Starting phenix.real_space_refine on Fri May 16 05:47:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ygo_39258/05_2025/8ygo_39258.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ygo_39258/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ygo_39258/05_2025/8ygo_39258.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ygo_39258/05_2025/8ygo_39258.map" model { file = "/net/cci-nas-00/data/ceres_data/8ygo_39258/05_2025/8ygo_39258.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ygo_39258/05_2025/8ygo_39258.cif" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 8.31, per 1000 atoms: 0.58 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: 3.12 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.47 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: 4.21 Time building geometry restraints manager: 3.74 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: 1.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 31.650 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.050 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (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 TRP 0.038 0.003 TRP B 448 HIS 0.003 0.001 HIS B 606 PHE 0.025 0.002 PHE A 921 TYR 0.034 0.002 TYR A 324 ARG 0.020 0.001 ARG B 517 Details of bonding type rmsd hydrogen bonds : bond 0.18738 ( 693) hydrogen bonds : angle 5.72210 ( 1977) covalent geometry : bond 0.00390 (14519) covalent geometry : angle 0.71036 (19530) *********************** 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 : 1.751 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: 0.3078 (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: 0.6579 (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: 0.7345 (mp) REVERT: A 554 ASP cc_start: 0.7838 (m-30) cc_final: 0.7538 (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: 0.7511 (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: 0.7262 (t) REVERT: B 680 GLU cc_start: 0.7988 (pm20) cc_final: 0.7764 (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: 0.2776 time to fit residues: 125.6502 Evaluate side-chains 303 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 297 time to evaluate : 1.458 ------------------------------------------------------------------------------- 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 143 optimal weight: 0.9990 chunk 128 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 44 optimal weight: 0.0670 chunk 86 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 133 optimal weight: 6.9990 chunk 51 optimal weight: 0.0980 chunk 81 optimal weight: 0.9980 chunk 99 optimal weight: 0.5980 chunk 154 optimal weight: 3.9990 overall best weight: 0.5520 ------------------------------------------------------------------------------- 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 ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 351 ASN ** B 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 867 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.187413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.160773 restraints weight = 21025.533| |-----------------------------------------------------------------------------| r_work (start): 0.4008 rms_B_bonded: 3.04 r_work: 0.3865 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 moved from start: 0.1158 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= 0.140 Angle : 0.623 12.905 19530 Z= 0.330 Chirality : 0.042 0.213 2070 Planarity : 0.003 0.050 2504 Dihedral : 5.253 54.865 1889 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.95 % Favored : 92.53 % Rotamer: Outliers : 3.72 % Allowed : 27.56 % Favored : 68.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.21), residues: 1699 helix: 1.30 (0.18), residues: 925 sheet: -1.43 (0.46), residues: 126 loop : -1.90 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 448 HIS 0.006 0.001 HIS B 786 PHE 0.042 0.002 PHE A 544 TYR 0.018 0.001 TYR D 192 ARG 0.006 0.000 ARG B 517 Details of bonding type rmsd hydrogen bonds : bond 0.04937 ( 693) hydrogen bonds : angle 4.40816 ( 1977) covalent geometry : bond 0.00291 (14519) covalent geometry : angle 0.62336 (19530) *********************** 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 351 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 293 time to evaluate : 1.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 MET cc_start: 0.4465 (tpt) cc_final: 0.4171 (tpt) REVERT: A 396 MET cc_start: 0.7637 (OUTLIER) cc_final: 0.7198 (ttp) REVERT: A 423 LYS cc_start: 0.8432 (mttt) cc_final: 0.8217 (mttt) REVERT: A 445 LEU cc_start: 0.7470 (tp) cc_final: 0.7104 (tt) REVERT: A 543 GLU cc_start: 0.6579 (tp30) cc_final: 0.6376 (tp30) REVERT: A 548 ASN cc_start: 0.4411 (OUTLIER) cc_final: 0.3965 (p0) REVERT: A 554 ASP cc_start: 0.7798 (m-30) cc_final: 0.7352 (m-30) REVERT: A 626 GLU cc_start: 0.7811 (tm-30) cc_final: 0.7597 (tm-30) REVERT: A 685 GLU cc_start: 0.7331 (tp30) cc_final: 0.7069 (tp30) REVERT: A 777 ASP cc_start: 0.7566 (OUTLIER) cc_final: 0.7290 (m-30) REVERT: A 831 LYS cc_start: 0.6328 (mtmm) cc_final: 0.6109 (mtmm) REVERT: A 913 MET cc_start: 0.7510 (mmm) cc_final: 0.6682 (tpp) REVERT: A 923 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7799 (mp0) REVERT: B 394 ILE cc_start: 0.8577 (mm) cc_final: 0.8345 (mt) REVERT: B 438 LYS cc_start: 0.8220 (mtpt) cc_final: 0.7994 (mtpp) REVERT: B 486 THR cc_start: 0.7662 (m) cc_final: 0.7413 (t) REVERT: B 570 SER cc_start: 0.8391 (m) cc_final: 0.8109 (t) REVERT: B 722 PHE cc_start: 0.8649 (OUTLIER) cc_final: 0.8116 (t80) REVERT: B 797 ASN cc_start: 0.7195 (OUTLIER) cc_final: 0.6671 (t0) REVERT: B 948 ASN cc_start: 0.6751 (t0) cc_final: 0.6504 (t0) REVERT: B 981 ILE cc_start: 0.7447 (OUTLIER) cc_final: 0.7174 (mp) REVERT: D 34 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.8057 (mm-40) REVERT: D 51 TYR cc_start: 0.6440 (OUTLIER) cc_final: 0.6206 (m-10) REVERT: D 172 GLU cc_start: 0.7683 (pm20) cc_final: 0.7287 (pm20) outliers start: 58 outliers final: 25 residues processed: 329 average time/residue: 0.2876 time to fit residues: 134.7911 Evaluate side-chains 317 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 284 time to evaluate : 1.425 ------------------------------------------------------------------------------- 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 762 THR Chi-restraints excluded: chain A residue 777 ASP 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 432 ILE Chi-restraints excluded: chain B residue 444 CYS Chi-restraints excluded: chain B residue 495 LEU 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 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 147 optimal weight: 5.9990 chunk 44 optimal weight: 0.0470 chunk 36 optimal weight: 0.6980 chunk 136 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 79 optimal weight: 0.3980 chunk 169 optimal weight: 9.9990 chunk 85 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 overall best weight: 0.5880 ------------------------------------------------------------------------------- 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 A 961 ASN ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 867 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.187044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.160137 restraints weight = 21123.471| |-----------------------------------------------------------------------------| r_work (start): 0.3999 rms_B_bonded: 3.06 r_work: 0.3857 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6835 moved from start: 0.1506 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= 0.128 Angle : 0.579 11.084 19530 Z= 0.309 Chirality : 0.041 0.211 2070 Planarity : 0.003 0.057 2504 Dihedral : 4.738 48.723 1881 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.47 % Allowed : 7.18 % Favored : 92.35 % Rotamer: Outliers : 4.42 % Allowed : 26.35 % Favored : 69.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.21), residues: 1699 helix: 1.40 (0.18), residues: 936 sheet: -1.32 (0.47), residues: 126 loop : -1.93 (0.23), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 919 HIS 0.003 0.001 HIS B 786 PHE 0.030 0.001 PHE A 544 TYR 0.015 0.001 TYR A 649 ARG 0.006 0.000 ARG B 517 Details of bonding type rmsd hydrogen bonds : bond 0.04536 ( 693) hydrogen bonds : angle 4.22121 ( 1977) covalent geometry : bond 0.00277 (14519) covalent geometry : angle 0.57916 (19530) *********************** 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 366 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 297 time to evaluate : 1.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 THR cc_start: 0.5726 (OUTLIER) cc_final: 0.4783 (p) REVERT: A 357 MET cc_start: 0.4541 (tpt) cc_final: 0.4231 (tpt) REVERT: A 395 CYS cc_start: 0.7356 (m) cc_final: 0.7147 (m) REVERT: A 396 MET cc_start: 0.7631 (OUTLIER) cc_final: 0.7275 (ttp) REVERT: A 423 LYS cc_start: 0.8408 (mttt) cc_final: 0.8170 (mttt) REVERT: A 442 LEU cc_start: 0.7807 (mt) cc_final: 0.7494 (mp) REVERT: A 445 LEU cc_start: 0.7485 (tp) cc_final: 0.7158 (tt) REVERT: A 548 ASN cc_start: 0.4557 (OUTLIER) cc_final: 0.4091 (p0) REVERT: A 551 LEU cc_start: 0.5909 (OUTLIER) cc_final: 0.5681 (mt) REVERT: A 554 ASP cc_start: 0.7774 (m-30) cc_final: 0.7286 (m-30) REVERT: A 626 GLU cc_start: 0.7837 (tm-30) cc_final: 0.7628 (tm-30) REVERT: A 685 GLU cc_start: 0.7341 (tp30) cc_final: 0.7072 (tp30) REVERT: A 777 ASP cc_start: 0.7594 (m-30) cc_final: 0.7317 (m-30) REVERT: A 913 MET cc_start: 0.7590 (mmm) cc_final: 0.7289 (tpp) REVERT: A 923 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7747 (mp0) REVERT: B 315 LYS cc_start: 0.8060 (mmtm) cc_final: 0.7400 (mmmt) REVERT: B 438 LYS cc_start: 0.8246 (mtpt) cc_final: 0.8026 (mtpp) REVERT: B 480 ARG cc_start: 0.6960 (mmt180) cc_final: 0.4942 (mmt180) REVERT: B 486 THR cc_start: 0.7693 (m) cc_final: 0.7462 (t) REVERT: B 487 GLN cc_start: 0.7906 (mt0) cc_final: 0.7567 (mt0) REVERT: B 570 SER cc_start: 0.8355 (m) cc_final: 0.8075 (t) REVERT: B 722 PHE cc_start: 0.8600 (OUTLIER) cc_final: 0.8162 (t80) REVERT: B 948 ASN cc_start: 0.6910 (t0) cc_final: 0.6660 (t0) REVERT: B 963 ASN cc_start: 0.7116 (t0) cc_final: 0.6882 (t0) REVERT: B 981 ILE cc_start: 0.7455 (OUTLIER) cc_final: 0.7182 (mp) REVERT: C 77 GLN cc_start: 0.4922 (OUTLIER) cc_final: 0.4589 (tp-100) REVERT: D 34 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.7972 (mm-40) REVERT: D 51 TYR cc_start: 0.6320 (OUTLIER) cc_final: 0.5949 (m-80) REVERT: D 172 GLU cc_start: 0.7744 (pm20) cc_final: 0.7257 (pm20) outliers start: 69 outliers final: 31 residues processed: 340 average time/residue: 0.2754 time to fit residues: 133.4779 Evaluate side-chains 337 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 297 time to evaluate : 1.814 ------------------------------------------------------------------------------- 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 391 ASN 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 802 ARG 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 51 TYR 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 123 optimal weight: 3.9990 chunk 144 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 106 optimal weight: 0.5980 chunk 162 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 = 0.4299 r_free = 0.4299 target = 0.184230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.157216 restraints weight = 20952.024| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 3.05 r_work: 0.3821 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14519 Z= 0.163 Angle : 0.602 12.599 19530 Z= 0.319 Chirality : 0.042 0.234 2070 Planarity : 0.003 0.051 2504 Dihedral : 4.748 44.062 1879 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.47 % Allowed : 7.30 % Favored : 92.23 % Rotamer: Outliers : 4.42 % Allowed : 26.99 % Favored : 68.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.21), residues: 1699 helix: 1.39 (0.17), residues: 934 sheet: -1.32 (0.47), residues: 126 loop : -1.92 (0.23), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 919 HIS 0.003 0.001 HIS A 415 PHE 0.033 0.002 PHE A 544 TYR 0.018 0.002 TYR A 649 ARG 0.006 0.000 ARG B 517 Details of bonding type rmsd hydrogen bonds : bond 0.04892 ( 693) hydrogen bonds : angle 4.20216 ( 1977) covalent geometry : bond 0.00372 (14519) covalent geometry : angle 0.60196 (19530) *********************** 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 380 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 311 time to evaluate : 1.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 THR cc_start: 0.5996 (OUTLIER) cc_final: 0.5063 (p) REVERT: A 357 MET cc_start: 0.4697 (tpt) cc_final: 0.4393 (tpt) REVERT: A 395 CYS cc_start: 0.7393 (m) cc_final: 0.7183 (m) REVERT: A 396 MET cc_start: 0.7688 (OUTLIER) cc_final: 0.7333 (ttp) REVERT: A 423 LYS cc_start: 0.8475 (mttt) cc_final: 0.8216 (mttt) REVERT: A 442 LEU cc_start: 0.7853 (mt) cc_final: 0.7563 (mp) REVERT: A 445 LEU cc_start: 0.7502 (tp) cc_final: 0.7208 (tt) REVERT: A 548 ASN cc_start: 0.4525 (OUTLIER) cc_final: 0.3913 (p0) REVERT: A 554 ASP cc_start: 0.7919 (m-30) cc_final: 0.7387 (m-30) REVERT: A 626 GLU cc_start: 0.7864 (tm-30) cc_final: 0.7662 (tm-30) REVERT: A 685 GLU cc_start: 0.7359 (tp30) cc_final: 0.7104 (tp30) REVERT: A 777 ASP cc_start: 0.7617 (m-30) cc_final: 0.7335 (m-30) REVERT: A 829 GLN cc_start: 0.6127 (OUTLIER) cc_final: 0.5910 (mm-40) REVERT: A 912 TYR cc_start: 0.7968 (m-80) cc_final: 0.7579 (m-80) REVERT: A 921 PHE cc_start: 0.7780 (t80) cc_final: 0.7572 (t80) REVERT: A 923 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7747 (mp0) REVERT: A 976 MET cc_start: 0.7700 (mtm) cc_final: 0.7359 (ptt) REVERT: B 315 LYS cc_start: 0.8146 (mmtm) cc_final: 0.7510 (mmmt) REVERT: B 480 ARG cc_start: 0.7260 (mmt180) cc_final: 0.5204 (mmt180) REVERT: B 487 GLN cc_start: 0.7973 (mt0) cc_final: 0.7639 (mt0) REVERT: B 517 ARG cc_start: 0.8051 (mtm110) cc_final: 0.7756 (ttm-80) REVERT: B 570 SER cc_start: 0.8490 (m) cc_final: 0.8223 (t) REVERT: B 697 LYS cc_start: 0.8134 (tppp) cc_final: 0.7777 (tppp) REVERT: B 948 ASN cc_start: 0.6981 (t0) cc_final: 0.6710 (t0) REVERT: B 963 ASN cc_start: 0.7142 (t0) cc_final: 0.6937 (t0) REVERT: B 981 ILE cc_start: 0.7431 (OUTLIER) cc_final: 0.7162 (mp) REVERT: B 982 GLU cc_start: 0.8162 (pt0) cc_final: 0.7882 (pt0) REVERT: C 77 GLN cc_start: 0.4931 (OUTLIER) cc_final: 0.4614 (tp-100) REVERT: D 34 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.8003 (mm-40) REVERT: D 50 LEU cc_start: 0.4749 (OUTLIER) cc_final: 0.4497 (pp) REVERT: D 51 TYR cc_start: 0.6459 (OUTLIER) cc_final: 0.6048 (m-80) REVERT: D 172 GLU cc_start: 0.7794 (pm20) cc_final: 0.7318 (pm20) outliers start: 69 outliers final: 39 residues processed: 357 average time/residue: 0.2842 time to fit residues: 144.1273 Evaluate side-chains 354 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 306 time to evaluate : 1.492 ------------------------------------------------------------------------------- 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 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 829 GLN Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 934 ILE 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 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 831 LYS Chi-restraints excluded: chain B residue 859 VAL 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 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 18 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 162 optimal weight: 5.9990 chunk 152 optimal weight: 0.0370 chunk 28 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 120 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 128 optimal weight: 6.9990 chunk 135 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 797 ASN ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 905 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.185368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.158253 restraints weight = 21098.892| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 3.09 r_work: 0.3831 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14519 Z= 0.130 Angle : 0.581 10.508 19530 Z= 0.308 Chirality : 0.042 0.210 2070 Planarity : 0.003 0.050 2504 Dihedral : 4.694 46.225 1879 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.18 % Favored : 92.47 % Rotamer: Outliers : 4.49 % Allowed : 27.82 % Favored : 67.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.21), residues: 1699 helix: 1.47 (0.17), residues: 936 sheet: -1.22 (0.48), residues: 126 loop : -1.96 (0.23), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 919 HIS 0.003 0.001 HIS B 881 PHE 0.025 0.001 PHE A 544 TYR 0.019 0.001 TYR D 192 ARG 0.006 0.000 ARG B 502 Details of bonding type rmsd hydrogen bonds : bond 0.04457 ( 693) hydrogen bonds : angle 4.15359 ( 1977) covalent geometry : bond 0.00288 (14519) covalent geometry : angle 0.58051 (19530) *********************** 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 381 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 311 time to evaluate : 1.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 THR cc_start: 0.5994 (OUTLIER) cc_final: 0.5080 (p) REVERT: A 350 LYS cc_start: 0.7819 (mmmm) cc_final: 0.7575 (mmmm) REVERT: A 357 MET cc_start: 0.4471 (tpt) cc_final: 0.4120 (tpt) REVERT: A 396 MET cc_start: 0.7680 (OUTLIER) cc_final: 0.7348 (ttp) REVERT: A 423 LYS cc_start: 0.8431 (mttt) cc_final: 0.8150 (mttt) REVERT: A 442 LEU cc_start: 0.7895 (mt) cc_final: 0.7610 (mp) REVERT: A 445 LEU cc_start: 0.7514 (tp) cc_final: 0.7228 (tt) REVERT: A 548 ASN cc_start: 0.4517 (OUTLIER) cc_final: 0.4003 (p0) REVERT: A 553 ASP cc_start: 0.7822 (t0) cc_final: 0.7523 (t0) REVERT: A 685 GLU cc_start: 0.7322 (tp30) cc_final: 0.7069 (tp30) REVERT: A 777 ASP cc_start: 0.7583 (m-30) cc_final: 0.7311 (m-30) REVERT: A 829 GLN cc_start: 0.6119 (OUTLIER) cc_final: 0.5897 (mm-40) REVERT: A 912 TYR cc_start: 0.7955 (m-80) cc_final: 0.7617 (m-80) REVERT: A 921 PHE cc_start: 0.7778 (t80) cc_final: 0.7545 (t80) REVERT: A 923 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7706 (mp0) REVERT: A 976 MET cc_start: 0.7563 (mtm) cc_final: 0.7289 (ptt) REVERT: B 487 GLN cc_start: 0.7928 (mt0) cc_final: 0.7712 (mt0) REVERT: B 510 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7660 (mp0) REVERT: B 570 SER cc_start: 0.8439 (m) cc_final: 0.8182 (t) REVERT: B 697 LYS cc_start: 0.8141 (tppp) cc_final: 0.7730 (tppp) REVERT: B 722 PHE cc_start: 0.8593 (OUTLIER) cc_final: 0.7868 (t80) REVERT: B 948 ASN cc_start: 0.7006 (t0) cc_final: 0.6725 (t0) REVERT: B 981 ILE cc_start: 0.7426 (OUTLIER) cc_final: 0.7172 (mp) REVERT: B 982 GLU cc_start: 0.8169 (pt0) cc_final: 0.7892 (pt0) REVERT: C 77 GLN cc_start: 0.4928 (OUTLIER) cc_final: 0.4576 (tp-100) REVERT: D 34 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.8035 (mm-40) REVERT: D 51 TYR cc_start: 0.6412 (OUTLIER) cc_final: 0.5973 (m-10) REVERT: D 172 GLU cc_start: 0.7751 (pm20) cc_final: 0.7289 (pm20) REVERT: D 174 GLU cc_start: 0.7493 (tm-30) cc_final: 0.7288 (tm-30) outliers start: 70 outliers final: 44 residues processed: 355 average time/residue: 0.2671 time to fit residues: 135.6398 Evaluate side-chains 354 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 301 time to evaluate : 1.417 ------------------------------------------------------------------------------- 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 548 ASN Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 570 SER 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 808 ILE Chi-restraints excluded: chain A residue 829 GLN Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 970 ILE 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 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 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 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 153 optimal weight: 7.9990 chunk 148 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 39 optimal weight: 0.5980 chunk 131 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 113 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 116 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 70 optimal weight: 20.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 797 ASN ** 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 = 0.4305 r_free = 0.4305 target = 0.184897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.158527 restraints weight = 21136.568| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 2.90 r_work: 0.3842 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14519 Z= 0.140 Angle : 0.587 9.690 19530 Z= 0.311 Chirality : 0.041 0.211 2070 Planarity : 0.003 0.049 2504 Dihedral : 4.672 44.735 1879 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.41 % Allowed : 7.06 % Favored : 92.53 % Rotamer: Outliers : 5.06 % Allowed : 27.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.21), residues: 1699 helix: 1.48 (0.17), residues: 936 sheet: -1.12 (0.48), residues: 125 loop : -1.95 (0.23), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 919 HIS 0.003 0.001 HIS B 881 PHE 0.025 0.001 PHE D 67 TYR 0.019 0.001 TYR D 192 ARG 0.009 0.000 ARG B 517 Details of bonding type rmsd hydrogen bonds : bond 0.04521 ( 693) hydrogen bonds : angle 4.12412 ( 1977) covalent geometry : bond 0.00312 (14519) covalent geometry : angle 0.58730 (19530) *********************** 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 384 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 305 time to evaluate : 1.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 ASP cc_start: 0.7738 (t70) cc_final: 0.7537 (t70) REVERT: A 345 THR cc_start: 0.5984 (OUTLIER) cc_final: 0.5110 (p) REVERT: A 350 LYS cc_start: 0.7819 (mmmm) cc_final: 0.7581 (mmmm) REVERT: A 357 MET cc_start: 0.4750 (tpt) cc_final: 0.4510 (tpt) REVERT: A 423 LYS cc_start: 0.8421 (mttt) cc_final: 0.8147 (mttt) REVERT: A 442 LEU cc_start: 0.7943 (mt) cc_final: 0.7666 (mp) REVERT: A 445 LEU cc_start: 0.7499 (tp) cc_final: 0.7215 (tt) REVERT: A 543 GLU cc_start: 0.6824 (tp30) cc_final: 0.6558 (tp30) REVERT: A 548 ASN cc_start: 0.4640 (OUTLIER) cc_final: 0.4072 (p0) REVERT: A 553 ASP cc_start: 0.7857 (t0) cc_final: 0.7573 (t0) REVERT: A 685 GLU cc_start: 0.7334 (tp30) cc_final: 0.7108 (tp30) REVERT: A 777 ASP cc_start: 0.7549 (m-30) cc_final: 0.7210 (m-30) REVERT: A 829 GLN cc_start: 0.6208 (OUTLIER) cc_final: 0.5967 (mm-40) REVERT: A 912 TYR cc_start: 0.7945 (m-80) cc_final: 0.7577 (m-80) REVERT: A 921 PHE cc_start: 0.7801 (t80) cc_final: 0.7563 (t80) REVERT: A 923 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7713 (mp0) REVERT: B 306 ASP cc_start: 0.6401 (OUTLIER) cc_final: 0.6093 (p0) REVERT: B 517 ARG cc_start: 0.8030 (mtm110) cc_final: 0.7728 (ttm-80) REVERT: B 566 ARG cc_start: 0.8303 (tpp-160) cc_final: 0.8044 (mmt90) REVERT: B 570 SER cc_start: 0.8449 (m) cc_final: 0.8233 (t) REVERT: B 624 GLU cc_start: 0.6850 (OUTLIER) cc_final: 0.6356 (mm-30) REVERT: B 674 ASP cc_start: 0.8259 (t0) cc_final: 0.8049 (t0) REVERT: B 697 LYS cc_start: 0.8116 (tppp) cc_final: 0.7723 (tppp) REVERT: B 818 LYS cc_start: 0.6994 (mmmm) cc_final: 0.5849 (mmmm) REVERT: B 822 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7675 (mp0) REVERT: B 906 THR cc_start: 0.5824 (OUTLIER) cc_final: 0.5575 (m) REVERT: B 948 ASN cc_start: 0.7068 (t0) cc_final: 0.6767 (t0) REVERT: B 981 ILE cc_start: 0.7396 (OUTLIER) cc_final: 0.7142 (mp) REVERT: B 982 GLU cc_start: 0.8123 (pt0) cc_final: 0.7891 (pt0) REVERT: C 67 PHE cc_start: 0.6039 (t80) cc_final: 0.5796 (t80) REVERT: C 77 GLN cc_start: 0.4872 (OUTLIER) cc_final: 0.4517 (tp-100) REVERT: D 34 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.8098 (mm-40) REVERT: D 51 TYR cc_start: 0.6534 (OUTLIER) cc_final: 0.6114 (m-80) REVERT: D 172 GLU cc_start: 0.7781 (pm20) cc_final: 0.7365 (pm20) REVERT: D 174 GLU cc_start: 0.7446 (tm-30) cc_final: 0.7227 (tm-30) outliers start: 79 outliers final: 46 residues processed: 355 average time/residue: 0.2716 time to fit residues: 138.3099 Evaluate side-chains 358 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 301 time to evaluate : 1.438 ------------------------------------------------------------------------------- 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 570 SER 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 829 GLN Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 970 ILE 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 624 GLU 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 831 LYS Chi-restraints excluded: chain B residue 859 VAL 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 21 optimal weight: 0.4980 chunk 73 optimal weight: 2.9990 chunk 4 optimal weight: 0.0870 chunk 165 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 119 optimal weight: 0.9990 chunk 22 optimal weight: 0.0470 chunk 16 optimal weight: 0.0170 chunk 99 optimal weight: 1.9990 chunk 70 optimal weight: 20.0000 overall best weight: 0.2694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 503 HIS B 614 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.186945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.160877 restraints weight = 21176.521| |-----------------------------------------------------------------------------| r_work (start): 0.4013 rms_B_bonded: 2.91 r_work: 0.3876 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 14519 Z= 0.114 Angle : 0.578 13.976 19530 Z= 0.303 Chirality : 0.040 0.209 2070 Planarity : 0.003 0.046 2504 Dihedral : 4.584 47.011 1879 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.89 % Favored : 92.76 % Rotamer: Outliers : 4.42 % Allowed : 28.65 % Favored : 66.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.21), residues: 1699 helix: 1.62 (0.18), residues: 933 sheet: -1.07 (0.49), residues: 125 loop : -1.88 (0.23), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 919 HIS 0.003 0.000 HIS B 881 PHE 0.025 0.001 PHE D 67 TYR 0.012 0.001 TYR B 472 ARG 0.007 0.000 ARG B 517 Details of bonding type rmsd hydrogen bonds : bond 0.03917 ( 693) hydrogen bonds : angle 4.04695 ( 1977) covalent geometry : bond 0.00237 (14519) covalent geometry : angle 0.57797 (19530) *********************** 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 376 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 307 time to evaluate : 1.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 LYS cc_start: 0.7769 (mmmm) cc_final: 0.7502 (mmmm) REVERT: A 357 MET cc_start: 0.4713 (tpt) cc_final: 0.4512 (tpt) REVERT: A 423 LYS cc_start: 0.8423 (mttt) cc_final: 0.8150 (mttt) REVERT: A 440 PHE cc_start: 0.8128 (t80) cc_final: 0.7675 (t80) REVERT: A 442 LEU cc_start: 0.7989 (mt) cc_final: 0.7689 (mp) REVERT: A 445 LEU cc_start: 0.7517 (tp) cc_final: 0.7240 (tt) REVERT: A 548 ASN cc_start: 0.4558 (OUTLIER) cc_final: 0.4126 (p0) REVERT: A 553 ASP cc_start: 0.7774 (t0) cc_final: 0.7505 (t0) REVERT: A 685 GLU cc_start: 0.7260 (tp30) cc_final: 0.7060 (tp30) REVERT: A 777 ASP cc_start: 0.7422 (m-30) cc_final: 0.7120 (m-30) REVERT: A 829 GLN cc_start: 0.6143 (OUTLIER) cc_final: 0.5854 (mm110) REVERT: A 840 LYS cc_start: 0.6893 (OUTLIER) cc_final: 0.6198 (ptpt) REVERT: A 921 PHE cc_start: 0.7760 (t80) cc_final: 0.7515 (t80) REVERT: A 923 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7687 (mp0) REVERT: B 566 ARG cc_start: 0.8283 (tpp-160) cc_final: 0.8047 (mmt90) REVERT: B 624 GLU cc_start: 0.6743 (OUTLIER) cc_final: 0.6201 (mm-30) REVERT: B 697 LYS cc_start: 0.8105 (tppp) cc_final: 0.7704 (tppp) REVERT: B 722 PHE cc_start: 0.8539 (OUTLIER) cc_final: 0.7825 (t80) REVERT: B 727 LYS cc_start: 0.8226 (ttmt) cc_final: 0.7945 (ttmm) REVERT: B 748 ASP cc_start: 0.7480 (OUTLIER) cc_final: 0.7125 (m-30) REVERT: B 822 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7642 (mp0) REVERT: B 948 ASN cc_start: 0.7050 (t0) cc_final: 0.6755 (t0) REVERT: B 981 ILE cc_start: 0.7384 (OUTLIER) cc_final: 0.7136 (mp) REVERT: B 982 GLU cc_start: 0.8124 (pt0) cc_final: 0.7878 (pt0) REVERT: C 52 ILE cc_start: 0.4964 (OUTLIER) cc_final: 0.4596 (mm) REVERT: C 77 GLN cc_start: 0.4900 (OUTLIER) cc_final: 0.4558 (tp-100) REVERT: D 51 TYR cc_start: 0.6449 (OUTLIER) cc_final: 0.6010 (m-10) REVERT: D 172 GLU cc_start: 0.7719 (pm20) cc_final: 0.7311 (pm20) REVERT: D 174 GLU cc_start: 0.7409 (tm-30) cc_final: 0.7045 (tm-30) outliers start: 69 outliers final: 37 residues processed: 351 average time/residue: 0.2648 time to fit residues: 134.5026 Evaluate side-chains 347 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 299 time to evaluate : 1.466 ------------------------------------------------------------------------------- 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 498 LEU Chi-restraints excluded: chain A residue 518 GLU Chi-restraints excluded: chain A residue 548 ASN Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 570 SER Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 720 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 829 GLN Chi-restraints excluded: chain A residue 840 LYS 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 624 GLU 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 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 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 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 30 optimal weight: 0.4980 chunk 157 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 6 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 155 optimal weight: 20.0000 chunk 12 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 70 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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** B 614 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.184417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.158400 restraints weight = 20939.465| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 2.88 r_work: 0.3843 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 moved from start: 0.2564 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= 0.142 Angle : 0.609 13.565 19530 Z= 0.316 Chirality : 0.041 0.213 2070 Planarity : 0.003 0.044 2504 Dihedral : 4.629 42.689 1879 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.06 % Favored : 92.64 % Rotamer: Outliers : 4.36 % Allowed : 28.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.21), residues: 1699 helix: 1.56 (0.18), residues: 936 sheet: -1.11 (0.49), residues: 125 loop : -2.01 (0.23), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 919 HIS 0.003 0.001 HIS B 786 PHE 0.039 0.002 PHE D 32 TYR 0.016 0.001 TYR B 725 ARG 0.010 0.000 ARG B 517 Details of bonding type rmsd hydrogen bonds : bond 0.04463 ( 693) hydrogen bonds : angle 4.08204 ( 1977) covalent geometry : bond 0.00322 (14519) covalent geometry : angle 0.60862 (19530) *********************** 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 368 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 300 time to evaluate : 1.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 LYS cc_start: 0.7808 (mmmm) cc_final: 0.7525 (mmmm) REVERT: A 357 MET cc_start: 0.4630 (tpt) cc_final: 0.4409 (tpt) REVERT: A 423 LYS cc_start: 0.8464 (mttt) cc_final: 0.8202 (mttt) REVERT: A 442 LEU cc_start: 0.7955 (mt) cc_final: 0.7675 (mp) REVERT: A 445 LEU cc_start: 0.7500 (tp) cc_final: 0.7225 (tt) REVERT: A 548 ASN cc_start: 0.4447 (OUTLIER) cc_final: 0.3864 (p0) REVERT: A 553 ASP cc_start: 0.7846 (t0) cc_final: 0.7606 (t0) REVERT: A 685 GLU cc_start: 0.7321 (tp30) cc_final: 0.7111 (tp30) REVERT: A 697 LYS cc_start: 0.7985 (ttpp) cc_final: 0.7776 (ttpp) REVERT: A 717 LYS cc_start: 0.7599 (OUTLIER) cc_final: 0.7257 (mttt) REVERT: A 777 ASP cc_start: 0.7429 (m-30) cc_final: 0.7098 (m-30) REVERT: A 829 GLN cc_start: 0.6262 (OUTLIER) cc_final: 0.5961 (mm110) REVERT: A 840 LYS cc_start: 0.6952 (OUTLIER) cc_final: 0.6165 (ptpt) REVERT: A 921 PHE cc_start: 0.7781 (t80) cc_final: 0.7499 (t80) REVERT: A 923 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7706 (mp0) REVERT: B 450 GLU cc_start: 0.7388 (mp0) cc_final: 0.6916 (mp0) REVERT: B 566 ARG cc_start: 0.8303 (tpp-160) cc_final: 0.8062 (mmt90) REVERT: B 624 GLU cc_start: 0.6833 (OUTLIER) cc_final: 0.6321 (mm-30) REVERT: B 697 LYS cc_start: 0.8113 (tppp) cc_final: 0.7731 (tppp) REVERT: B 727 LYS cc_start: 0.8276 (ttmt) cc_final: 0.8025 (ttmm) REVERT: B 746 GLU cc_start: 0.7184 (pm20) cc_final: 0.6851 (pm20) REVERT: B 748 ASP cc_start: 0.7482 (OUTLIER) cc_final: 0.7120 (m-30) REVERT: B 797 ASN cc_start: 0.8191 (t0) cc_final: 0.7981 (t0) REVERT: B 822 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7612 (mp0) REVERT: B 948 ASN cc_start: 0.7075 (t0) cc_final: 0.6787 (t0) REVERT: B 981 ILE cc_start: 0.7390 (OUTLIER) cc_final: 0.7156 (mp) REVERT: B 982 GLU cc_start: 0.8121 (pt0) cc_final: 0.7888 (pt0) REVERT: C 77 GLN cc_start: 0.4861 (OUTLIER) cc_final: 0.4516 (tp-100) REVERT: D 51 TYR cc_start: 0.6663 (OUTLIER) cc_final: 0.6237 (m-10) REVERT: D 172 GLU cc_start: 0.7754 (pm20) cc_final: 0.7354 (pm20) REVERT: D 174 GLU cc_start: 0.7362 (tm-30) cc_final: 0.7151 (tm-30) outliers start: 68 outliers final: 44 residues processed: 345 average time/residue: 0.2725 time to fit residues: 134.4913 Evaluate side-chains 350 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 296 time to evaluate : 1.524 ------------------------------------------------------------------------------- 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 498 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 518 GLU Chi-restraints excluded: chain A residue 543 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 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 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 829 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 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 624 GLU Chi-restraints excluded: chain B residue 676 ILE 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 799 LEU Chi-restraints excluded: chain B residue 822 GLU 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 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 51 TYR Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 62 THR 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 91 optimal weight: 0.8980 chunk 156 optimal weight: 0.3980 chunk 4 optimal weight: 0.0000 chunk 86 optimal weight: 0.3980 chunk 43 optimal weight: 0.8980 chunk 98 optimal weight: 0.0870 chunk 97 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 12 optimal weight: 0.4980 chunk 3 optimal weight: 3.9990 overall best weight: 0.2762 ------------------------------------------------------------------------------- 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** B 614 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.186662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.160768 restraints weight = 21094.857| |-----------------------------------------------------------------------------| r_work (start): 0.4030 rms_B_bonded: 2.91 r_work: 0.3896 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 14519 Z= 0.119 Angle : 0.604 12.815 19530 Z= 0.314 Chirality : 0.041 0.233 2070 Planarity : 0.003 0.044 2504 Dihedral : 4.617 45.920 1879 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.65 % Favored : 93.05 % Rotamer: Outliers : 3.85 % Allowed : 28.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.21), residues: 1699 helix: 1.65 (0.18), residues: 932 sheet: -1.07 (0.49), residues: 125 loop : -1.94 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 919 HIS 0.004 0.001 HIS B 881 PHE 0.032 0.001 PHE D 32 TYR 0.015 0.001 TYR B 539 ARG 0.009 0.000 ARG B 517 Details of bonding type rmsd hydrogen bonds : bond 0.03904 ( 693) hydrogen bonds : angle 4.03836 ( 1977) covalent geometry : bond 0.00260 (14519) covalent geometry : angle 0.60442 (19530) *********************** 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 362 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 302 time to evaluate : 1.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 LYS cc_start: 0.7810 (mmmm) cc_final: 0.7544 (mmmm) REVERT: A 357 MET cc_start: 0.4432 (tpt) cc_final: 0.4227 (tpt) REVERT: A 423 LYS cc_start: 0.8409 (mttt) cc_final: 0.8190 (mttt) REVERT: A 440 PHE cc_start: 0.8041 (t80) cc_final: 0.7733 (t80) REVERT: A 442 LEU cc_start: 0.8033 (mt) cc_final: 0.7733 (mp) REVERT: A 445 LEU cc_start: 0.7532 (tp) cc_final: 0.7278 (tt) REVERT: A 548 ASN cc_start: 0.4606 (OUTLIER) cc_final: 0.4069 (p0) REVERT: A 553 ASP cc_start: 0.7778 (t0) cc_final: 0.7568 (t0) REVERT: A 717 LYS cc_start: 0.7524 (OUTLIER) cc_final: 0.7136 (mttt) REVERT: A 777 ASP cc_start: 0.7383 (m-30) cc_final: 0.7055 (m-30) REVERT: A 829 GLN cc_start: 0.6110 (OUTLIER) cc_final: 0.5827 (mm110) REVERT: A 840 LYS cc_start: 0.6906 (OUTLIER) cc_final: 0.6284 (ptpt) REVERT: A 923 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7682 (mp0) REVERT: A 944 VAL cc_start: 0.8738 (m) cc_final: 0.8420 (p) REVERT: B 357 MET cc_start: 0.7173 (mmm) cc_final: 0.6866 (mmm) REVERT: B 450 GLU cc_start: 0.7293 (mp0) cc_final: 0.6895 (mp0) REVERT: B 566 ARG cc_start: 0.8319 (tpp-160) cc_final: 0.8088 (mmt90) REVERT: B 624 GLU cc_start: 0.6771 (OUTLIER) cc_final: 0.6210 (mm-30) REVERT: B 697 LYS cc_start: 0.8120 (tppp) cc_final: 0.7769 (tppp) REVERT: B 727 LYS cc_start: 0.8208 (ttmt) cc_final: 0.7973 (ttmm) REVERT: B 748 ASP cc_start: 0.7378 (OUTLIER) cc_final: 0.7046 (m-30) REVERT: B 797 ASN cc_start: 0.8152 (t0) cc_final: 0.7923 (t0) REVERT: B 822 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7588 (mp0) REVERT: B 948 ASN cc_start: 0.7045 (t0) cc_final: 0.6751 (t0) REVERT: B 981 ILE cc_start: 0.7322 (OUTLIER) cc_final: 0.7085 (mp) REVERT: C 52 ILE cc_start: 0.4859 (OUTLIER) cc_final: 0.4516 (mm) REVERT: C 77 GLN cc_start: 0.4879 (OUTLIER) cc_final: 0.4498 (tp-100) REVERT: D 51 TYR cc_start: 0.6631 (OUTLIER) cc_final: 0.6232 (m-10) REVERT: D 172 GLU cc_start: 0.7705 (pm20) cc_final: 0.7353 (pm20) outliers start: 60 outliers final: 38 residues processed: 339 average time/residue: 0.2630 time to fit residues: 128.2753 Evaluate side-chains 344 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 295 time to evaluate : 1.411 ------------------------------------------------------------------------------- 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 518 GLU Chi-restraints excluded: chain A residue 543 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 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 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 829 GLN Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain A residue 970 ILE 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 624 GLU Chi-restraints excluded: chain B residue 685 GLU 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 913 MET Chi-restraints excluded: chain B residue 981 ILE Chi-restraints excluded: chain B residue 998 GLU 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 51 TYR 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 156 optimal weight: 0.0060 chunk 108 optimal weight: 0.6980 chunk 101 optimal weight: 0.9990 chunk 64 optimal weight: 0.0980 chunk 155 optimal weight: 10.0000 chunk 116 optimal weight: 1.9990 chunk 139 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 124 optimal weight: 2.9990 chunk 145 optimal weight: 0.0980 overall best weight: 0.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 698 GLN A 881 HIS ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 614 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.187168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.161244 restraints weight = 21028.474| |-----------------------------------------------------------------------------| r_work (start): 0.4034 rms_B_bonded: 2.90 r_work: 0.3897 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6830 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 14519 Z= 0.119 Angle : 0.623 12.419 19530 Z= 0.319 Chirality : 0.041 0.229 2070 Planarity : 0.003 0.054 2504 Dihedral : 4.567 45.458 1879 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.71 % Favored : 93.00 % Rotamer: Outliers : 3.33 % Allowed : 29.62 % Favored : 67.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.21), residues: 1699 helix: 1.67 (0.18), residues: 931 sheet: -1.00 (0.50), residues: 125 loop : -1.96 (0.22), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 919 HIS 0.003 0.001 HIS B 881 PHE 0.029 0.001 PHE D 32 TYR 0.015 0.001 TYR B 539 ARG 0.013 0.000 ARG B 517 Details of bonding type rmsd hydrogen bonds : bond 0.03852 ( 693) hydrogen bonds : angle 4.01232 ( 1977) covalent geometry : bond 0.00262 (14519) covalent geometry : angle 0.62321 (19530) ********************** 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 352 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 300 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 LYS cc_start: 0.7817 (mmmm) cc_final: 0.7529 (mmmm) REVERT: A 357 MET cc_start: 0.4478 (tpt) cc_final: 0.4210 (tpt) REVERT: A 423 LYS cc_start: 0.8398 (mttt) cc_final: 0.8174 (mttt) REVERT: A 440 PHE cc_start: 0.8015 (t80) cc_final: 0.7703 (t80) REVERT: A 442 LEU cc_start: 0.8040 (mt) cc_final: 0.7739 (mp) REVERT: A 445 LEU cc_start: 0.7535 (tp) cc_final: 0.7294 (tt) REVERT: A 553 ASP cc_start: 0.7758 (t0) cc_final: 0.7552 (t0) REVERT: A 717 LYS cc_start: 0.7557 (OUTLIER) cc_final: 0.7125 (mttt) REVERT: A 777 ASP cc_start: 0.7377 (m-30) cc_final: 0.7060 (m-30) REVERT: A 829 GLN cc_start: 0.6186 (OUTLIER) cc_final: 0.5839 (mm110) REVERT: A 840 LYS cc_start: 0.6749 (OUTLIER) cc_final: 0.6193 (ptpt) REVERT: A 923 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7692 (mp0) REVERT: B 357 MET cc_start: 0.7182 (mmm) cc_final: 0.6880 (mmm) REVERT: B 450 GLU cc_start: 0.7316 (mp0) cc_final: 0.6908 (mp0) REVERT: B 566 ARG cc_start: 0.8333 (tpp-160) cc_final: 0.8105 (mmt90) REVERT: B 624 GLU cc_start: 0.6748 (OUTLIER) cc_final: 0.5975 (mm-30) REVERT: B 697 LYS cc_start: 0.8135 (tppp) cc_final: 0.7777 (tppp) REVERT: B 722 PHE cc_start: 0.8572 (OUTLIER) cc_final: 0.7864 (t80) REVERT: B 727 LYS cc_start: 0.8186 (ttmt) cc_final: 0.7957 (ttmm) REVERT: B 748 ASP cc_start: 0.7372 (OUTLIER) cc_final: 0.7036 (m-30) REVERT: B 797 ASN cc_start: 0.8160 (t0) cc_final: 0.7881 (t0) REVERT: B 822 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7586 (mp0) REVERT: B 948 ASN cc_start: 0.7050 (t0) cc_final: 0.6756 (t0) REVERT: B 981 ILE cc_start: 0.7343 (OUTLIER) cc_final: 0.7133 (mp) REVERT: C 52 ILE cc_start: 0.4844 (OUTLIER) cc_final: 0.4497 (mm) REVERT: C 77 GLN cc_start: 0.4860 (OUTLIER) cc_final: 0.4573 (tp-100) REVERT: D 51 TYR cc_start: 0.6520 (OUTLIER) cc_final: 0.6181 (m-10) REVERT: D 58 GLU cc_start: 0.6935 (pp20) cc_final: 0.6192 (pp20) REVERT: D 172 GLU cc_start: 0.7707 (pm20) cc_final: 0.7340 (pm20) outliers start: 52 outliers final: 36 residues processed: 332 average time/residue: 0.2729 time to fit residues: 130.5569 Evaluate side-chains 340 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 293 time to evaluate : 1.400 ------------------------------------------------------------------------------- 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 518 GLU Chi-restraints excluded: chain A residue 543 GLU 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 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 829 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 421 MET Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 444 CYS Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 624 GLU Chi-restraints excluded: chain B residue 685 GLU 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 906 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 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 51 TYR 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 149 optimal weight: 9.9990 chunk 99 optimal weight: 0.9990 chunk 24 optimal weight: 0.4980 chunk 142 optimal weight: 0.9980 chunk 155 optimal weight: 0.9980 chunk 69 optimal weight: 0.4980 chunk 27 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 70 optimal weight: 20.0000 chunk 67 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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** B 391 ASN B 614 ASN C 77 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.185024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.159036 restraints weight = 21168.032| |-----------------------------------------------------------------------------| r_work (start): 0.4008 rms_B_bonded: 2.90 r_work: 0.3872 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 14519 Z= 0.142 Angle : 0.638 12.049 19530 Z= 0.327 Chirality : 0.042 0.240 2070 Planarity : 0.003 0.053 2504 Dihedral : 4.629 42.377 1879 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.18 % Favored : 92.53 % Rotamer: Outliers : 3.27 % Allowed : 29.42 % Favored : 67.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.21), residues: 1699 helix: 1.65 (0.18), residues: 931 sheet: -1.10 (0.48), residues: 130 loop : -1.99 (0.23), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 919 HIS 0.004 0.001 HIS B 786 PHE 0.032 0.001 PHE D 32 TYR 0.017 0.001 TYR B 539 ARG 0.012 0.000 ARG B 517 Details of bonding type rmsd hydrogen bonds : bond 0.04303 ( 693) hydrogen bonds : angle 4.03616 ( 1977) covalent geometry : bond 0.00322 (14519) covalent geometry : angle 0.63822 (19530) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6662.25 seconds wall clock time: 116 minutes 33.02 seconds (6993.02 seconds total)