Starting phenix.real_space_refine on Thu Jun 12 15:59:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ygo_39258/06_2025/8ygo_39258.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ygo_39258/06_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_39258/06_2025/8ygo_39258.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ygo_39258/06_2025/8ygo_39258.map" model { file = "/net/cci-nas-00/data/ceres_data/8ygo_39258/06_2025/8ygo_39258.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ygo_39258/06_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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 8.93, per 1000 atoms: 0.63 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: 3.28 Conformation dependent library (CDL) restraints added in 1.7 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: 1.48 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: 4.29 Time building geometry restraints manager: 3.94 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: 1.430 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: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 33.290 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.150 ------------------------------------------------------------------------------- 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 : 1.430 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: 0.3027 time to fit residues: 138.2438 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 : 1.410 ------------------------------------------------------------------------------- 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 = 0.187416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.160782 restraints weight = 21025.926| |-----------------------------------------------------------------------------| r_work (start): 0.4008 rms_B_bonded: 3.04 r_work: 0.3864 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3864 ------------------------------------------------------------------------------- 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 12.906 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 : 27.50 % Favored : 68.78 % 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 4.40820 ( 1977) covalent geometry : bond 0.00291 (14519) covalent geometry : angle 0.62337 (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 : 2.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 MET cc_start: 0.4471 (tpt) cc_final: 0.4175 (tpt) REVERT: A 396 MET cc_start: 0.7637 (OUTLIER) cc_final: 0.7197 (ttp) REVERT: A 423 LYS cc_start: 0.8428 (mttt) cc_final: 0.8212 (mttt) REVERT: A 445 LEU cc_start: 0.7470 (tp) cc_final: 0.7105 (tt) REVERT: A 543 GLU cc_start: 0.6580 (tp30) cc_final: 0.6376 (tp30) REVERT: A 548 ASN cc_start: 0.4413 (OUTLIER) cc_final: 0.3968 (p0) REVERT: A 554 ASP cc_start: 0.7799 (m-30) cc_final: 0.7354 (m-30) REVERT: A 626 GLU cc_start: 0.7813 (tm-30) cc_final: 0.7599 (tm-30) REVERT: A 685 GLU cc_start: 0.7332 (tp30) cc_final: 0.7070 (tp30) REVERT: A 777 ASP cc_start: 0.7566 (OUTLIER) cc_final: 0.7290 (m-30) REVERT: A 831 LYS cc_start: 0.6327 (mtmm) cc_final: 0.6110 (mtmm) REVERT: A 913 MET cc_start: 0.7511 (mmm) cc_final: 0.6680 (tpp) REVERT: A 923 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7800 (mp0) REVERT: B 394 ILE cc_start: 0.8577 (mm) cc_final: 0.8346 (mt) REVERT: B 438 LYS cc_start: 0.8222 (mtpt) cc_final: 0.7997 (mtpp) REVERT: B 486 THR cc_start: 0.7659 (m) cc_final: 0.7411 (t) REVERT: B 570 SER cc_start: 0.8393 (m) cc_final: 0.8111 (t) REVERT: B 722 PHE cc_start: 0.8648 (OUTLIER) cc_final: 0.8114 (t80) REVERT: B 797 ASN cc_start: 0.7194 (OUTLIER) cc_final: 0.6669 (t0) REVERT: B 948 ASN cc_start: 0.6758 (t0) cc_final: 0.6512 (t0) REVERT: B 981 ILE cc_start: 0.7446 (OUTLIER) cc_final: 0.7173 (mp) REVERT: D 34 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.8057 (mm-40) REVERT: D 51 TYR cc_start: 0.6434 (OUTLIER) cc_final: 0.6201 (m-10) REVERT: D 172 GLU cc_start: 0.7684 (pm20) cc_final: 0.7287 (pm20) outliers start: 58 outliers final: 25 residues processed: 329 average time/residue: 0.3170 time to fit residues: 152.4240 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 : 1.659 ------------------------------------------------------------------------------- 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: 7.9990 chunk 44 optimal weight: 0.0070 chunk 36 optimal weight: 0.4980 chunk 136 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 79 optimal weight: 0.0870 chunk 169 optimal weight: 9.9990 chunk 85 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 overall best weight: 0.4576 ------------------------------------------------------------------------------- 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 = 0.4338 r_free = 0.4338 target = 0.187787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.160897 restraints weight = 21157.286| |-----------------------------------------------------------------------------| r_work (start): 0.4008 rms_B_bonded: 3.07 r_work: 0.3866 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 moved from start: 0.1479 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= 0.123 Angle : 0.575 11.232 19530 Z= 0.307 Chirality : 0.041 0.210 2070 Planarity : 0.003 0.056 2504 Dihedral : 4.727 48.822 1881 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.47 % Allowed : 7.24 % Favored : 92.29 % Rotamer: Outliers : 4.29 % Allowed : 26.67 % Favored : 69.04 % 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: -0.00 (0.21), residues: 1699 helix: 1.41 (0.18), residues: 936 sheet: -1.33 (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 881 PHE 0.029 0.001 PHE A 544 TYR 0.013 0.001 TYR A 649 ARG 0.005 0.000 ARG B 517 Details of bonding type rmsd hydrogen bonds : bond 0.04442 ( 693) hydrogen bonds : angle 4.22911 ( 1977) covalent geometry : bond 0.00263 (14519) covalent geometry : angle 0.57541 (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 361 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 294 time to evaluate : 1.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 THR cc_start: 0.5646 (OUTLIER) cc_final: 0.4661 (p) REVERT: A 357 MET cc_start: 0.4479 (tpt) cc_final: 0.4191 (tpt) REVERT: A 396 MET cc_start: 0.7610 (OUTLIER) cc_final: 0.7253 (ttp) REVERT: A 423 LYS cc_start: 0.8381 (mttt) cc_final: 0.8158 (mttt) REVERT: A 442 LEU cc_start: 0.7806 (mt) cc_final: 0.7472 (mp) REVERT: A 445 LEU cc_start: 0.7488 (tp) cc_final: 0.7157 (tt) REVERT: A 498 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7347 (tp) REVERT: A 548 ASN cc_start: 0.4523 (OUTLIER) cc_final: 0.4102 (p0) REVERT: A 554 ASP cc_start: 0.7778 (m-30) cc_final: 0.7291 (m-30) REVERT: A 626 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7616 (tm-30) REVERT: A 685 GLU cc_start: 0.7323 (tp30) cc_final: 0.7065 (tp30) REVERT: A 777 ASP cc_start: 0.7583 (m-30) cc_final: 0.7298 (m-30) REVERT: A 913 MET cc_start: 0.7545 (mmm) cc_final: 0.7233 (tpp) REVERT: A 923 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7733 (mp0) REVERT: B 315 LYS cc_start: 0.8058 (mmtm) cc_final: 0.7405 (mmmt) REVERT: B 394 ILE cc_start: 0.8565 (mm) cc_final: 0.8357 (mt) REVERT: B 438 LYS cc_start: 0.8238 (mtpt) cc_final: 0.8019 (mtpp) REVERT: B 480 ARG cc_start: 0.6882 (mmt180) cc_final: 0.4893 (mmt180) REVERT: B 486 THR cc_start: 0.7650 (m) cc_final: 0.7415 (t) REVERT: B 570 SER cc_start: 0.8336 (m) cc_final: 0.8059 (t) REVERT: B 722 PHE cc_start: 0.8584 (OUTLIER) cc_final: 0.8133 (t80) REVERT: B 797 ASN cc_start: 0.7318 (OUTLIER) cc_final: 0.7107 (t0) REVERT: B 948 ASN cc_start: 0.6877 (t0) cc_final: 0.6624 (t0) REVERT: B 963 ASN cc_start: 0.7106 (t0) cc_final: 0.6871 (t0) REVERT: B 981 ILE cc_start: 0.7451 (OUTLIER) cc_final: 0.7178 (mp) REVERT: C 77 GLN cc_start: 0.4923 (OUTLIER) cc_final: 0.4590 (tp-100) REVERT: D 34 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7942 (mm-40) REVERT: D 51 TYR cc_start: 0.6310 (OUTLIER) cc_final: 0.5974 (m-10) REVERT: D 172 GLU cc_start: 0.7727 (pm20) cc_final: 0.7251 (pm20) outliers start: 67 outliers final: 33 residues processed: 336 average time/residue: 0.2988 time to fit residues: 144.3636 Evaluate side-chains 330 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 287 time to evaluate : 1.640 ------------------------------------------------------------------------------- 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 391 ASN Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 548 ASN Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 782 GLN 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 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 685 GLU Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 797 ASN Chi-restraints excluded: chain B residue 802 ARG Chi-restraints excluded: chain B residue 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: 4.9990 chunk 144 optimal weight: 0.0370 chunk 107 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 chunk 162 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 81 optimal weight: 0.0060 chunk 20 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 67 optimal weight: 0.4980 overall best weight: 0.4276 ------------------------------------------------------------------------------- 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 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 867 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.188031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.161353 restraints weight = 20959.890| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 3.05 r_work: 0.3873 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14519 Z= 0.118 Angle : 0.568 12.181 19530 Z= 0.301 Chirality : 0.040 0.209 2070 Planarity : 0.003 0.051 2504 Dihedral : 4.730 48.448 1881 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.47 % Allowed : 7.24 % Favored : 92.29 % Rotamer: Outliers : 4.62 % Allowed : 26.99 % Favored : 68.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (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: 0.09 (0.21), residues: 1699 helix: 1.49 (0.18), residues: 936 sheet: -1.26 (0.48), residues: 126 loop : -1.90 (0.23), residues: 637 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 0.027 0.001 PHE A 544 TYR 0.015 0.001 TYR A 324 ARG 0.005 0.000 ARG B 517 Details of bonding type rmsd hydrogen bonds : bond 0.04129 ( 693) hydrogen bonds : angle 4.12186 ( 1977) covalent geometry : bond 0.00257 (14519) covalent geometry : angle 0.56802 (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 367 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 295 time to evaluate : 1.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 MET cc_start: 0.4499 (tpt) cc_final: 0.4192 (tpt) REVERT: A 396 MET cc_start: 0.7611 (OUTLIER) cc_final: 0.7208 (ttp) REVERT: A 423 LYS cc_start: 0.8402 (mttt) cc_final: 0.8136 (mttt) REVERT: A 440 PHE cc_start: 0.8075 (t80) cc_final: 0.7621 (t80) REVERT: A 442 LEU cc_start: 0.7846 (mt) cc_final: 0.7483 (mp) REVERT: A 445 LEU cc_start: 0.7475 (tp) cc_final: 0.7162 (tt) REVERT: A 548 ASN cc_start: 0.4512 (OUTLIER) cc_final: 0.4092 (p0) REVERT: A 554 ASP cc_start: 0.7810 (m-30) cc_final: 0.7263 (m-30) REVERT: A 626 GLU cc_start: 0.7831 (tm-30) cc_final: 0.7622 (tm-30) REVERT: A 685 GLU cc_start: 0.7317 (tp30) cc_final: 0.7079 (tp30) REVERT: A 777 ASP cc_start: 0.7568 (m-30) cc_final: 0.7284 (m-30) REVERT: A 829 GLN cc_start: 0.6078 (OUTLIER) cc_final: 0.5849 (mm-40) REVERT: A 840 LYS cc_start: 0.6874 (OUTLIER) cc_final: 0.6294 (ptpt) REVERT: A 913 MET cc_start: 0.7543 (mmm) cc_final: 0.7334 (tpp) REVERT: A 921 PHE cc_start: 0.7688 (t80) cc_final: 0.7488 (t80) REVERT: A 923 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7713 (mp0) REVERT: B 315 LYS cc_start: 0.8045 (mmtm) cc_final: 0.7420 (mmmt) REVERT: B 414 TYR cc_start: 0.8144 (t80) cc_final: 0.7733 (t80) REVERT: B 486 THR cc_start: 0.7634 (m) cc_final: 0.7401 (t) REVERT: B 487 GLN cc_start: 0.7860 (mt0) cc_final: 0.7511 (mt0) REVERT: B 570 SER cc_start: 0.8319 (m) cc_final: 0.8054 (t) REVERT: B 697 LYS cc_start: 0.8151 (tppp) cc_final: 0.7804 (tppp) REVERT: B 722 PHE cc_start: 0.8561 (OUTLIER) cc_final: 0.8038 (t80) REVERT: B 948 ASN cc_start: 0.6875 (t0) cc_final: 0.6616 (t0) REVERT: B 981 ILE cc_start: 0.7422 (OUTLIER) cc_final: 0.7140 (mp) REVERT: C 77 GLN cc_start: 0.4902 (OUTLIER) cc_final: 0.4568 (tp-100) REVERT: D 34 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.7956 (mm-40) REVERT: D 51 TYR cc_start: 0.6316 (OUTLIER) cc_final: 0.5883 (m-10) REVERT: D 172 GLU cc_start: 0.7713 (pm20) cc_final: 0.7254 (pm20) outliers start: 72 outliers final: 43 residues processed: 341 average time/residue: 0.2964 time to fit residues: 145.0349 Evaluate side-chains 343 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 291 time to evaluate : 1.434 ------------------------------------------------------------------------------- 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 358 GLU 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 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 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 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 432 ILE Chi-restraints excluded: chain B residue 444 CYS Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 685 GLU Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 797 ASN Chi-restraints excluded: chain B residue 822 GLU Chi-restraints excluded: chain B residue 859 VAL Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 878 THR Chi-restraints excluded: chain B residue 906 THR Chi-restraints excluded: chain B residue 913 MET Chi-restraints excluded: chain B residue 981 ILE Chi-restraints excluded: chain C residue 14 LYS 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 51 TYR Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 188 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: 2.9990 chunk 26 optimal weight: 0.5980 chunk 162 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 135 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 B 905 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.183399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.156452 restraints weight = 21140.833| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 3.02 r_work: 0.3817 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6898 moved from start: 0.1895 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= 0.167 Angle : 0.599 10.624 19530 Z= 0.319 Chirality : 0.042 0.221 2070 Planarity : 0.004 0.047 2504 Dihedral : 4.920 58.068 1881 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.24 % Favored : 92.41 % Rotamer: Outliers : 4.36 % Allowed : 27.37 % Favored : 68.27 % 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: 0.01 (0.21), residues: 1699 helix: 1.43 (0.18), residues: 935 sheet: -1.27 (0.47), residues: 126 loop : -1.93 (0.23), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 919 HIS 0.004 0.001 HIS A 415 PHE 0.029 0.002 PHE A 544 TYR 0.024 0.002 TYR B 725 ARG 0.007 0.001 ARG B 517 Details of bonding type rmsd hydrogen bonds : bond 0.04992 ( 693) hydrogen bonds : angle 4.17606 ( 1977) covalent geometry : bond 0.00384 (14519) covalent geometry : angle 0.59920 (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 377 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 309 time to evaluate : 2.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 LYS cc_start: 0.7877 (mmmm) cc_final: 0.7631 (mmmm) REVERT: A 357 MET cc_start: 0.4633 (tpt) cc_final: 0.4323 (tpt) REVERT: A 396 MET cc_start: 0.7684 (OUTLIER) cc_final: 0.7314 (ttp) REVERT: A 423 LYS cc_start: 0.8452 (mttt) cc_final: 0.8014 (mttt) REVERT: A 442 LEU cc_start: 0.7883 (mt) cc_final: 0.7579 (mp) REVERT: A 445 LEU cc_start: 0.7484 (tp) cc_final: 0.7197 (tt) REVERT: A 548 ASN cc_start: 0.4398 (OUTLIER) cc_final: 0.3750 (p0) REVERT: A 553 ASP cc_start: 0.7843 (t0) cc_final: 0.7549 (t0) REVERT: A 626 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7662 (tm-30) REVERT: A 685 GLU cc_start: 0.7348 (tp30) cc_final: 0.7087 (tp30) REVERT: A 717 LYS cc_start: 0.7918 (OUTLIER) cc_final: 0.7548 (mttt) REVERT: A 777 ASP cc_start: 0.7596 (m-30) cc_final: 0.7297 (m-30) REVERT: A 812 GLU cc_start: 0.6840 (tm-30) cc_final: 0.6613 (tm-30) REVERT: A 829 GLN cc_start: 0.6180 (OUTLIER) cc_final: 0.5965 (mm-40) REVERT: A 840 LYS cc_start: 0.7077 (OUTLIER) cc_final: 0.6319 (ptpt) REVERT: A 921 PHE cc_start: 0.7776 (t80) cc_final: 0.7561 (t80) REVERT: A 923 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7709 (mp0) REVERT: A 976 MET cc_start: 0.7593 (mtm) cc_final: 0.7316 (ptt) REVERT: B 438 LYS cc_start: 0.8278 (mtpt) cc_final: 0.8027 (mtpp) REVERT: B 487 GLN cc_start: 0.7973 (mt0) cc_final: 0.7700 (mt0) REVERT: B 517 ARG cc_start: 0.8032 (mtm110) cc_final: 0.7727 (ttm-80) REVERT: B 570 SER cc_start: 0.8492 (m) cc_final: 0.8235 (t) REVERT: B 697 LYS cc_start: 0.8139 (tppp) cc_final: 0.7733 (tppp) REVERT: B 948 ASN cc_start: 0.7061 (t0) cc_final: 0.6782 (t0) REVERT: B 981 ILE cc_start: 0.7438 (OUTLIER) cc_final: 0.7173 (mp) REVERT: C 77 GLN cc_start: 0.4932 (OUTLIER) cc_final: 0.4602 (tp-100) REVERT: D 34 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.8024 (mm-40) REVERT: D 50 LEU cc_start: 0.4751 (OUTLIER) cc_final: 0.4480 (pp) REVERT: D 51 TYR cc_start: 0.6461 (OUTLIER) cc_final: 0.6042 (m-80) REVERT: D 172 GLU cc_start: 0.7768 (pm20) cc_final: 0.7304 (pm20) REVERT: D 174 GLU cc_start: 0.7465 (tm-30) cc_final: 0.7248 (tm-30) outliers start: 68 outliers final: 42 residues processed: 352 average time/residue: 0.3175 time to fit residues: 159.6017 Evaluate side-chains 354 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 302 time to evaluate : 1.709 ------------------------------------------------------------------------------- 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 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 717 LYS 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 836 ASP Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 970 ILE Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 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 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 797 ASN Chi-restraints excluded: chain B residue 831 LYS Chi-restraints excluded: chain B residue 859 VAL Chi-restraints excluded: chain B residue 878 THR Chi-restraints excluded: chain B residue 902 LYS Chi-restraints excluded: chain B residue 913 MET Chi-restraints excluded: chain B residue 981 ILE Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 77 GLN Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 34 GLN Chi-restraints excluded: chain D residue 48 LYS Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 219 LYS Chi-restraints excluded: chain D residue 226 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 153 optimal weight: 7.9990 chunk 148 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 70 optimal weight: 30.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 A 910 ASN ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 797 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 = 0.4255 r_free = 0.4255 target = 0.180044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.153210 restraints weight = 21109.400| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 2.97 r_work: 0.3774 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14519 Z= 0.207 Angle : 0.643 9.977 19530 Z= 0.343 Chirality : 0.044 0.217 2070 Planarity : 0.004 0.047 2504 Dihedral : 5.072 47.490 1881 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.53 % Favored : 92.11 % Rotamer: Outliers : 5.51 % Allowed : 27.82 % Favored : 66.67 % 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: -0.31 (0.21), residues: 1699 helix: 1.13 (0.17), residues: 948 sheet: -1.25 (0.49), residues: 120 loop : -2.12 (0.23), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 919 HIS 0.004 0.001 HIS A 415 PHE 0.029 0.002 PHE A 544 TYR 0.025 0.002 TYR B 471 ARG 0.007 0.001 ARG B 802 Details of bonding type rmsd hydrogen bonds : bond 0.05670 ( 693) hydrogen bonds : angle 4.30297 ( 1977) covalent geometry : bond 0.00479 (14519) covalent geometry : angle 0.64283 (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 410 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 324 time to evaluate : 1.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 LYS cc_start: 0.7857 (mmmm) cc_final: 0.7596 (mmmm) REVERT: A 357 MET cc_start: 0.5002 (tpt) cc_final: 0.4781 (tpt) REVERT: A 396 MET cc_start: 0.7648 (OUTLIER) cc_final: 0.7344 (ttp) REVERT: A 404 ASN cc_start: 0.7990 (p0) cc_final: 0.7752 (p0) REVERT: A 423 LYS cc_start: 0.8526 (mttt) cc_final: 0.8275 (mttt) REVERT: A 442 LEU cc_start: 0.7801 (mt) cc_final: 0.7525 (mp) REVERT: A 445 LEU cc_start: 0.7533 (tp) cc_final: 0.7262 (tt) REVERT: A 502 ARG cc_start: 0.7534 (ptt180) cc_final: 0.7279 (ptt180) REVERT: A 548 ASN cc_start: 0.4458 (OUTLIER) cc_final: 0.3629 (p0) REVERT: A 553 ASP cc_start: 0.7899 (t0) cc_final: 0.7638 (t0) REVERT: A 666 ASN cc_start: 0.8462 (m-40) cc_final: 0.8251 (m-40) REVERT: A 685 GLU cc_start: 0.7394 (tp30) cc_final: 0.7110 (tp30) REVERT: A 777 ASP cc_start: 0.7668 (m-30) cc_final: 0.7303 (m-30) REVERT: A 829 GLN cc_start: 0.6245 (OUTLIER) cc_final: 0.5984 (mm-40) REVERT: A 912 TYR cc_start: 0.7950 (m-80) cc_final: 0.7683 (m-80) REVERT: A 921 PHE cc_start: 0.7812 (t80) cc_final: 0.7537 (t80) REVERT: A 923 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7702 (mp0) REVERT: A 976 MET cc_start: 0.7649 (mtm) cc_final: 0.7430 (ptt) REVERT: B 438 LYS cc_start: 0.8298 (mtpt) cc_final: 0.8048 (mtpp) REVERT: B 510 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7609 (mp0) REVERT: B 566 ARG cc_start: 0.8270 (tpp-160) cc_final: 0.8015 (mmt90) REVERT: B 570 SER cc_start: 0.8558 (m) cc_final: 0.8300 (t) REVERT: B 697 LYS cc_start: 0.8073 (tppp) cc_final: 0.7663 (tppp) REVERT: B 746 GLU cc_start: 0.7283 (pm20) cc_final: 0.7040 (pm20) REVERT: B 906 THR cc_start: 0.7070 (OUTLIER) cc_final: 0.6864 (m) REVERT: B 948 ASN cc_start: 0.7242 (t0) cc_final: 0.6937 (t0) REVERT: B 981 ILE cc_start: 0.7437 (OUTLIER) cc_final: 0.7207 (mp) REVERT: B 982 GLU cc_start: 0.8213 (pt0) cc_final: 0.7955 (pt0) REVERT: C 13 PHE cc_start: 0.4878 (OUTLIER) cc_final: 0.4346 (m-80) REVERT: C 77 GLN cc_start: 0.4839 (OUTLIER) cc_final: 0.4547 (tp-100) REVERT: D 34 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.8070 (mm-40) REVERT: D 50 LEU cc_start: 0.4974 (OUTLIER) cc_final: 0.4671 (pp) REVERT: D 51 TYR cc_start: 0.6639 (OUTLIER) cc_final: 0.6211 (m-80) REVERT: D 172 GLU cc_start: 0.7806 (pm20) cc_final: 0.7297 (pm20) REVERT: D 174 GLU cc_start: 0.7414 (tm-30) cc_final: 0.7095 (tm-30) outliers start: 86 outliers final: 47 residues processed: 379 average time/residue: 0.3538 time to fit residues: 193.8457 Evaluate side-chains 365 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 308 time to evaluate : 1.535 ------------------------------------------------------------------------------- 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 396 MET Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 512 LEU 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 570 SER Chi-restraints excluded: chain A residue 646 PHE Chi-restraints excluded: chain A residue 695 ILE 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 821 SER Chi-restraints excluded: chain A residue 829 GLN Chi-restraints excluded: chain A residue 834 GLN Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 970 ILE Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 377 GLN Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 444 CYS Chi-restraints excluded: chain B residue 490 THR 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 744 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 13 PHE 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 31 SER Chi-restraints excluded: chain D residue 34 GLN Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 226 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 21 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 4 optimal weight: 5.9990 chunk 165 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 119 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 70 optimal weight: 20.0000 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 536 GLN ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.182047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.155805 restraints weight = 20939.365| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 2.89 r_work: 0.3817 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14519 Z= 0.148 Angle : 0.618 14.334 19530 Z= 0.325 Chirality : 0.042 0.227 2070 Planarity : 0.003 0.049 2504 Dihedral : 4.842 44.668 1879 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.59 % Favored : 92.17 % Rotamer: Outliers : 4.62 % Allowed : 28.97 % Favored : 66.41 % 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: -0.14 (0.21), residues: 1699 helix: 1.31 (0.17), residues: 944 sheet: -1.20 (0.47), residues: 130 loop : -2.10 (0.23), residues: 625 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 0.030 0.002 PHE A 544 TYR 0.017 0.001 TYR B 471 ARG 0.010 0.001 ARG B 517 Details of bonding type rmsd hydrogen bonds : bond 0.04795 ( 693) hydrogen bonds : angle 4.17534 ( 1977) covalent geometry : bond 0.00331 (14519) covalent geometry : angle 0.61771 (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 375 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 303 time to evaluate : 1.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 LYS cc_start: 0.7896 (mmmm) cc_final: 0.7600 (mmmm) REVERT: A 357 MET cc_start: 0.4734 (tpt) cc_final: 0.4504 (tpt) REVERT: A 396 MET cc_start: 0.7625 (OUTLIER) cc_final: 0.7329 (ttp) REVERT: A 404 ASN cc_start: 0.7953 (p0) cc_final: 0.7666 (p0) REVERT: A 423 LYS cc_start: 0.8471 (mttt) cc_final: 0.8217 (mttt) REVERT: A 442 LEU cc_start: 0.7922 (mt) cc_final: 0.7637 (mp) REVERT: A 445 LEU cc_start: 0.7549 (tp) cc_final: 0.7304 (tt) REVERT: A 502 ARG cc_start: 0.7432 (ptt180) cc_final: 0.7182 (ptt180) REVERT: A 548 ASN cc_start: 0.4406 (OUTLIER) cc_final: 0.3781 (p0) REVERT: A 553 ASP cc_start: 0.7867 (t0) cc_final: 0.7649 (t0) REVERT: A 628 THR cc_start: 0.8756 (m) cc_final: 0.8437 (p) REVERT: A 685 GLU cc_start: 0.7339 (tp30) cc_final: 0.7105 (tp30) REVERT: A 697 LYS cc_start: 0.8075 (ttpp) cc_final: 0.7860 (ttpp) REVERT: A 717 LYS cc_start: 0.7610 (OUTLIER) cc_final: 0.7259 (mttt) REVERT: A 777 ASP cc_start: 0.7487 (m-30) cc_final: 0.7143 (m-30) REVERT: A 812 GLU cc_start: 0.7082 (tm-30) cc_final: 0.6759 (tm-30) REVERT: A 829 GLN cc_start: 0.6204 (OUTLIER) cc_final: 0.5893 (mm110) REVERT: A 912 TYR cc_start: 0.7939 (m-80) cc_final: 0.7553 (m-80) REVERT: A 921 PHE cc_start: 0.7792 (t80) cc_final: 0.7517 (t80) REVERT: A 923 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7732 (mp0) REVERT: A 944 VAL cc_start: 0.8744 (m) cc_final: 0.8467 (p) REVERT: B 438 LYS cc_start: 0.8176 (mtpt) cc_final: 0.7943 (mtpp) REVERT: B 510 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7560 (mp0) REVERT: B 517 ARG cc_start: 0.8048 (mtm110) cc_final: 0.7732 (ttm-80) REVERT: B 566 ARG cc_start: 0.8280 (tpp-160) cc_final: 0.8041 (mmt90) REVERT: B 570 SER cc_start: 0.8496 (m) cc_final: 0.8286 (t) REVERT: B 624 GLU cc_start: 0.6876 (OUTLIER) cc_final: 0.6386 (mm-30) REVERT: B 697 LYS cc_start: 0.8046 (tppp) cc_final: 0.7668 (tppp) REVERT: B 727 LYS cc_start: 0.8357 (ttmt) cc_final: 0.8050 (ttmm) REVERT: B 748 ASP cc_start: 0.7602 (OUTLIER) cc_final: 0.7235 (m-30) REVERT: B 771 ILE cc_start: 0.7978 (mm) cc_final: 0.7768 (mp) REVERT: B 948 ASN cc_start: 0.7273 (t0) cc_final: 0.6950 (t0) REVERT: B 981 ILE cc_start: 0.7410 (OUTLIER) cc_final: 0.7186 (mp) REVERT: B 982 GLU cc_start: 0.8160 (pt0) cc_final: 0.7932 (pt0) REVERT: C 13 PHE cc_start: 0.4818 (OUTLIER) cc_final: 0.4303 (m-80) REVERT: C 77 GLN cc_start: 0.4807 (OUTLIER) cc_final: 0.4468 (tp-100) REVERT: D 34 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.8099 (mm-40) REVERT: D 50 LEU cc_start: 0.4974 (OUTLIER) cc_final: 0.4674 (pp) REVERT: D 51 TYR cc_start: 0.6615 (OUTLIER) cc_final: 0.6166 (m-80) REVERT: D 58 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.6276 (pp20) REVERT: D 172 GLU cc_start: 0.7787 (pm20) cc_final: 0.7301 (pm20) REVERT: D 174 GLU cc_start: 0.7349 (tm-30) cc_final: 0.7074 (tm-30) outliers start: 72 outliers final: 46 residues processed: 349 average time/residue: 0.2745 time to fit residues: 138.6902 Evaluate side-chains 355 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 296 time to evaluate : 1.538 ------------------------------------------------------------------------------- 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 396 MET Chi-restraints excluded: chain A residue 459 ILE 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 646 PHE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 717 LYS 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 821 SER Chi-restraints excluded: chain A residue 829 GLN Chi-restraints excluded: chain A residue 833 LYS Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 377 GLN Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 444 CYS Chi-restraints excluded: chain B residue 490 THR 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 748 ASP Chi-restraints excluded: chain B residue 822 GLU Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 831 LYS 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 13 PHE 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 34 GLN Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 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: 0.9990 chunk 157 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 155 optimal weight: 6.9990 chunk 12 optimal weight: 0.3980 chunk 40 optimal weight: 1.9990 chunk 70 optimal weight: 20.0000 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.182244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.156119 restraints weight = 20809.320| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 2.87 r_work: 0.3823 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14519 Z= 0.145 Angle : 0.614 13.728 19530 Z= 0.320 Chirality : 0.042 0.224 2070 Planarity : 0.003 0.050 2504 Dihedral : 4.795 44.400 1879 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.65 % Favored : 92.05 % Rotamer: Outliers : 5.00 % Allowed : 28.78 % Favored : 66.22 % 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: -0.14 (0.21), residues: 1699 helix: 1.33 (0.17), residues: 949 sheet: -1.15 (0.47), residues: 130 loop : -2.19 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 919 HIS 0.004 0.001 HIS A 975 PHE 0.026 0.001 PHE A 544 TYR 0.019 0.001 TYR B 725 ARG 0.008 0.000 ARG B 627 Details of bonding type rmsd hydrogen bonds : bond 0.04687 ( 693) hydrogen bonds : angle 4.13481 ( 1977) covalent geometry : bond 0.00329 (14519) covalent geometry : angle 0.61423 (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 387 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 309 time to evaluate : 1.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 LYS cc_start: 0.7849 (mmmm) cc_final: 0.7614 (mmmm) REVERT: A 357 MET cc_start: 0.4730 (tpt) cc_final: 0.4485 (tpt) REVERT: A 393 VAL cc_start: 0.7161 (t) cc_final: 0.6952 (m) REVERT: A 396 MET cc_start: 0.7635 (OUTLIER) cc_final: 0.7345 (ttp) REVERT: A 404 ASN cc_start: 0.7969 (p0) cc_final: 0.7665 (p0) REVERT: A 423 LYS cc_start: 0.8462 (mttt) cc_final: 0.8212 (mttt) REVERT: A 442 LEU cc_start: 0.7951 (mt) cc_final: 0.7671 (mp) REVERT: A 445 LEU cc_start: 0.7521 (tp) cc_final: 0.7293 (tt) REVERT: A 502 ARG cc_start: 0.7408 (ptt180) cc_final: 0.7160 (ptt180) REVERT: A 548 ASN cc_start: 0.4523 (OUTLIER) cc_final: 0.3799 (p0) REVERT: A 553 ASP cc_start: 0.7863 (t0) cc_final: 0.7658 (t0) REVERT: A 685 GLU cc_start: 0.7329 (tp30) cc_final: 0.7108 (tp30) REVERT: A 717 LYS cc_start: 0.7695 (OUTLIER) cc_final: 0.7327 (mttt) REVERT: A 777 ASP cc_start: 0.7460 (m-30) cc_final: 0.7137 (m-30) REVERT: A 812 GLU cc_start: 0.7014 (tm-30) cc_final: 0.6745 (tm-30) REVERT: A 829 GLN cc_start: 0.6262 (OUTLIER) cc_final: 0.5919 (mm110) REVERT: A 944 VAL cc_start: 0.8745 (m) cc_final: 0.8460 (p) REVERT: B 357 MET cc_start: 0.7475 (mmm) cc_final: 0.7214 (mmm) REVERT: B 438 LYS cc_start: 0.8151 (mtpt) cc_final: 0.7916 (mtpp) REVERT: B 510 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7581 (mp0) REVERT: B 527 LEU cc_start: 0.8422 (tp) cc_final: 0.8170 (tp) REVERT: B 566 ARG cc_start: 0.8276 (tpp-160) cc_final: 0.8023 (mmt90) REVERT: B 570 SER cc_start: 0.8486 (m) cc_final: 0.8285 (t) REVERT: B 624 GLU cc_start: 0.6872 (OUTLIER) cc_final: 0.6369 (mm-30) REVERT: B 697 LYS cc_start: 0.8025 (tppp) cc_final: 0.7650 (tppp) REVERT: B 727 LYS cc_start: 0.8336 (ttmt) cc_final: 0.8050 (ttmm) REVERT: B 748 ASP cc_start: 0.7563 (OUTLIER) cc_final: 0.7202 (m-30) REVERT: B 822 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7637 (mp0) REVERT: B 948 ASN cc_start: 0.7333 (t0) cc_final: 0.7005 (t0) REVERT: B 981 ILE cc_start: 0.7423 (OUTLIER) cc_final: 0.7209 (mp) REVERT: B 982 GLU cc_start: 0.8140 (pt0) cc_final: 0.7926 (pt0) REVERT: C 13 PHE cc_start: 0.4883 (OUTLIER) cc_final: 0.4369 (m-80) REVERT: C 52 ILE cc_start: 0.5062 (OUTLIER) cc_final: 0.4680 (mm) REVERT: C 77 GLN cc_start: 0.4798 (OUTLIER) cc_final: 0.4456 (tp-100) REVERT: D 50 LEU cc_start: 0.5046 (OUTLIER) cc_final: 0.4727 (pp) REVERT: D 51 TYR cc_start: 0.6683 (OUTLIER) cc_final: 0.6194 (m-80) REVERT: D 58 GLU cc_start: 0.6967 (OUTLIER) cc_final: 0.6348 (pp20) REVERT: D 172 GLU cc_start: 0.7785 (pm20) cc_final: 0.7297 (pm20) REVERT: D 174 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.7016 (tm-30) outliers start: 78 outliers final: 45 residues processed: 358 average time/residue: 0.2656 time to fit residues: 138.4768 Evaluate side-chains 367 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 307 time to evaluate : 1.420 ------------------------------------------------------------------------------- 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 358 GLU Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 459 ILE 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 646 PHE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 717 LYS 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 821 SER Chi-restraints excluded: chain A residue 829 GLN Chi-restraints excluded: chain A residue 833 LYS Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 377 GLN Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 444 CYS Chi-restraints excluded: chain B residue 490 THR 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 748 ASP Chi-restraints excluded: chain B residue 822 GLU Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 831 LYS Chi-restraints excluded: chain B residue 859 VAL Chi-restraints excluded: chain B residue 878 THR Chi-restraints excluded: chain B residue 902 LYS Chi-restraints excluded: chain B residue 913 MET Chi-restraints excluded: chain B residue 981 ILE Chi-restraints excluded: chain C residue 13 PHE 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 50 LEU Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 174 GLU 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: 0.4980 chunk 156 optimal weight: 0.3980 chunk 4 optimal weight: 8.9990 chunk 86 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 98 optimal weight: 0.0470 chunk 97 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.5278 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.183872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.157920 restraints weight = 20908.472| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 2.89 r_work: 0.3841 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14519 Z= 0.126 Angle : 0.624 12.964 19530 Z= 0.320 Chirality : 0.042 0.228 2070 Planarity : 0.003 0.050 2504 Dihedral : 4.720 45.254 1879 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.42 % Favored : 92.29 % Rotamer: Outliers : 3.78 % Allowed : 30.00 % Favored : 66.22 % 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: 0.07 (0.21), residues: 1699 helix: 1.52 (0.18), residues: 937 sheet: -0.98 (0.49), residues: 127 loop : -2.06 (0.23), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 919 HIS 0.003 0.001 HIS B 881 PHE 0.036 0.001 PHE D 32 TYR 0.013 0.001 TYR B 472 ARG 0.013 0.000 ARG B 517 Details of bonding type rmsd hydrogen bonds : bond 0.04205 ( 693) hydrogen bonds : angle 4.03813 ( 1977) covalent geometry : bond 0.00275 (14519) covalent geometry : angle 0.62402 (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 366 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 307 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 LYS cc_start: 0.7853 (mmmm) cc_final: 0.7566 (mmmm) REVERT: A 357 MET cc_start: 0.4663 (tpt) cc_final: 0.4431 (tpt) REVERT: A 396 MET cc_start: 0.7582 (OUTLIER) cc_final: 0.7351 (ttp) REVERT: A 404 ASN cc_start: 0.7943 (p0) cc_final: 0.7611 (p0) REVERT: A 423 LYS cc_start: 0.8493 (mttt) cc_final: 0.8224 (mttt) REVERT: A 442 LEU cc_start: 0.7958 (mt) cc_final: 0.7661 (mp) REVERT: A 445 LEU cc_start: 0.7541 (tp) cc_final: 0.7319 (tt) REVERT: A 502 ARG cc_start: 0.7313 (ptt180) cc_final: 0.7084 (ptt180) REVERT: A 548 ASN cc_start: 0.4402 (OUTLIER) cc_final: 0.3812 (p0) REVERT: A 597 GLU cc_start: 0.7218 (mp0) cc_final: 0.6865 (mp0) REVERT: A 628 THR cc_start: 0.8710 (OUTLIER) cc_final: 0.8437 (p) REVERT: A 685 GLU cc_start: 0.7283 (tp30) cc_final: 0.7071 (tp30) REVERT: A 717 LYS cc_start: 0.7626 (OUTLIER) cc_final: 0.7253 (mttt) REVERT: A 777 ASP cc_start: 0.7399 (m-30) cc_final: 0.7058 (m-30) REVERT: A 812 GLU cc_start: 0.6820 (tm-30) cc_final: 0.6582 (tm-30) REVERT: A 829 GLN cc_start: 0.6261 (OUTLIER) cc_final: 0.5846 (mm110) REVERT: A 840 LYS cc_start: 0.6950 (OUTLIER) cc_final: 0.6099 (ptpt) REVERT: A 944 VAL cc_start: 0.8748 (m) cc_final: 0.8450 (p) REVERT: B 357 MET cc_start: 0.7458 (mmm) cc_final: 0.7250 (mmm) REVERT: B 391 ASN cc_start: 0.6390 (m-40) cc_final: 0.6169 (m-40) REVERT: B 438 LYS cc_start: 0.8123 (mtpt) cc_final: 0.7868 (mtpp) REVERT: B 510 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7586 (mp0) REVERT: B 566 ARG cc_start: 0.8276 (tpp-160) cc_final: 0.8025 (mmt90) REVERT: B 624 GLU cc_start: 0.6862 (OUTLIER) cc_final: 0.6319 (mm-30) REVERT: B 697 LYS cc_start: 0.8034 (tppp) cc_final: 0.7669 (tppp) REVERT: B 727 LYS cc_start: 0.8311 (ttmt) cc_final: 0.8040 (ttmm) REVERT: B 748 ASP cc_start: 0.7518 (OUTLIER) cc_final: 0.7149 (m-30) REVERT: B 822 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7611 (mp0) REVERT: B 948 ASN cc_start: 0.7298 (t0) cc_final: 0.6977 (t0) REVERT: B 981 ILE cc_start: 0.7414 (OUTLIER) cc_final: 0.7189 (mp) REVERT: B 982 GLU cc_start: 0.8160 (pt0) cc_final: 0.7936 (pt0) REVERT: C 52 ILE cc_start: 0.5027 (OUTLIER) cc_final: 0.4680 (mm) REVERT: C 77 GLN cc_start: 0.4766 (OUTLIER) cc_final: 0.4483 (tp-100) REVERT: D 34 GLN cc_start: 0.8335 (mm-40) cc_final: 0.7892 (mm-40) REVERT: D 50 LEU cc_start: 0.4811 (OUTLIER) cc_final: 0.4439 (pp) REVERT: D 51 TYR cc_start: 0.6673 (OUTLIER) cc_final: 0.6141 (m-80) REVERT: D 172 GLU cc_start: 0.7736 (pm20) cc_final: 0.7237 (pm20) REVERT: D 174 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.7036 (tm-30) outliers start: 59 outliers final: 41 residues processed: 346 average time/residue: 0.2923 time to fit residues: 146.9586 Evaluate side-chains 357 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 301 time to evaluate : 1.688 ------------------------------------------------------------------------------- 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 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 628 THR Chi-restraints excluded: chain A residue 634 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 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 829 GLN Chi-restraints excluded: chain A residue 833 LYS Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 377 GLN Chi-restraints excluded: chain B residue 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 695 ILE Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 748 ASP Chi-restraints excluded: chain B residue 822 GLU Chi-restraints excluded: chain B residue 831 LYS Chi-restraints excluded: chain B residue 878 THR Chi-restraints excluded: chain B residue 902 LYS Chi-restraints excluded: chain B residue 913 MET Chi-restraints excluded: chain B residue 981 ILE Chi-restraints excluded: chain C residue 52 ILE 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 50 LEU Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 174 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 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: 0.2980 chunk 108 optimal weight: 0.0010 chunk 101 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 155 optimal weight: 9.9990 chunk 116 optimal weight: 2.9990 chunk 139 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 124 optimal weight: 0.9980 chunk 145 optimal weight: 0.8980 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 698 GLN ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.183907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.158119 restraints weight = 20728.608| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 2.86 r_work: 0.3840 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14519 Z= 0.130 Angle : 0.636 12.691 19530 Z= 0.326 Chirality : 0.042 0.226 2070 Planarity : 0.003 0.048 2504 Dihedral : 4.700 44.108 1879 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.30 % Favored : 92.41 % Rotamer: Outliers : 3.72 % Allowed : 29.94 % Favored : 66.35 % 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: 0.08 (0.21), residues: 1699 helix: 1.57 (0.18), residues: 932 sheet: -1.02 (0.49), residues: 125 loop : -2.11 (0.22), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 919 HIS 0.003 0.001 HIS B 881 PHE 0.038 0.001 PHE D 32 TYR 0.017 0.001 TYR B 539 ARG 0.010 0.000 ARG B 517 Details of bonding type rmsd hydrogen bonds : bond 0.04228 ( 693) hydrogen bonds : angle 4.01744 ( 1977) covalent geometry : bond 0.00286 (14519) covalent geometry : angle 0.63584 (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: 58 poor density : 294 time to evaluate : 1.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 LYS cc_start: 0.7848 (mmmm) cc_final: 0.7551 (mmmm) REVERT: A 357 MET cc_start: 0.4671 (tpt) cc_final: 0.4454 (tpt) REVERT: A 396 MET cc_start: 0.7598 (OUTLIER) cc_final: 0.7384 (ttp) REVERT: A 404 ASN cc_start: 0.7934 (p0) cc_final: 0.7588 (p0) REVERT: A 423 LYS cc_start: 0.8489 (mttt) cc_final: 0.8258 (mttt) REVERT: A 442 LEU cc_start: 0.7965 (mt) cc_final: 0.7655 (mp) REVERT: A 445 LEU cc_start: 0.7537 (tp) cc_final: 0.7300 (tt) REVERT: A 502 ARG cc_start: 0.7284 (ptt180) cc_final: 0.7052 (ptt180) REVERT: A 548 ASN cc_start: 0.4411 (OUTLIER) cc_final: 0.4055 (m-40) REVERT: A 597 GLU cc_start: 0.7220 (mp0) cc_final: 0.6871 (mp0) REVERT: A 628 THR cc_start: 0.8742 (OUTLIER) cc_final: 0.8457 (p) REVERT: A 685 GLU cc_start: 0.7316 (tp30) cc_final: 0.7104 (tp30) REVERT: A 717 LYS cc_start: 0.7693 (OUTLIER) cc_final: 0.7311 (mttt) REVERT: A 777 ASP cc_start: 0.7395 (m-30) cc_final: 0.7067 (m-30) REVERT: A 812 GLU cc_start: 0.6820 (tm-30) cc_final: 0.6608 (tm-30) REVERT: A 829 GLN cc_start: 0.6343 (OUTLIER) cc_final: 0.5852 (mm110) REVERT: A 944 VAL cc_start: 0.8752 (m) cc_final: 0.8466 (p) REVERT: B 391 ASN cc_start: 0.6402 (m-40) cc_final: 0.6138 (m-40) REVERT: B 438 LYS cc_start: 0.8063 (mtpt) cc_final: 0.7803 (mtpp) REVERT: B 510 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7571 (mp0) REVERT: B 527 LEU cc_start: 0.8422 (tp) cc_final: 0.8112 (tp) REVERT: B 566 ARG cc_start: 0.8295 (tpp-160) cc_final: 0.8053 (mmt90) REVERT: B 624 GLU cc_start: 0.6869 (OUTLIER) cc_final: 0.6332 (mm-30) REVERT: B 697 LYS cc_start: 0.8029 (tppp) cc_final: 0.7670 (tppp) REVERT: B 727 LYS cc_start: 0.8287 (ttmt) cc_final: 0.8020 (ttmm) REVERT: B 748 ASP cc_start: 0.7496 (OUTLIER) cc_final: 0.7131 (m-30) REVERT: B 822 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7616 (mp0) REVERT: B 981 ILE cc_start: 0.7417 (OUTLIER) cc_final: 0.7195 (mp) REVERT: B 982 GLU cc_start: 0.8155 (pt0) cc_final: 0.7937 (pt0) REVERT: C 52 ILE cc_start: 0.5014 (OUTLIER) cc_final: 0.4647 (mm) REVERT: C 77 GLN cc_start: 0.4772 (OUTLIER) cc_final: 0.4490 (tp-100) REVERT: D 51 TYR cc_start: 0.6700 (OUTLIER) cc_final: 0.6466 (m-80) REVERT: D 172 GLU cc_start: 0.7736 (pm20) cc_final: 0.7286 (pm20) REVERT: D 174 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.7050 (tm-30) outliers start: 58 outliers final: 36 residues processed: 333 average time/residue: 0.2716 time to fit residues: 129.6374 Evaluate side-chains 341 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 292 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 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 628 THR Chi-restraints excluded: chain A residue 634 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 829 GLN Chi-restraints excluded: chain A residue 833 LYS Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 377 GLN Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 444 CYS 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 748 ASP Chi-restraints excluded: chain B residue 822 GLU Chi-restraints excluded: chain B residue 878 THR Chi-restraints excluded: chain B residue 902 LYS Chi-restraints excluded: chain B residue 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 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 51 TYR Chi-restraints excluded: chain D residue 174 GLU 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: 8.9990 chunk 99 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 142 optimal weight: 8.9990 chunk 155 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 70 optimal weight: 30.0000 chunk 67 optimal weight: 3.9990 chunk 102 optimal weight: 0.6980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.180000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.153960 restraints weight = 20991.344| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 2.89 r_work: 0.3790 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 14519 Z= 0.203 Angle : 0.689 12.482 19530 Z= 0.355 Chirality : 0.045 0.249 2070 Planarity : 0.004 0.046 2504 Dihedral : 4.846 41.359 1879 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.71 % Favored : 92.05 % Rotamer: Outliers : 3.65 % Allowed : 29.94 % Favored : 66.41 % 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: -0.16 (0.21), residues: 1699 helix: 1.37 (0.17), residues: 935 sheet: -1.16 (0.48), residues: 130 loop : -2.22 (0.23), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 919 HIS 0.004 0.001 HIS A 415 PHE 0.042 0.002 PHE D 32 TYR 0.022 0.002 TYR B 539 ARG 0.011 0.001 ARG B 517 Details of bonding type rmsd hydrogen bonds : bond 0.05311 ( 693) hydrogen bonds : angle 4.18584 ( 1977) covalent geometry : bond 0.00476 (14519) covalent geometry : angle 0.68933 (19530) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7199.63 seconds wall clock time: 127 minutes 17.92 seconds (7637.92 seconds total)