 ASN cc_start: 0.7008 (t0) cc_final: 0.6705 (t0) REVERT: B 981 ILE cc_start: 0.7398 (OUTLIER) cc_final: 0.7159 (mp) REVERT: C 77 GLN cc_start: 0.4865 (OUTLIER) cc_final: 0.4523 (tp-100) REVERT: D 34 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.8075 (mm-40) REVERT: D 50 LEU cc_start: 0.4473 (OUTLIER) cc_final: 0.4088 (pp) REVERT: D 51 TYR cc_start: 0.6308 (OUTLIER) cc_final: 0.5797 (m-10) REVERT: D 172 GLU cc_start: 0.7752 (pm20) cc_final: 0.7305 (pm20) outliers start: 77 outliers final: 46 residues processed: 347 average time/residue: 0.1239 time to fit residues: 62.5938 Evaluate side-chains 348 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 292 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 548 ASN Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 782 GLN Chi-restraints excluded: chain A residue 808 ILE Chi-restraints excluded: chain A residue 821 SER Chi-restraints excluded: chain A residue 833 LYS Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 970 ILE Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 377 GLN Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 444 CYS Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 685 GLU Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 822 GLU Chi-restraints excluded: chain B residue 859 VAL Chi-restraints excluded: chain B residue 878 THR Chi-restraints excluded: chain B residue 902 LYS Chi-restraints excluded: chain B residue 913 MET Chi-restraints excluded: chain B residue 981 ILE Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 77 GLN Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 34 GLN Chi-restraints excluded: chain D residue 48 LYS Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 226 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 131 optimal weight: 0.8980 chunk 16 optimal weight: 0.1980 chunk 139 optimal weight: 0.4980 chunk 136 optimal weight: 0.8980 chunk 14 optimal weight: 0.0570 chunk 38 optimal weight: 0.9990 chunk 118 optimal weight: 0.8980 chunk 146 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 ASN A 797 ASN ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.186174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.160034 restraints weight = 21099.719| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 2.90 r_work: 0.3872 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14519 Z= 0.119 Angle : 0.574 14.183 19530 Z= 0.301 Chirality : 0.041 0.207 2070 Planarity : 0.003 0.050 2504 Dihedral : 4.583 47.381 1879 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.06 % Favored : 92.58 % Rotamer: Outliers : 4.81 % Allowed : 27.50 % Favored : 67.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.15 (0.21), residues: 1699 helix: 1.56 (0.18), residues: 939 sheet: -1.15 (0.49), residues: 125 loop : -1.94 (0.23), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 517 TYR 0.012 0.001 TYR B 725 PHE 0.024 0.001 PHE A 646 TRP 0.017 0.001 TRP B 919 HIS 0.003 0.001 HIS B 881 Details of bonding type rmsd covalent geometry : bond 0.00258 (14519) covalent geometry : angle 0.57420 (19530) hydrogen bonds : bond 0.04086 ( 693) hydrogen bonds : angle 4.01791 ( 1977) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 298 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 LYS cc_start: 0.7759 (mmmm) cc_final: 0.7482 (mmmm) REVERT: A 423 LYS cc_start: 0.8459 (mttt) cc_final: 0.8151 (mttt) REVERT: A 440 PHE cc_start: 0.7979 (t80) cc_final: 0.7667 (t80) REVERT: A 442 LEU cc_start: 0.7981 (mt) cc_final: 0.7665 (mp) REVERT: A 445 LEU cc_start: 0.7502 (tp) cc_final: 0.7219 (tt) REVERT: A 548 ASN cc_start: 0.4485 (OUTLIER) cc_final: 0.4017 (p0) REVERT: A 553 ASP cc_start: 0.7824 (t0) cc_final: 0.7552 (t0) REVERT: A 593 ARG cc_start: 0.5941 (ttt90) cc_final: 0.3277 (ttt90) REVERT: A 685 GLU cc_start: 0.7262 (tp30) cc_final: 0.7052 (tp30) REVERT: A 777 ASP cc_start: 0.7441 (m-30) cc_final: 0.7140 (m-30) REVERT: A 921 PHE cc_start: 0.7725 (t80) cc_final: 0.7460 (t80) REVERT: A 923 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7701 (mp0) REVERT: B 436 TYR cc_start: 0.6745 (t80) cc_final: 0.6420 (t80) REVERT: B 570 SER cc_start: 0.8395 (m) cc_final: 0.8177 (t) REVERT: B 697 LYS cc_start: 0.8120 (tppp) cc_final: 0.7723 (tppp) REVERT: B 722 PHE cc_start: 0.8623 (OUTLIER) cc_final: 0.7826 (t80) REVERT: B 948 ASN cc_start: 0.7060 (t0) cc_final: 0.6739 (t0) REVERT: B 981 ILE cc_start: 0.7420 (OUTLIER) cc_final: 0.7155 (mp) REVERT: C 52 ILE cc_start: 0.4955 (OUTLIER) cc_final: 0.4582 (mm) REVERT: C 77 GLN cc_start: 0.4795 (OUTLIER) cc_final: 0.4457 (tp-100) REVERT: D 50 LEU cc_start: 0.4250 (OUTLIER) cc_final: 0.3854 (pp) REVERT: D 51 TYR cc_start: 0.6234 (OUTLIER) cc_final: 0.5699 (m-10) REVERT: D 172 GLU cc_start: 0.7732 (pm20) cc_final: 0.7307 (pm20) outliers start: 75 outliers final: 44 residues processed: 348 average time/residue: 0.1263 time to fit residues: 63.8099 Evaluate side-chains 345 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 294 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 548 ASN Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 782 GLN Chi-restraints excluded: chain A residue 808 ILE Chi-restraints excluded: chain A residue 821 SER Chi-restraints excluded: chain A residue 833 LYS Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 377 GLN Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 444 CYS Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 685 GLU Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 822 GLU Chi-restraints excluded: chain B residue 859 VAL Chi-restraints excluded: chain B residue 878 THR Chi-restraints excluded: chain B residue 913 MET Chi-restraints excluded: chain B residue 981 ILE Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 77 GLN Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 48 LYS Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 226 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 12 optimal weight: 0.4980 chunk 146 optimal weight: 0.0170 chunk 20 optimal weight: 0.1980 chunk 50 optimal weight: 0.3980 chunk 135 optimal weight: 1.9990 chunk 153 optimal weight: 0.9990 chunk 155 optimal weight: 6.9990 chunk 116 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 698 GLN ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.186881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.160759 restraints weight = 21066.789| |-----------------------------------------------------------------------------| r_work (start): 0.4015 rms_B_bonded: 2.91 r_work: 0.3880 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14519 Z= 0.116 Angle : 0.588 13.355 19530 Z= 0.305 Chirality : 0.041 0.212 2070 Planarity : 0.003 0.044 2504 Dihedral : 4.556 47.559 1879 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.06 % Favored : 92.64 % Rotamer: Outliers : 3.78 % Allowed : 28.65 % Favored : 67.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.25 (0.21), residues: 1699 helix: 1.65 (0.18), residues: 933 sheet: -1.11 (0.49), residues: 125 loop : -1.88 (0.23), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 517 TYR 0.012 0.001 TYR B 472 PHE 0.035 0.001 PHE D 32 TRP 0.012 0.001 TRP B 919 HIS 0.003 0.001 HIS B 881 Details of bonding type rmsd covalent geometry : bond 0.00252 (14519) covalent geometry : angle 0.58759 (19530) hydrogen bonds : bond 0.03904 ( 693) hydrogen bonds : angle 3.99278 ( 1977) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 293 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 LYS cc_start: 0.7735 (mmmm) cc_final: 0.7485 (mmmm) REVERT: A 423 LYS cc_start: 0.8469 (mttt) cc_final: 0.8193 (mttt) REVERT: A 440 PHE cc_start: 0.8003 (t80) cc_final: 0.7673 (t80) REVERT: A 442 LEU cc_start: 0.7995 (mt) cc_final: 0.7687 (mp) REVERT: A 445 LEU cc_start: 0.7520 (tp) cc_final: 0.7242 (tt) REVERT: A 548 ASN cc_start: 0.4535 (OUTLIER) cc_final: 0.4078 (p0) REVERT: A 553 ASP cc_start: 0.7818 (t0) cc_final: 0.7580 (t0) REVERT: A 593 ARG cc_start: 0.5903 (ttt90) cc_final: 0.3196 (ttt90) REVERT: A 717 LYS cc_start: 0.7826 (OUTLIER) cc_final: 0.7083 (mttt) REVERT: A 748 ASP cc_start: 0.6943 (t0) cc_final: 0.6471 (t0) REVERT: A 777 ASP cc_start: 0.7451 (m-30) cc_final: 0.7124 (m-30) REVERT: A 829 GLN cc_start: 0.6433 (OUTLIER) cc_final: 0.5909 (mm110) REVERT: A 840 LYS cc_start: 0.6866 (OUTLIER) cc_final: 0.6207 (ptpt) REVERT: A 921 PHE cc_start: 0.7717 (t80) cc_final: 0.7449 (t80) REVERT: A 923 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7674 (mp0) REVERT: B 436 TYR cc_start: 0.6605 (t80) cc_final: 0.6242 (t80) REVERT: B 450 GLU cc_start: 0.7409 (mp0) cc_final: 0.6956 (mp0) REVERT: B 570 SER cc_start: 0.8397 (m) cc_final: 0.8184 (t) REVERT: B 697 LYS cc_start: 0.8146 (tppp) cc_final: 0.7766 (tppp) REVERT: B 722 PHE cc_start: 0.8632 (OUTLIER) cc_final: 0.7913 (t80) REVERT: B 748 ASP cc_start: 0.7467 (OUTLIER) cc_final: 0.7112 (m-30) REVERT: B 822 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7626 (mp0) REVERT: B 948 ASN cc_start: 0.7069 (t0) cc_final: 0.6757 (t0) REVERT: B 981 ILE cc_start: 0.7451 (OUTLIER) cc_final: 0.7193 (mp) REVERT: C 52 ILE cc_start: 0.4891 (OUTLIER) cc_final: 0.4554 (mm) REVERT: C 77 GLN cc_start: 0.4813 (OUTLIER) cc_final: 0.4469 (tp-100) REVERT: D 50 LEU cc_start: 0.4115 (OUTLIER) cc_final: 0.3715 (pp) REVERT: D 51 TYR cc_start: 0.6188 (OUTLIER) cc_final: 0.5662 (m-10) REVERT: D 172 GLU cc_start: 0.7724 (pm20) cc_final: 0.7307 (pm20) outliers start: 59 outliers final: 39 residues processed: 335 average time/residue: 0.1195 time to fit residues: 58.6315 Evaluate side-chains 339 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 288 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 548 ASN Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 698 GLN Chi-restraints excluded: chain A residue 717 LYS Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 782 GLN Chi-restraints excluded: chain A residue 808 ILE Chi-restraints excluded: chain A residue 821 SER Chi-restraints excluded: chain A residue 829 GLN Chi-restraints excluded: chain A residue 833 LYS Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 377 GLN Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 444 CYS Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 685 GLU Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 748 ASP Chi-restraints excluded: chain B residue 822 GLU Chi-restraints excluded: chain B residue 878 THR Chi-restraints excluded: chain B residue 902 LYS Chi-restraints excluded: chain B residue 981 ILE Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 77 GLN Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 48 LYS Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 226 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 142 optimal weight: 10.0000 chunk 141 optimal weight: 0.3980 chunk 65 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 67 optimal weight: 0.0980 chunk 150 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 155 optimal weight: 0.0870 chunk 33 optimal weight: 0.6980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 698 GLN A 797 ASN ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.186960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.160832 restraints weight = 21053.937| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 2.89 r_work: 0.3882 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14519 Z= 0.117 Angle : 0.596 12.915 19530 Z= 0.309 Chirality : 0.041 0.234 2070 Planarity : 0.003 0.045 2504 Dihedral : 4.541 47.264 1879 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.95 % Favored : 92.76 % Rotamer: Outliers : 3.97 % Allowed : 28.53 % Favored : 67.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.29 (0.21), residues: 1699 helix: 1.68 (0.18), residues: 932 sheet: -1.10 (0.49), residues: 125 loop : -1.86 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 517 TYR 0.015 0.001 TYR B 539 PHE 0.032 0.001 PHE D 32 TRP 0.015 0.001 TRP B 919 HIS 0.003 0.001 HIS B 881 Details of bonding type rmsd covalent geometry : bond 0.00255 (14519) covalent geometry : angle 0.59601 (19530) hydrogen bonds : bond 0.03879 ( 693) hydrogen bonds : angle 3.98337 ( 1977) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 288 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 LYS cc_start: 0.7766 (mmmm) cc_final: 0.7476 (mmmm) REVERT: A 423 LYS cc_start: 0.8456 (mttt) cc_final: 0.8204 (mttt) REVERT: A 440 PHE cc_start: 0.8012 (t80) cc_final: 0.7676 (t80) REVERT: A 442 LEU cc_start: 0.7985 (mt) cc_final: 0.7672 (mp) REVERT: A 445 LEU cc_start: 0.7515 (tp) cc_final: 0.7236 (tt) REVERT: A 553 ASP cc_start: 0.7837 (t0) cc_final: 0.7610 (t0) REVERT: A 593 ARG cc_start: 0.6030 (ttt90) cc_final: 0.3428 (ttt90) REVERT: A 717 LYS cc_start: 0.7862 (OUTLIER) cc_final: 0.7171 (mttt) REVERT: A 748 ASP cc_start: 0.6928 (t0) cc_final: 0.6428 (t0) REVERT: A 777 ASP cc_start: 0.7435 (m-30) cc_final: 0.7118 (m-30) REVERT: A 829 GLN cc_start: 0.6311 (OUTLIER) cc_final: 0.5710 (mm110) REVERT: A 840 LYS cc_start: 0.6865 (OUTLIER) cc_final: 0.6173 (ptpt) REVERT: A 921 PHE cc_start: 0.7691 (t80) cc_final: 0.7430 (t80) REVERT: A 923 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7671 (mp0) REVERT: B 357 MET cc_start: 0.7173 (mmm) cc_final: 0.6878 (mmm) REVERT: B 436 TYR cc_start: 0.6569 (t80) cc_final: 0.6202 (t80) REVERT: B 450 GLU cc_start: 0.7388 (mp0) cc_final: 0.6935 (mp0) REVERT: B 566 ARG cc_start: 0.8294 (tpp-160) cc_final: 0.8061 (mmt90) REVERT: B 697 LYS cc_start: 0.8135 (tppp) cc_final: 0.7756 (tppp) REVERT: B 722 PHE cc_start: 0.8631 (OUTLIER) cc_final: 0.7919 (t80) REVERT: B 748 ASP cc_start: 0.7445 (OUTLIER) cc_final: 0.7089 (m-30) REVERT: B 822 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7641 (mp0) REVERT: B 948 ASN cc_start: 0.7045 (t0) cc_final: 0.6730 (t0) REVERT: B 981 ILE cc_start: 0.7435 (OUTLIER) cc_final: 0.7186 (mp) REVERT: C 52 ILE cc_start: 0.4866 (OUTLIER) cc_final: 0.4524 (mm) REVERT: C 77 GLN cc_start: 0.4791 (OUTLIER) cc_final: 0.4435 (tp-100) REVERT: D 50 LEU cc_start: 0.4133 (OUTLIER) cc_final: 0.3722 (pp) REVERT: D 51 TYR cc_start: 0.6185 (OUTLIER) cc_final: 0.5703 (m-10) REVERT: D 172 GLU cc_start: 0.7744 (pm20) cc_final: 0.7344 (pm20) outliers start: 62 outliers final: 43 residues processed: 333 average time/residue: 0.1308 time to fit residues: 62.8841 Evaluate side-chains 338 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 284 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 698 GLN Chi-restraints excluded: chain A residue 717 LYS Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 782 GLN Chi-restraints excluded: chain A residue 808 ILE Chi-restraints excluded: chain A residue 821 SER Chi-restraints excluded: chain A residue 829 GLN Chi-restraints excluded: chain A residue 833 LYS Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 377 GLN Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 444 CYS Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 685 GLU Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 748 ASP Chi-restraints excluded: chain B residue 822 GLU Chi-restraints excluded: chain B residue 878 THR Chi-restraints excluded: chain B residue 902 LYS Chi-restraints excluded: chain B residue 981 ILE Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 77 GLN Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 48 LYS Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 226 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 144 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 23 optimal weight: 0.0470 chunk 159 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.186188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.159880 restraints weight = 21128.151| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 2.93 r_work: 0.3865 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6854 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14519 Z= 0.127 Angle : 0.616 12.635 19530 Z= 0.317 Chirality : 0.041 0.229 2070 Planarity : 0.003 0.058 2504 Dihedral : 4.548 45.863 1879 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.12 % Favored : 92.58 % Rotamer: Outliers : 3.59 % Allowed : 28.78 % Favored : 67.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.20 (0.21), residues: 1699 helix: 1.61 (0.18), residues: 937 sheet: -1.11 (0.49), residues: 125 loop : -1.93 (0.23), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 517 TYR 0.017 0.001 TYR B 996 PHE 0.032 0.001 PHE D 32 TRP 0.017 0.001 TRP B 919 HIS 0.003 0.001 HIS B 881 Details of bonding type rmsd covalent geometry : bond 0.00282 (14519) covalent geometry : angle 0.61566 (19530) hydrogen bonds : bond 0.04053 ( 693) hydrogen bonds : angle 3.99009 ( 1977) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 286 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 LYS cc_start: 0.7751 (mmmm) cc_final: 0.7479 (mmmm) REVERT: A 423 LYS cc_start: 0.8450 (mttt) cc_final: 0.8175 (mttt) REVERT: A 442 LEU cc_start: 0.7945 (mt) cc_final: 0.7634 (mp) REVERT: A 445 LEU cc_start: 0.7520 (tp) cc_final: 0.7234 (tt) REVERT: A 498 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7212 (tp) REVERT: A 553 ASP cc_start: 0.7859 (t0) cc_final: 0.7636 (t0) REVERT: A 593 ARG cc_start: 0.6055 (ttt90) cc_final: 0.3502 (ttt90) REVERT: A 717 LYS cc_start: 0.7879 (OUTLIER) cc_final: 0.7210 (mttt) REVERT: A 748 ASP cc_start: 0.6986 (t0) cc_final: 0.6396 (t0) REVERT: A 777 ASP cc_start: 0.7474 (m-30) cc_final: 0.7151 (m-30) REVERT: A 829 GLN cc_start: 0.6268 (OUTLIER) cc_final: 0.5594 (mm110) REVERT: A 840 LYS cc_start: 0.6876 (OUTLIER) cc_final: 0.6093 (ptpt) REVERT: A 921 PHE cc_start: 0.7668 (t80) cc_final: 0.7410 (t80) REVERT: A 923 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7693 (mp0) REVERT: B 436 TYR cc_start: 0.6567 (t80) cc_final: 0.6202 (t80) REVERT: B 566 ARG cc_start: 0.8277 (tpp-160) cc_final: 0.8044 (mmt90) REVERT: B 586 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7546 (mp) REVERT: B 697 LYS cc_start: 0.8136 (tppp) cc_final: 0.7745 (tppp) REVERT: B 722 PHE cc_start: 0.8637 (OUTLIER) cc_final: 0.7840 (t80) REVERT: B 746 GLU cc_start: 0.7206 (pm20) cc_final: 0.6923 (pm20) REVERT: B 748 ASP cc_start: 0.7490 (OUTLIER) cc_final: 0.7129 (m-30) REVERT: B 822 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7620 (mp0) REVERT: B 948 ASN cc_start: 0.7177 (t0) cc_final: 0.6872 (t0) REVERT: B 981 ILE cc_start: 0.7452 (OUTLIER) cc_final: 0.7215 (mp) REVERT: C 52 ILE cc_start: 0.4854 (OUTLIER) cc_final: 0.4488 (mm) REVERT: C 77 GLN cc_start: 0.4770 (OUTLIER) cc_final: 0.4417 (tp-100) REVERT: D 50 LEU cc_start: 0.4200 (OUTLIER) cc_final: 0.3785 (pp) REVERT: D 51 TYR cc_start: 0.6249 (OUTLIER) cc_final: 0.5739 (m-10) REVERT: D 58 GLU cc_start: 0.6959 (pp20) cc_final: 0.6144 (pp20) REVERT: D 172 GLU cc_start: 0.7736 (pm20) cc_final: 0.7329 (pm20) outliers start: 56 outliers final: 39 residues processed: 327 average time/residue: 0.1262 time to fit residues: 59.5499 Evaluate side-chains 334 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 282 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 717 LYS Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 782 GLN Chi-restraints excluded: chain A residue 808 ILE Chi-restraints excluded: chain A residue 821 SER Chi-restraints excluded: chain A residue 829 GLN Chi-restraints excluded: chain A residue 833 LYS Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 377 GLN Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 444 CYS Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 685 GLU Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 748 ASP Chi-restraints excluded: chain B residue 822 GLU Chi-restraints excluded: chain B residue 878 THR Chi-restraints excluded: chain B residue 902 LYS Chi-restraints excluded: chain B residue 981 ILE Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 77 GLN Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 48 LYS Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 226 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 58 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 17 optimal weight: 0.5980 chunk 3 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 44 optimal weight: 0.0020 chunk 19 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 698 GLN ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.185540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.159474 restraints weight = 21084.391| |-----------------------------------------------------------------------------| r_work (start): 0.3996 rms_B_bonded: 2.89 r_work: 0.3860 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14519 Z= 0.131 Angle : 0.623 12.102 19530 Z= 0.321 Chirality : 0.042 0.242 2070 Planarity : 0.003 0.056 2504 Dihedral : 4.598 45.167 1879 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.30 % Favored : 92.41 % Rotamer: Outliers : 3.85 % Allowed : 28.85 % Favored : 67.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.19 (0.21), residues: 1699 helix: 1.59 (0.18), residues: 938 sheet: -1.07 (0.49), residues: 125 loop : -1.94 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 517 TYR 0.016 0.001 TYR B 539 PHE 0.031 0.001 PHE D 32 TRP 0.017 0.001 TRP B 919 HIS 0.004 0.001 HIS B 881 Details of bonding type rmsd covalent geometry : bond 0.00292 (14519) covalent geometry : angle 0.62292 (19530) hydrogen bonds : bond 0.04166 ( 693) hydrogen bonds : angle 4.01316 ( 1977) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3231.95 seconds wall clock time: 56 minutes 21.72 seconds (3381.72 seconds total)