Starting phenix.real_space_refine on Sat May 24 12:32:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8juz_36667/05_2025/8juz_36667_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8juz_36667/05_2025/8juz_36667.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8juz_36667/05_2025/8juz_36667.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8juz_36667/05_2025/8juz_36667.map" model { file = "/net/cci-nas-00/data/ceres_data/8juz_36667/05_2025/8juz_36667_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8juz_36667/05_2025/8juz_36667_neut.cif" } resolution = 4.29 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 17 5.49 5 S 110 5.16 5 C 16130 2.51 5 N 4361 2.21 5 O 4656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 25274 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4149 Classifications: {'peptide': 522} Link IDs: {'CIS': 3, 'PCIS': 2, 'PTRANS': 30, 'TRANS': 486} Chain breaks: 5 Chain: "B" Number of atoms: 4210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4210 Classifications: {'peptide': 529} Link IDs: {'CIS': 3, 'PCIS': 2, 'PTRANS': 32, 'TRANS': 491} Chain breaks: 2 Chain: "C" Number of atoms: 4199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4199 Classifications: {'peptide': 528} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 493} Chain breaks: 2 Chain: "D" Number of atoms: 4213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4213 Classifications: {'peptide': 530} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 495} Chain breaks: 2 Chain: "E" Number of atoms: 4202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4202 Classifications: {'peptide': 528} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 32, 'TRANS': 491} Chain breaks: 2 Chain: "F" Number of atoms: 4119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 4119 Classifications: {'peptide': 518} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 30, 'TRANS': 483} Chain breaks: 4 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 14.86, per 1000 atoms: 0.59 Number of scatterers: 25274 At special positions: 0 Unit cell: (148.5, 152.9, 146.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 110 16.00 P 17 15.00 O 4656 8.00 N 4361 7.00 C 16130 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.35 Conformation dependent library (CDL) restraints added in 3.3 seconds 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6022 Finding SS restraints... Secondary structure from input PDB file: 159 helices and 13 sheets defined 53.5% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.76 Creating SS restraints... Processing helix chain 'A' and resid 432 through 440 removed outlier: 3.580A pdb=" N GLU A 440 " --> pdb=" O ALA A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 448 removed outlier: 3.617A pdb=" N LEU A 446 " --> pdb=" O VAL A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 485 removed outlier: 3.504A pdb=" N VAL A 476 " --> pdb=" O GLY A 472 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ALA A 477 " --> pdb=" O LYS A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 524 removed outlier: 4.080A pdb=" N ARG A 511 " --> pdb=" O GLY A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 536 Processing helix chain 'A' and resid 548 through 562 Processing helix chain 'A' and resid 576 through 580 removed outlier: 3.844A pdb=" N SER A 579 " --> pdb=" O ARG A 576 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE A 580 " --> pdb=" O LEU A 577 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 576 through 580' Processing helix chain 'A' and resid 581 through 585 Processing helix chain 'A' and resid 600 through 612 Processing helix chain 'A' and resid 620 through 631 Processing helix chain 'A' and resid 636 through 655 removed outlier: 3.743A pdb=" N ALA A 647 " --> pdb=" O CYS A 643 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A 648 " --> pdb=" O ALA A 644 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N TYR A 655 " --> pdb=" O LEU A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 659 removed outlier: 3.756A pdb=" N TYR A 659 " --> pdb=" O PRO A 656 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 656 through 659' Processing helix chain 'A' and resid 679 through 685 removed outlier: 3.915A pdb=" N LYS A 685 " --> pdb=" O VAL A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 721 removed outlier: 6.048A pdb=" N ASN A 711 " --> pdb=" O PRO A 707 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N THR A 712 " --> pdb=" O LEU A 708 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU A 717 " --> pdb=" O VAL A 713 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU A 718 " --> pdb=" O ASP A 714 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA A 719 " --> pdb=" O LYS A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 729 Processing helix chain 'A' and resid 808 through 817 Processing helix chain 'A' and resid 826 through 831 Processing helix chain 'A' and resid 838 through 852 removed outlier: 4.031A pdb=" N CYS A 842 " --> pdb=" O PRO A 838 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA A 843 " --> pdb=" O GLU A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 866 Processing helix chain 'A' and resid 870 through 881 removed outlier: 3.620A pdb=" N LEU A 881 " --> pdb=" O PHE A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 909 Processing helix chain 'A' and resid 910 through 911 No H-bonds generated for 'chain 'A' and resid 910 through 911' Processing helix chain 'A' and resid 912 through 916 Processing helix chain 'A' and resid 926 through 938 removed outlier: 4.519A pdb=" N ASP A 935 " --> pdb=" O LYS A 931 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LEU A 936 " --> pdb=" O PHE A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 943 removed outlier: 3.811A pdb=" N LYS A 943 " --> pdb=" O GLN A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1344 removed outlier: 3.939A pdb=" N ASN A1335 " --> pdb=" O GLU A1331 " (cutoff:3.500A) Processing helix chain 'A' and resid 1348 through 1366 removed outlier: 3.504A pdb=" N LEU A1355 " --> pdb=" O GLN A1351 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N TYR A1356 " --> pdb=" O LEU A1352 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN A1361 " --> pdb=" O ALA A1357 " (cutoff:3.500A) Processing helix chain 'A' and resid 1375 through 1386 removed outlier: 3.506A pdb=" N GLU A1384 " --> pdb=" O GLU A1380 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 443 removed outlier: 3.559A pdb=" N VAL B 442 " --> pdb=" O LEU B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 447 Processing helix chain 'B' and resid 450 through 456 removed outlier: 3.636A pdb=" N PHE B 455 " --> pdb=" O VAL B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 485 removed outlier: 3.635A pdb=" N VAL B 476 " --> pdb=" O GLY B 472 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ALA B 477 " --> pdb=" O LYS B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 523 removed outlier: 4.041A pdb=" N LEU B 513 " --> pdb=" O SER B 509 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ARG B 514 " --> pdb=" O GLU B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 536 Processing helix chain 'B' and resid 545 through 560 removed outlier: 3.966A pdb=" N SER B 549 " --> pdb=" O ASP B 545 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASP B 560 " --> pdb=" O LEU B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 580 Processing helix chain 'B' and resid 600 through 612 removed outlier: 3.819A pdb=" N ARG B 604 " --> pdb=" O ASP B 600 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LYS B 605 " --> pdb=" O LYS B 601 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLU B 606 " --> pdb=" O GLU B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 629 Processing helix chain 'B' and resid 636 through 655 removed outlier: 3.796A pdb=" N LYS B 640 " --> pdb=" O GLY B 636 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA B 647 " --> pdb=" O CYS B 643 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU B 648 " --> pdb=" O ALA B 644 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N CYS B 649 " --> pdb=" O GLU B 645 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA B 650 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU B 651 " --> pdb=" O ALA B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 675 through 686 removed outlier: 4.152A pdb=" N PHE B 679 " --> pdb=" O SER B 675 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLU B 680 " --> pdb=" O ALA B 676 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL B 681 " --> pdb=" O LYS B 677 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA B 682 " --> pdb=" O ASP B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 693 removed outlier: 3.520A pdb=" N ARG B 692 " --> pdb=" O ALA B 689 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ALA B 693 " --> pdb=" O SER B 690 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 689 through 693' Processing helix chain 'B' and resid 705 through 724 removed outlier: 7.044A pdb=" N ASN B 711 " --> pdb=" O PRO B 707 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N THR B 712 " --> pdb=" O LEU B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 728 Processing helix chain 'B' and resid 804 through 817 removed outlier: 3.550A pdb=" N LEU B 809 " --> pdb=" O GLN B 805 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ALA B 810 " --> pdb=" O GLY B 806 " (cutoff:3.500A) Proline residue: B 811 - end of helix Processing helix chain 'B' and resid 826 through 831 Processing helix chain 'B' and resid 837 through 852 Processing helix chain 'B' and resid 861 through 866 Processing helix chain 'B' and resid 867 through 869 No H-bonds generated for 'chain 'B' and resid 867 through 869' Processing helix chain 'B' and resid 870 through 883 Processing helix chain 'B' and resid 899 through 903 Processing helix chain 'B' and resid 904 through 909 Processing helix chain 'B' and resid 910 through 911 No H-bonds generated for 'chain 'B' and resid 910 through 911' Processing helix chain 'B' and resid 912 through 916 Processing helix chain 'B' and resid 925 through 935 removed outlier: 4.274A pdb=" N ASP B 935 " --> pdb=" O LYS B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 935 through 940 removed outlier: 3.531A pdb=" N LYS B 939 " --> pdb=" O ASP B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 1331 through 1344 removed outlier: 3.864A pdb=" N ASN B1335 " --> pdb=" O GLU B1331 " (cutoff:3.500A) Processing helix chain 'B' and resid 1348 through 1365 removed outlier: 3.600A pdb=" N ILE B1359 " --> pdb=" O LEU B1355 " (cutoff:3.500A) Processing helix chain 'B' and resid 1375 through 1386 removed outlier: 3.563A pdb=" N GLU B1384 " --> pdb=" O GLU B1380 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 443 removed outlier: 4.038A pdb=" N GLU C 440 " --> pdb=" O ALA C 436 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N MET C 441 " --> pdb=" O ALA C 437 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL C 442 " --> pdb=" O LEU C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 448 Processing helix chain 'C' and resid 451 through 456 removed outlier: 3.712A pdb=" N PHE C 455 " --> pdb=" O VAL C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 486 removed outlier: 3.692A pdb=" N ALA C 477 " --> pdb=" O LYS C 473 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN C 486 " --> pdb=" O ASN C 482 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 523 removed outlier: 3.587A pdb=" N ARG C 514 " --> pdb=" O GLU C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 536 Processing helix chain 'C' and resid 546 through 559 Processing helix chain 'C' and resid 576 through 580 removed outlier: 3.509A pdb=" N SER C 579 " --> pdb=" O ARG C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 585 Processing helix chain 'C' and resid 600 through 612 Processing helix chain 'C' and resid 620 through 631 removed outlier: 3.875A pdb=" N GLU C 629 " --> pdb=" O GLU C 625 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASN C 630 " --> pdb=" O GLU C 626 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS C 631 " --> pdb=" O LEU C 627 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 655 removed outlier: 4.145A pdb=" N ALA C 647 " --> pdb=" O CYS C 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 686 removed outlier: 3.748A pdb=" N PHE C 679 " --> pdb=" O SER C 675 " (cutoff:3.500A) Processing helix chain 'C' and resid 689 through 693 removed outlier: 3.743A pdb=" N ARG C 692 " --> pdb=" O ALA C 689 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ALA C 693 " --> pdb=" O SER C 690 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 689 through 693' Processing helix chain 'C' and resid 705 through 708 Processing helix chain 'C' and resid 709 through 724 Processing helix chain 'C' and resid 809 through 817 Processing helix chain 'C' and resid 826 through 831 Processing helix chain 'C' and resid 837 through 852 Processing helix chain 'C' and resid 861 through 866 Processing helix chain 'C' and resid 870 through 881 removed outlier: 3.574A pdb=" N LEU C 881 " --> pdb=" O PHE C 877 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 916 Processing helix chain 'C' and resid 925 through 939 removed outlier: 3.518A pdb=" N PHE C 933 " --> pdb=" O ARG C 929 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ASP C 935 " --> pdb=" O LYS C 931 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N LEU C 936 " --> pdb=" O PHE C 932 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS C 939 " --> pdb=" O ASP C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 1331 through 1344 removed outlier: 3.548A pdb=" N ASN C1335 " --> pdb=" O GLU C1331 " (cutoff:3.500A) Processing helix chain 'C' and resid 1348 through 1366 removed outlier: 4.028A pdb=" N CYS C1362 " --> pdb=" O VAL C1358 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE C1363 " --> pdb=" O ILE C1359 " (cutoff:3.500A) Processing helix chain 'C' and resid 1374 through 1386 removed outlier: 4.364A pdb=" N LYS C1378 " --> pdb=" O SER C1374 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 448 removed outlier: 3.523A pdb=" N GLU D 440 " --> pdb=" O ALA D 436 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N MET D 441 " --> pdb=" O ALA D 437 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL D 442 " --> pdb=" O LEU D 438 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N PHE D 444 " --> pdb=" O GLU D 440 " (cutoff:3.500A) Proline residue: D 445 - end of helix Processing helix chain 'D' and resid 451 through 456 removed outlier: 4.167A pdb=" N PHE D 455 " --> pdb=" O VAL D 451 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 486 removed outlier: 3.718A pdb=" N ALA D 477 " --> pdb=" O LYS D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 507 through 523 removed outlier: 3.602A pdb=" N LEU D 513 " --> pdb=" O SER D 509 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG D 514 " --> pdb=" O GLU D 510 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET D 523 " --> pdb=" O GLN D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 536 Processing helix chain 'D' and resid 546 through 557 Processing helix chain 'D' and resid 600 through 612 Processing helix chain 'D' and resid 620 through 631 removed outlier: 4.007A pdb=" N ASN D 630 " --> pdb=" O GLU D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 655 removed outlier: 3.815A pdb=" N CYS D 643 " --> pdb=" O ILE D 639 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA D 644 " --> pdb=" O LYS D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 677 through 685 removed outlier: 3.779A pdb=" N VAL D 681 " --> pdb=" O LYS D 677 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LYS D 685 " --> pdb=" O VAL D 681 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 693 removed outlier: 3.707A pdb=" N ARG D 692 " --> pdb=" O ALA D 689 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ALA D 693 " --> pdb=" O SER D 690 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 689 through 693' Processing helix chain 'D' and resid 705 through 724 removed outlier: 5.677A pdb=" N ASN D 711 " --> pdb=" O PRO D 707 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N THR D 712 " --> pdb=" O LEU D 708 " (cutoff:3.500A) Processing helix chain 'D' and resid 808 through 817 removed outlier: 3.937A pdb=" N ALA D 812 " --> pdb=" O HIS D 808 " (cutoff:3.500A) Processing helix chain 'D' and resid 826 through 831 Processing helix chain 'D' and resid 837 through 852 removed outlier: 3.624A pdb=" N THR D 841 " --> pdb=" O SER D 837 " (cutoff:3.500A) Processing helix chain 'D' and resid 861 through 866 Processing helix chain 'D' and resid 870 through 882 removed outlier: 3.801A pdb=" N GLN D 882 " --> pdb=" O THR D 878 " (cutoff:3.500A) Processing helix chain 'D' and resid 899 through 903 Processing helix chain 'D' and resid 904 through 910 removed outlier: 3.794A pdb=" N LEU D 910 " --> pdb=" O GLU D 906 " (cutoff:3.500A) Processing helix chain 'D' and resid 911 through 916 removed outlier: 6.360A pdb=" N ASP D 914 " --> pdb=" O PHE D 911 " (cutoff:3.500A) Processing helix chain 'D' and resid 925 through 938 removed outlier: 4.312A pdb=" N ASP D 935 " --> pdb=" O LYS D 931 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N LEU D 936 " --> pdb=" O PHE D 932 " (cutoff:3.500A) Processing helix chain 'D' and resid 1331 through 1344 removed outlier: 4.173A pdb=" N ASN D1335 " --> pdb=" O GLU D1331 " (cutoff:3.500A) Processing helix chain 'D' and resid 1348 through 1366 removed outlier: 4.032A pdb=" N HIS D1366 " --> pdb=" O CYS D1362 " (cutoff:3.500A) Processing helix chain 'D' and resid 1375 through 1386 Processing helix chain 'E' and resid 433 through 440 removed outlier: 3.914A pdb=" N ALA E 437 " --> pdb=" O ASN E 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 443 through 448 removed outlier: 3.832A pdb=" N LEU E 447 " --> pdb=" O VAL E 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 450 through 455 removed outlier: 4.506A pdb=" N LYS E 454 " --> pdb=" O GLU E 450 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N PHE E 455 " --> pdb=" O VAL E 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 450 through 455' Processing helix chain 'E' and resid 474 through 486 Processing helix chain 'E' and resid 510 through 523 removed outlier: 3.740A pdb=" N ARG E 514 " --> pdb=" O GLU E 510 " (cutoff:3.500A) Processing helix chain 'E' and resid 533 through 536 Processing helix chain 'E' and resid 545 through 561 removed outlier: 4.218A pdb=" N SER E 549 " --> pdb=" O ASP E 545 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU E 558 " --> pdb=" O THR E 554 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLY E 561 " --> pdb=" O ALA E 557 " (cutoff:3.500A) Processing helix chain 'E' and resid 600 through 612 Processing helix chain 'E' and resid 620 through 631 removed outlier: 4.256A pdb=" N ASN E 630 " --> pdb=" O GLU E 626 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYS E 631 " --> pdb=" O LEU E 627 " (cutoff:3.500A) Processing helix chain 'E' and resid 635 through 655 removed outlier: 3.692A pdb=" N ALA E 644 " --> pdb=" O LYS E 640 " (cutoff:3.500A) Processing helix chain 'E' and resid 675 through 686 removed outlier: 3.605A pdb=" N LYS E 685 " --> pdb=" O VAL E 681 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET E 686 " --> pdb=" O ALA E 682 " (cutoff:3.500A) Processing helix chain 'E' and resid 705 through 724 removed outlier: 6.717A pdb=" N ASN E 711 " --> pdb=" O PRO E 707 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N THR E 712 " --> pdb=" O LEU E 708 " (cutoff:3.500A) Processing helix chain 'E' and resid 725 through 728 Processing helix chain 'E' and resid 800 through 804 removed outlier: 4.033A pdb=" N GLY E 804 " --> pdb=" O PRO E 801 " (cutoff:3.500A) Processing helix chain 'E' and resid 808 through 817 Processing helix chain 'E' and resid 826 through 831 Processing helix chain 'E' and resid 837 through 852 removed outlier: 3.523A pdb=" N THR E 852 " --> pdb=" O GLU E 848 " (cutoff:3.500A) Processing helix chain 'E' and resid 861 through 866 Processing helix chain 'E' and resid 870 through 881 removed outlier: 3.836A pdb=" N LEU E 881 " --> pdb=" O PHE E 877 " (cutoff:3.500A) Processing helix chain 'E' and resid 882 through 884 No H-bonds generated for 'chain 'E' and resid 882 through 884' Processing helix chain 'E' and resid 904 through 909 removed outlier: 3.771A pdb=" N GLU E 909 " --> pdb=" O GLU E 905 " (cutoff:3.500A) Processing helix chain 'E' and resid 912 through 916 Processing helix chain 'E' and resid 925 through 935 removed outlier: 3.987A pdb=" N ASP E 935 " --> pdb=" O LYS E 931 " (cutoff:3.500A) Processing helix chain 'E' and resid 1331 through 1344 Processing helix chain 'E' and resid 1348 through 1365 Processing helix chain 'E' and resid 1375 through 1386 Processing helix chain 'F' and resid 431 through 448 removed outlier: 3.642A pdb=" N ALA F 436 " --> pdb=" O SER F 432 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N MET F 441 " --> pdb=" O ALA F 437 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL F 442 " --> pdb=" O LEU F 438 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N PHE F 444 " --> pdb=" O GLU F 440 " (cutoff:3.500A) Proline residue: F 445 - end of helix Processing helix chain 'F' and resid 449 through 452 removed outlier: 3.681A pdb=" N PHE F 452 " --> pdb=" O PRO F 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 449 through 452' Processing helix chain 'F' and resid 472 through 486 Processing helix chain 'F' and resid 509 through 520 removed outlier: 4.290A pdb=" N LEU F 513 " --> pdb=" O SER F 509 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG F 514 " --> pdb=" O GLU F 510 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ASP F 518 " --> pdb=" O ARG F 514 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN F 519 " --> pdb=" O LEU F 515 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA F 520 " --> pdb=" O LEU F 516 " (cutoff:3.500A) Processing helix chain 'F' and resid 532 through 537 removed outlier: 4.487A pdb=" N LEU F 536 " --> pdb=" O GLN F 532 " (cutoff:3.500A) Processing helix chain 'F' and resid 545 through 562 removed outlier: 3.928A pdb=" N ASP F 560 " --> pdb=" O LEU F 556 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY F 561 " --> pdb=" O ALA F 557 " (cutoff:3.500A) Processing helix chain 'F' and resid 576 through 580 removed outlier: 3.699A pdb=" N ILE F 580 " --> pdb=" O LEU F 577 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 585 Processing helix chain 'F' and resid 602 through 612 removed outlier: 4.089A pdb=" N GLU F 606 " --> pdb=" O GLU F 602 " (cutoff:3.500A) Processing helix chain 'F' and resid 620 through 631 removed outlier: 3.616A pdb=" N LEU F 624 " --> pdb=" O LEU F 620 " (cutoff:3.500A) Processing helix chain 'F' and resid 636 through 654 removed outlier: 3.651A pdb=" N CYS F 643 " --> pdb=" O ILE F 639 " (cutoff:3.500A) Processing helix chain 'F' and resid 655 through 659 removed outlier: 3.907A pdb=" N TYR F 659 " --> pdb=" O PRO F 656 " (cutoff:3.500A) Processing helix chain 'F' and resid 675 through 683 removed outlier: 3.809A pdb=" N PHE F 679 " --> pdb=" O SER F 675 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU F 680 " --> pdb=" O ALA F 676 " (cutoff:3.500A) Processing helix chain 'F' and resid 705 through 724 removed outlier: 3.574A pdb=" N LEU F 709 " --> pdb=" O VAL F 705 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ASN F 711 " --> pdb=" O PRO F 707 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N THR F 712 " --> pdb=" O LEU F 708 " (cutoff:3.500A) Processing helix chain 'F' and resid 808 through 817 Processing helix chain 'F' and resid 826 through 831 Processing helix chain 'F' and resid 837 through 852 removed outlier: 3.776A pdb=" N GLN F 844 " --> pdb=" O GLU F 840 " (cutoff:3.500A) Processing helix chain 'F' and resid 861 through 866 removed outlier: 3.590A pdb=" N TRP F 866 " --> pdb=" O ILE F 862 " (cutoff:3.500A) Processing helix chain 'F' and resid 870 through 883 removed outlier: 3.576A pdb=" N LYS F 874 " --> pdb=" O GLY F 870 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA F 875 " --> pdb=" O PRO F 871 " (cutoff:3.500A) Processing helix chain 'F' and resid 899 through 903 Processing helix chain 'F' and resid 904 through 909 Processing helix chain 'F' and resid 925 through 933 removed outlier: 3.740A pdb=" N PHE F 933 " --> pdb=" O ARG F 929 " (cutoff:3.500A) Processing helix chain 'F' and resid 1332 through 1344 Processing helix chain 'F' and resid 1348 through 1366 removed outlier: 3.520A pdb=" N ILE F1363 " --> pdb=" O ILE F1359 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR F1364 " --> pdb=" O SER F1360 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N HIS F1366 " --> pdb=" O CYS F1362 " (cutoff:3.500A) Processing helix chain 'F' and resid 1374 through 1386 removed outlier: 3.633A pdb=" N GLU F1384 " --> pdb=" O GLU F1380 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 492 through 497 removed outlier: 6.110A pdb=" N ALA A 492 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N PHE A 529 " --> pdb=" O ALA A 492 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N PHE A 494 " --> pdb=" O PHE A 529 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ASP A 531 " --> pdb=" O PHE A 494 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ARG A 496 " --> pdb=" O ASP A 531 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL A 569 " --> pdb=" O SER A 526 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY A 572 " --> pdb=" O CYS A 463 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ARG A 592 " --> pdb=" O GLY A 462 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 821 through 824 removed outlier: 6.687A pdb=" N THR A 821 " --> pdb=" O ILE A 856 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N TYR A 858 " --> pdb=" O THR A 821 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TYR A 823 " --> pdb=" O TYR A 858 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N SER A 855 " --> pdb=" O LEU A 891 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N LEU A 893 " --> pdb=" O SER A 855 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL A 857 " --> pdb=" O LEU A 893 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N THR A 895 " --> pdb=" O VAL A 857 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N VAL A 859 " --> pdb=" O THR A 895 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE A 795 " --> pdb=" O LEU A 892 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA A 894 " --> pdb=" O ILE A 795 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 494 through 496 removed outlier: 3.651A pdb=" N VAL B 569 " --> pdb=" O SER B 526 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA B 573 " --> pdb=" O PHE B 530 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY B 572 " --> pdb=" O CYS B 463 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N PHE B 594 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU B 464 " --> pdb=" O PHE B 594 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 821 through 824 removed outlier: 6.642A pdb=" N THR B 821 " --> pdb=" O ILE B 856 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N TYR B 858 " --> pdb=" O THR B 821 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N TYR B 823 " --> pdb=" O TYR B 858 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR B 895 " --> pdb=" O VAL B 859 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA B 894 " --> pdb=" O ILE B 795 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 494 through 496 removed outlier: 4.152A pdb=" N VAL C 569 " --> pdb=" O SER C 526 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA C 573 " --> pdb=" O PHE C 530 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY C 572 " --> pdb=" O CYS C 463 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLY C 462 " --> pdb=" O ARG C 592 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N PHE C 594 " --> pdb=" O GLY C 462 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU C 464 " --> pdb=" O PHE C 594 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 822 through 824 removed outlier: 7.026A pdb=" N TYR C 823 " --> pdb=" O TYR C 858 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N SER C 855 " --> pdb=" O LEU C 891 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N LEU C 893 " --> pdb=" O SER C 855 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N VAL C 857 " --> pdb=" O LEU C 893 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N THR C 895 " --> pdb=" O VAL C 857 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N VAL C 859 " --> pdb=" O THR C 895 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE C 795 " --> pdb=" O ALA C 894 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N SER C 896 " --> pdb=" O ILE C 795 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE C 797 " --> pdb=" O SER C 896 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N PHE C 919 " --> pdb=" O ARG C 794 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU C 796 " --> pdb=" O PHE C 919 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 492 through 496 removed outlier: 3.689A pdb=" N VAL D 569 " --> pdb=" O SER D 526 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY D 572 " --> pdb=" O CYS D 463 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N PHE D 594 " --> pdb=" O GLY D 462 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU D 464 " --> pdb=" O PHE D 594 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 821 through 824 removed outlier: 3.775A pdb=" N THR D 895 " --> pdb=" O VAL D 859 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE D 795 " --> pdb=" O ALA D 894 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N SER D 896 " --> pdb=" O ILE D 795 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ILE D 797 " --> pdb=" O SER D 896 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU D 796 " --> pdb=" O PHE D 919 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 463 through 466 removed outlier: 6.507A pdb=" N LEU E 464 " --> pdb=" O PHE E 594 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 492 through 495 removed outlier: 3.554A pdb=" N ILE E 527 " --> pdb=" O ALA E 492 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL E 569 " --> pdb=" O SER E 526 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 821 through 824 removed outlier: 3.700A pdb=" N THR E 895 " --> pdb=" O VAL E 859 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA E 894 " --> pdb=" O ILE E 795 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 492 through 494 removed outlier: 6.303A pdb=" N ALA F 492 " --> pdb=" O ILE F 527 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N PHE F 529 " --> pdb=" O ALA F 492 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N PHE F 494 " --> pdb=" O PHE F 529 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N ASP F 531 " --> pdb=" O PHE F 494 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N SER F 526 " --> pdb=" O VAL F 569 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N ILE F 571 " --> pdb=" O SER F 526 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ILE F 528 " --> pdb=" O ILE F 571 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N ALA F 573 " --> pdb=" O ILE F 528 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N PHE F 530 " --> pdb=" O ALA F 573 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N CYS F 463 " --> pdb=" O VAL F 570 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY F 572 " --> pdb=" O CYS F 463 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 821 through 824 removed outlier: 3.698A pdb=" N THR F 895 " --> pdb=" O VAL F 859 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE F 795 " --> pdb=" O LEU F 892 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ALA F 894 " --> pdb=" O ILE F 795 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N PHE F 919 " --> pdb=" O ARG F 794 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU F 796 " --> pdb=" O PHE F 919 " (cutoff:3.500A) 1008 hydrogen bonds defined for protein. 2883 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: 7.75 Time building geometry restraints manager: 7.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7388 1.33 - 1.45: 3717 1.45 - 1.57: 14537 1.57 - 1.69: 28 1.69 - 1.81: 159 Bond restraints: 25829 Sorted by residual: bond pdb=" C4 ATP C1401 " pdb=" C5 ATP C1401 " ideal model delta sigma weight residual 1.388 1.472 -0.084 1.00e-02 1.00e+04 7.01e+01 bond pdb=" C4 ATP B1401 " pdb=" C5 ATP B1401 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.96e+01 bond pdb=" C4 ATP D1401 " pdb=" C5 ATP D1401 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.78e+01 bond pdb=" C5 ATP C1401 " pdb=" C6 ATP C1401 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.39e+01 bond pdb=" C5 ATP D1401 " pdb=" C6 ATP D1401 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.29e+01 ... (remaining 25824 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.90: 34847 3.90 - 7.81: 147 7.81 - 11.71: 14 11.71 - 15.62: 0 15.62 - 19.52: 6 Bond angle restraints: 35014 Sorted by residual: angle pdb=" PB ATP D1401 " pdb=" O3B ATP D1401 " pdb=" PG ATP D1401 " ideal model delta sigma weight residual 139.87 120.35 19.52 1.00e+00 1.00e+00 3.81e+02 angle pdb=" PB ATP C1401 " pdb=" O3B ATP C1401 " pdb=" PG ATP C1401 " ideal model delta sigma weight residual 139.87 120.53 19.34 1.00e+00 1.00e+00 3.74e+02 angle pdb=" PB ATP B1401 " pdb=" O3B ATP B1401 " pdb=" PG ATP B1401 " ideal model delta sigma weight residual 139.87 120.81 19.06 1.00e+00 1.00e+00 3.63e+02 angle pdb=" PA ATP C1401 " pdb=" O3A ATP C1401 " pdb=" PB ATP C1401 " ideal model delta sigma weight residual 136.83 120.42 16.41 1.00e+00 1.00e+00 2.69e+02 angle pdb=" PA ATP B1401 " pdb=" O3A ATP B1401 " pdb=" PB ATP B1401 " ideal model delta sigma weight residual 136.83 120.51 16.32 1.00e+00 1.00e+00 2.66e+02 ... (remaining 35009 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.53: 14599 21.53 - 43.07: 1119 43.07 - 64.60: 116 64.60 - 86.13: 63 86.13 - 107.66: 9 Dihedral angle restraints: 15906 sinusoidal: 6675 harmonic: 9231 Sorted by residual: dihedral pdb=" C5' ADP A1401 " pdb=" O5' ADP A1401 " pdb=" PA ADP A1401 " pdb=" O2A ADP A1401 " ideal model delta sinusoidal sigma weight residual -60.00 47.67 -107.66 1 2.00e+01 2.50e-03 3.13e+01 dihedral pdb=" O1B ADP A1401 " pdb=" O3A ADP A1401 " pdb=" PB ADP A1401 " pdb=" PA ADP A1401 " ideal model delta sinusoidal sigma weight residual -60.00 -149.55 89.55 1 2.00e+01 2.50e-03 2.38e+01 dihedral pdb=" CA PHE B 911 " pdb=" C PHE B 911 " pdb=" N ILE B 912 " pdb=" CA ILE B 912 " ideal model delta harmonic sigma weight residual -180.00 -158.07 -21.93 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 15903 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2800 0.041 - 0.081: 862 0.081 - 0.122: 258 0.122 - 0.163: 24 0.163 - 0.204: 4 Chirality restraints: 3948 Sorted by residual: chirality pdb=" CA GLU E1382 " pdb=" N GLU E1382 " pdb=" C GLU E1382 " pdb=" CB GLU E1382 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA ASN A 616 " pdb=" N ASN A 616 " pdb=" C ASN A 616 " pdb=" CB ASN A 616 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.36e-01 chirality pdb=" CB ILE B 672 " pdb=" CA ILE B 672 " pdb=" CG1 ILE B 672 " pdb=" CG2 ILE B 672 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.19 2.00e-01 2.50e+01 9.26e-01 ... (remaining 3945 not shown) Planarity restraints: 4488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D 586 " -0.032 5.00e-02 4.00e+02 4.80e-02 3.69e+00 pdb=" N PRO D 587 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO D 587 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 587 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG F 586 " -0.030 5.00e-02 4.00e+02 4.52e-02 3.27e+00 pdb=" N PRO F 587 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO F 587 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 587 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 865 " -0.010 2.00e-02 2.50e+03 1.11e-02 3.09e+00 pdb=" CG TRP E 865 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP E 865 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP E 865 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 865 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP E 865 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP E 865 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 865 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 865 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP E 865 " -0.000 2.00e-02 2.50e+03 ... (remaining 4485 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 458 2.68 - 3.24: 25087 3.24 - 3.79: 37111 3.79 - 4.35: 46992 4.35 - 4.90: 76572 Nonbonded interactions: 186220 Sorted by model distance: nonbonded pdb=" OE1 GLU D 440 " pdb=" OH TYR E 659 " model vdw 2.131 3.040 nonbonded pdb=" O GLN F 657 " pdb=" OG1 THR F 661 " model vdw 2.178 3.040 nonbonded pdb=" O ARG F 576 " pdb=" OG SER F 579 " model vdw 2.220 3.040 nonbonded pdb=" OD2 ASP C 668 " pdb=" OG SER C 670 " model vdw 2.221 3.040 nonbonded pdb=" O LYS C 706 " pdb=" NE2 GLN C 710 " model vdw 2.232 3.120 ... (remaining 186215 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' and (resid 422 through 598 or resid 601 through 688 or resid 696 thro \ ugh 727 or resid 787 through 943 or resid 1331 through 1388)) selection = (chain 'B' and (resid 422 through 539 or resid 546 through 598 or resid 601 thro \ ugh 659 or resid 666 through 688 or resid 696 through 727 or resid 787 through 9 \ 23 or resid 925 through 943 or resid 1331 through 1388)) selection = (chain 'C' and (resid 422 through 539 or resid 546 through 598 or resid 601 thro \ ugh 659 or resid 666 through 688 or resid 696 through 727 or resid 787 through 9 \ 23 or resid 925 through 943 or resid 1331 through 1388)) selection = (chain 'D' and (resid 422 through 539 or resid 546 through 598 or resid 601 thro \ ugh 659 or resid 666 through 688 or resid 696 through 727 or resid 787 through 9 \ 23 or resid 925 through 943 or resid 1331 through 1388)) selection = (chain 'E' and (resid 422 through 539 or resid 546 through 598 or resid 601 thro \ ugh 659 or resid 666 through 688 or resid 696 through 727 or resid 787 through 9 \ 23 or resid 925 through 943 or resid 1331 through 1388)) selection = (chain 'F' and (resid 422 through 539 or resid 546 through 659 or resid 666 thro \ ugh 727 or resid 787 through 923 or resid 925 through 943 or resid 1331 through \ 1388)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 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: 0.030 Extract box with map and model: 0.830 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 53.600 Find NCS groups from input model: 1.690 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4999 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 : 0.006 0.677 25831 Z= 0.554 Angle : 0.723 19.522 35014 Z= 0.456 Chirality : 0.042 0.204 3948 Planarity : 0.004 0.052 4488 Dihedral : 15.177 107.663 9884 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.56 % Favored : 93.34 % Rotamer: Outliers : 0.07 % Allowed : 0.32 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.16), residues: 3109 helix: 0.67 (0.15), residues: 1391 sheet: 0.46 (0.28), residues: 377 loop : -1.22 (0.18), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP E 865 HIS 0.003 0.001 HIS C1366 PHE 0.010 0.001 PHE D 724 TYR 0.017 0.001 TYR C1364 ARG 0.006 0.000 ARG F 576 Details of bonding type rmsd hydrogen bonds : bond 0.20268 ( 1008) hydrogen bonds : angle 6.26622 ( 2883) covalent geometry : bond 0.00327 (25829) covalent geometry : angle 0.72320 (35014) Misc. bond : bond 0.58085 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 633 time to evaluate : 2.762 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 639 ILE cc_start: 0.5841 (mm) cc_final: 0.5626 (mm) REVERT: A 686 MET cc_start: 0.0558 (pmm) cc_final: 0.0348 (mtt) REVERT: A 1379 MET cc_start: -0.5244 (mmt) cc_final: -0.5847 (mmp) REVERT: B 686 MET cc_start: 0.3895 (ppp) cc_final: 0.3088 (ppp) REVERT: C 441 MET cc_start: 0.5248 (ttm) cc_final: 0.4284 (ttt) REVERT: C 642 ILE cc_start: 0.8023 (mm) cc_final: 0.7228 (tp) REVERT: C 876 THR cc_start: 0.8155 (m) cc_final: 0.7449 (p) REVERT: C 883 ASN cc_start: 0.7292 (m110) cc_final: 0.6992 (m-40) REVERT: D 789 MET cc_start: 0.6822 (ttp) cc_final: 0.6150 (ppp) REVERT: D 857 VAL cc_start: 0.9198 (t) cc_final: 0.8976 (m) REVERT: E 578 ASP cc_start: 0.1467 (m-30) cc_final: 0.1248 (m-30) REVERT: E 789 MET cc_start: 0.7885 (tpt) cc_final: 0.7614 (tpt) REVERT: E 827 ILE cc_start: 0.7117 (mm) cc_final: 0.6866 (mm) REVERT: F 548 HIS cc_start: 0.7333 (m90) cc_final: 0.6979 (m170) REVERT: F 789 MET cc_start: -0.1316 (ppp) cc_final: -0.1826 (ttt) REVERT: F 1355 LEU cc_start: 0.8742 (tp) cc_final: 0.8539 (tt) outliers start: 2 outliers final: 1 residues processed: 634 average time/residue: 0.3993 time to fit residues: 377.9850 Evaluate side-chains 294 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 293 time to evaluate : 2.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 0.6980 chunk 236 optimal weight: 0.2980 chunk 131 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 159 optimal weight: 4.9990 chunk 126 optimal weight: 0.8980 chunk 244 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 148 optimal weight: 4.9990 chunk 182 optimal weight: 2.9990 chunk 283 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 546 GLN ** A 861 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 548 HIS B 611 HIS B 882 GLN ** C 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 GLN C 882 GLN C1361 GLN D 532 GLN D 691 GLN D1361 GLN E 815 HIS E1330 HIS E1351 GLN ** F 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 611 HIS ** F 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.150089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.125479 restraints weight = 131130.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.126949 restraints weight = 98129.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.126897 restraints weight = 85660.920| |-----------------------------------------------------------------------------| r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6415 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25831 Z= 0.139 Angle : 0.668 10.625 35014 Z= 0.333 Chirality : 0.044 0.191 3948 Planarity : 0.005 0.051 4488 Dihedral : 8.938 105.531 3581 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.69 % Favored : 93.21 % Rotamer: Outliers : 0.14 % Allowed : 4.82 % Favored : 95.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.16), residues: 3109 helix: 0.64 (0.14), residues: 1422 sheet: 0.73 (0.28), residues: 375 loop : -1.17 (0.18), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 505 HIS 0.016 0.001 HIS A 861 PHE 0.031 0.001 PHE C 517 TYR 0.024 0.002 TYR C 823 ARG 0.010 0.001 ARG A 589 Details of bonding type rmsd hydrogen bonds : bond 0.04538 ( 1008) hydrogen bonds : angle 4.91134 ( 2883) covalent geometry : bond 0.00301 (25829) covalent geometry : angle 0.66767 (35014) Misc. bond : bond 0.00426 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 394 time to evaluate : 2.605 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 523 MET cc_start: 0.2338 (mmp) cc_final: 0.2021 (tpt) REVERT: A 825 LEU cc_start: 0.7694 (mt) cc_final: 0.7057 (tp) REVERT: A 858 TYR cc_start: 0.5807 (t80) cc_final: 0.5529 (t80) REVERT: A 861 HIS cc_start: 0.5609 (p-80) cc_final: 0.5097 (p90) REVERT: A 1379 MET cc_start: -0.4731 (mmt) cc_final: -0.5081 (mmp) REVERT: B 528 ILE cc_start: 0.7166 (mt) cc_final: 0.6960 (mt) REVERT: C 527 ILE cc_start: 0.6783 (mp) cc_final: 0.6545 (mp) REVERT: C 839 GLU cc_start: 0.8349 (mm-30) cc_final: 0.8132 (mm-30) REVERT: C 848 GLU cc_start: 0.8634 (tm-30) cc_final: 0.8330 (tm-30) REVERT: C 876 THR cc_start: 0.8260 (m) cc_final: 0.7648 (p) REVERT: C 1379 MET cc_start: 0.7963 (mmt) cc_final: 0.7656 (mmm) REVERT: C 1382 GLU cc_start: 0.7369 (tt0) cc_final: 0.7121 (tt0) REVERT: C 1384 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6756 (mp0) REVERT: D 424 ARG cc_start: 0.6101 (mmt180) cc_final: 0.5414 (tpp80) REVERT: D 444 PHE cc_start: 0.6279 (m-10) cc_final: 0.5731 (m-10) REVERT: D 789 MET cc_start: 0.7059 (ttp) cc_final: 0.6770 (ppp) REVERT: D 821 THR cc_start: 0.7665 (p) cc_final: 0.7401 (t) REVERT: D 857 VAL cc_start: 0.9264 (t) cc_final: 0.8986 (m) REVERT: E 620 LEU cc_start: 0.7354 (pt) cc_final: 0.7102 (mt) REVERT: E 670 SER cc_start: 0.6757 (m) cc_final: 0.6463 (p) REVERT: F 548 HIS cc_start: 0.8380 (m90) cc_final: 0.8118 (m90) REVERT: F 559 MET cc_start: 0.4267 (tmm) cc_final: 0.3960 (tmm) REVERT: F 652 ARG cc_start: 0.8871 (tmm160) cc_final: 0.8255 (ttm-80) REVERT: F 789 MET cc_start: -0.3142 (ppp) cc_final: -0.4103 (ttt) outliers start: 4 outliers final: 1 residues processed: 398 average time/residue: 0.3591 time to fit residues: 223.5321 Evaluate side-chains 251 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 249 time to evaluate : 2.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 126 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 chunk 210 optimal weight: 7.9990 chunk 8 optimal weight: 8.9990 chunk 278 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 chunk 199 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 137 optimal weight: 5.9990 chunk 117 optimal weight: 7.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 861 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1351 GLN ** C 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 808 HIS C 883 ASN C1361 GLN D 434 HIS ** D 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 611 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 691 GLN D1361 GLN E 726 HIS ** E 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 900 HIS ** E1351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 815 HIS ** F 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.140285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.114995 restraints weight = 127073.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.116201 restraints weight = 93977.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.116246 restraints weight = 75350.760| |-----------------------------------------------------------------------------| r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6758 moved from start: 0.4681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 25831 Z= 0.206 Angle : 0.786 12.344 35014 Z= 0.397 Chirality : 0.048 0.278 3948 Planarity : 0.007 0.188 4488 Dihedral : 9.053 101.653 3581 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.95 % Favored : 92.99 % Rotamer: Outliers : 0.25 % Allowed : 6.37 % Favored : 93.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.15), residues: 3109 helix: 0.35 (0.14), residues: 1440 sheet: 0.49 (0.27), residues: 379 loop : -1.22 (0.18), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 865 HIS 0.013 0.002 HIS C 863 PHE 0.049 0.002 PHE E 529 TYR 0.050 0.002 TYR B 466 ARG 0.042 0.001 ARG E 847 Details of bonding type rmsd hydrogen bonds : bond 0.04684 ( 1008) hydrogen bonds : angle 4.92519 ( 2883) covalent geometry : bond 0.00459 (25829) covalent geometry : angle 0.78616 (35014) Misc. bond : bond 0.02347 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 332 time to evaluate : 2.858 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 616 ASN cc_start: 0.3035 (p0) cc_final: 0.2021 (m-40) REVERT: A 639 ILE cc_start: 0.6437 (mm) cc_final: 0.6224 (mm) REVERT: A 789 MET cc_start: 0.1639 (ttt) cc_final: 0.0631 (ttt) REVERT: A 825 LEU cc_start: 0.7203 (mt) cc_final: 0.6449 (tt) REVERT: A 1379 MET cc_start: -0.4713 (mmt) cc_final: -0.5255 (mmp) REVERT: B 686 MET cc_start: 0.3445 (ppp) cc_final: 0.2860 (ppp) REVERT: C 876 THR cc_start: 0.8744 (m) cc_final: 0.8305 (p) REVERT: C 1379 MET cc_start: 0.7961 (mmt) cc_final: 0.7482 (mmp) REVERT: C 1382 GLU cc_start: 0.7628 (tt0) cc_final: 0.7164 (tt0) REVERT: D 789 MET cc_start: 0.7283 (ttp) cc_final: 0.6998 (ppp) REVERT: E 626 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8373 (mm-30) REVERT: E 627 LEU cc_start: 0.9091 (mt) cc_final: 0.8882 (mt) REVERT: E 1379 MET cc_start: 0.8814 (mpp) cc_final: 0.8365 (mpp) REVERT: F 531 ASP cc_start: 0.8431 (t0) cc_final: 0.7984 (p0) REVERT: F 551 ILE cc_start: 0.7819 (tt) cc_final: 0.7583 (tt) REVERT: F 626 GLU cc_start: 0.7882 (tm-30) cc_final: 0.7446 (tm-30) REVERT: F 863 HIS cc_start: 0.8122 (p90) cc_final: 0.7670 (p-80) REVERT: F 893 LEU cc_start: 0.5764 (mt) cc_final: 0.5335 (pp) REVERT: F 1382 GLU cc_start: 0.8742 (tm-30) cc_final: 0.8353 (tp30) outliers start: 7 outliers final: 1 residues processed: 337 average time/residue: 0.3684 time to fit residues: 194.3297 Evaluate side-chains 215 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 214 time to evaluate : 3.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 216 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 153 optimal weight: 2.9990 chunk 203 optimal weight: 1.9990 chunk 154 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 227 optimal weight: 0.8980 chunk 277 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 chunk 110 optimal weight: 0.0670 chunk 128 optimal weight: 0.0270 overall best weight: 0.5576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 863 HIS A1381 GLN B 548 HIS C 548 HIS C 691 GLN C 883 ASN D 458 GLN D 691 GLN D 726 HIS E 575 ASN ** E 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 863 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 548 HIS F 900 HIS ** F 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.141914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.117022 restraints weight = 126724.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.117114 restraints weight = 102559.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.117207 restraints weight = 91218.266| |-----------------------------------------------------------------------------| r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6735 moved from start: 0.5040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25831 Z= 0.119 Angle : 0.643 10.881 35014 Z= 0.314 Chirality : 0.044 0.180 3948 Planarity : 0.005 0.071 4488 Dihedral : 8.575 100.795 3581 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.01 % Favored : 93.92 % Rotamer: Outliers : 0.07 % Allowed : 3.35 % Favored : 96.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.16), residues: 3109 helix: 0.66 (0.14), residues: 1434 sheet: 0.59 (0.27), residues: 384 loop : -1.11 (0.18), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 505 HIS 0.006 0.001 HIS C 611 PHE 0.024 0.001 PHE C 517 TYR 0.015 0.001 TYR C1364 ARG 0.010 0.000 ARG C 592 Details of bonding type rmsd hydrogen bonds : bond 0.03478 ( 1008) hydrogen bonds : angle 4.59329 ( 2883) covalent geometry : bond 0.00256 (25829) covalent geometry : angle 0.64280 (35014) Misc. bond : bond 0.00413 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 320 time to evaluate : 2.664 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 441 MET cc_start: 0.0392 (tpp) cc_final: 0.0119 (tpp) REVERT: A 523 MET cc_start: 0.2792 (mmp) cc_final: 0.1852 (mtp) REVERT: A 616 ASN cc_start: 0.2851 (p0) cc_final: 0.2069 (m-40) REVERT: A 639 ILE cc_start: 0.6440 (mm) cc_final: 0.6224 (mm) REVERT: A 683 MET cc_start: -0.2358 (mmt) cc_final: -0.2826 (mtm) REVERT: A 825 LEU cc_start: 0.7629 (mt) cc_final: 0.6683 (tp) REVERT: A 1379 MET cc_start: -0.4709 (mmt) cc_final: -0.5298 (mmp) REVERT: B 528 ILE cc_start: 0.7576 (mt) cc_final: 0.7345 (mt) REVERT: B 686 MET cc_start: 0.4126 (ppp) cc_final: 0.3404 (ppp) REVERT: B 932 PHE cc_start: 0.7082 (t80) cc_final: 0.6611 (t80) REVERT: C 595 LEU cc_start: 0.9272 (tp) cc_final: 0.9014 (tt) REVERT: C 876 THR cc_start: 0.9092 (m) cc_final: 0.8692 (p) REVERT: C 1379 MET cc_start: 0.7940 (mmt) cc_final: 0.7602 (mmp) REVERT: C 1382 GLU cc_start: 0.7437 (tt0) cc_final: 0.6950 (tt0) REVERT: D 789 MET cc_start: 0.7244 (ttp) cc_final: 0.7007 (ppp) REVERT: E 620 LEU cc_start: 0.7411 (pt) cc_final: 0.7198 (mt) REVERT: E 1379 MET cc_start: 0.8705 (mpp) cc_final: 0.8320 (mpp) REVERT: F 531 ASP cc_start: 0.8394 (t0) cc_final: 0.7883 (p0) REVERT: F 863 HIS cc_start: 0.7999 (p90) cc_final: 0.7759 (p-80) REVERT: F 891 LEU cc_start: 0.8659 (tp) cc_final: 0.8414 (tp) REVERT: F 893 LEU cc_start: 0.6118 (mt) cc_final: 0.5645 (pp) outliers start: 2 outliers final: 0 residues processed: 322 average time/residue: 0.3627 time to fit residues: 181.7123 Evaluate side-chains 210 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 2.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 76 optimal weight: 0.0870 chunk 114 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 198 optimal weight: 2.9990 chunk 183 optimal weight: 10.0000 chunk 238 optimal weight: 3.9990 chunk 188 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 155 optimal weight: 0.0970 chunk 137 optimal weight: 5.9990 chunk 291 optimal weight: 1.9990 overall best weight: 1.6362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 548 HIS ** B 699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 883 ASN D 482 ASN D 691 GLN ** E 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1351 GLN F 548 HIS ** F 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.137390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.112164 restraints weight = 126321.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.112299 restraints weight = 98783.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.112795 restraints weight = 79071.013| |-----------------------------------------------------------------------------| r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 moved from start: 0.5841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 25831 Z= 0.155 Angle : 0.673 10.653 35014 Z= 0.333 Chirality : 0.044 0.222 3948 Planarity : 0.005 0.071 4488 Dihedral : 8.519 98.708 3581 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.53 % Favored : 93.41 % Rotamer: Outliers : 0.07 % Allowed : 3.06 % Favored : 96.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.16), residues: 3109 helix: 0.70 (0.14), residues: 1436 sheet: 0.49 (0.27), residues: 387 loop : -1.06 (0.19), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 615 HIS 0.008 0.001 HIS C 548 PHE 0.028 0.002 PHE D 933 TYR 0.016 0.002 TYR C1364 ARG 0.011 0.001 ARG E 524 Details of bonding type rmsd hydrogen bonds : bond 0.03686 ( 1008) hydrogen bonds : angle 4.54587 ( 2883) covalent geometry : bond 0.00335 (25829) covalent geometry : angle 0.67337 (35014) Misc. bond : bond 0.00254 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 300 time to evaluate : 3.046 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 616 ASN cc_start: 0.3092 (p0) cc_final: 0.2107 (m-40) REVERT: A 639 ILE cc_start: 0.6432 (mm) cc_final: 0.6199 (mm) REVERT: A 683 MET cc_start: -0.3284 (mmt) cc_final: -0.3757 (mtm) REVERT: A 825 LEU cc_start: 0.7068 (mt) cc_final: 0.5983 (tp) REVERT: A 1379 MET cc_start: -0.4714 (mmt) cc_final: -0.5137 (mmp) REVERT: B 686 MET cc_start: 0.4046 (ppp) cc_final: 0.3281 (ppp) REVERT: B 842 CYS cc_start: 0.8923 (t) cc_final: 0.8679 (t) REVERT: B 932 PHE cc_start: 0.7296 (t80) cc_final: 0.7000 (t80) REVERT: C 876 THR cc_start: 0.8994 (m) cc_final: 0.8509 (p) REVERT: C 1379 MET cc_start: 0.7679 (mmt) cc_final: 0.7221 (mmp) REVERT: C 1383 VAL cc_start: 0.8556 (t) cc_final: 0.8049 (p) REVERT: E 842 CYS cc_start: 0.8196 (t) cc_final: 0.7467 (t) REVERT: E 1379 MET cc_start: 0.8770 (mpp) cc_final: 0.8235 (mpp) REVERT: F 531 ASP cc_start: 0.8396 (t0) cc_final: 0.8026 (p0) REVERT: F 556 LEU cc_start: 0.7824 (pp) cc_final: 0.7296 (tp) REVERT: F 893 LEU cc_start: 0.6297 (mt) cc_final: 0.5847 (pp) REVERT: F 1382 GLU cc_start: 0.8781 (tm-30) cc_final: 0.8427 (tp30) outliers start: 2 outliers final: 1 residues processed: 302 average time/residue: 0.3534 time to fit residues: 172.2572 Evaluate side-chains 208 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 207 time to evaluate : 2.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 243 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 168 optimal weight: 2.9990 chunk 7 optimal weight: 20.0000 chunk 31 optimal weight: 9.9990 chunk 83 optimal weight: 8.9990 chunk 34 optimal weight: 10.0000 chunk 25 optimal weight: 0.2980 chunk 182 optimal weight: 0.9990 chunk 142 optimal weight: 1.9990 chunk 246 optimal weight: 0.9980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 699 GLN C 575 ASN ** C 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 883 ASN ** C1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 691 GLN E 726 HIS ** E 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 548 HIS ** F 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.135447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.107699 restraints weight = 118529.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.107770 restraints weight = 95478.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.108372 restraints weight = 77722.168| |-----------------------------------------------------------------------------| r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.6396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25831 Z= 0.135 Angle : 0.648 10.520 35014 Z= 0.318 Chirality : 0.044 0.200 3948 Planarity : 0.005 0.069 4488 Dihedral : 8.527 99.951 3581 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.14 % Favored : 93.79 % Rotamer: Outliers : 0.07 % Allowed : 2.52 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.16), residues: 3109 helix: 0.70 (0.14), residues: 1444 sheet: 0.46 (0.27), residues: 375 loop : -1.03 (0.19), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP F 866 HIS 0.008 0.001 HIS A 611 PHE 0.030 0.001 PHE C 517 TYR 0.011 0.001 TYR B1364 ARG 0.007 0.000 ARG D 496 Details of bonding type rmsd hydrogen bonds : bond 0.03469 ( 1008) hydrogen bonds : angle 4.61379 ( 2883) covalent geometry : bond 0.00300 (25829) covalent geometry : angle 0.64848 (35014) Misc. bond : bond 0.00232 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 282 time to evaluate : 3.040 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 616 ASN cc_start: 0.3805 (p0) cc_final: 0.2876 (m-40) REVERT: A 639 ILE cc_start: 0.6512 (mm) cc_final: 0.6257 (mm) REVERT: A 683 MET cc_start: -0.3021 (mmt) cc_final: -0.3577 (mtm) REVERT: A 825 LEU cc_start: 0.6847 (mt) cc_final: 0.5722 (tp) REVERT: A 1379 MET cc_start: -0.4296 (mmt) cc_final: -0.4780 (mmp) REVERT: B 495 MET cc_start: 0.7271 (tmm) cc_final: 0.7015 (tmm) REVERT: B 528 ILE cc_start: 0.7632 (mt) cc_final: 0.7368 (mt) REVERT: B 686 MET cc_start: 0.3782 (ppp) cc_final: 0.3128 (ppp) REVERT: B 842 CYS cc_start: 0.8912 (t) cc_final: 0.8634 (t) REVERT: B 932 PHE cc_start: 0.7260 (t80) cc_final: 0.6883 (t80) REVERT: C 595 LEU cc_start: 0.9205 (tp) cc_final: 0.8970 (tt) REVERT: C 876 THR cc_start: 0.9161 (m) cc_final: 0.8722 (p) REVERT: C 1379 MET cc_start: 0.7805 (mmt) cc_final: 0.7276 (mmp) REVERT: E 638 ASP cc_start: 0.8812 (m-30) cc_final: 0.8391 (m-30) REVERT: E 1379 MET cc_start: 0.8636 (mpp) cc_final: 0.8005 (mpp) REVERT: F 531 ASP cc_start: 0.8428 (t0) cc_final: 0.7981 (p0) REVERT: F 626 GLU cc_start: 0.7748 (tm-30) cc_final: 0.7287 (tm-30) REVERT: F 825 LEU cc_start: 0.8450 (tp) cc_final: 0.8208 (tp) REVERT: F 866 TRP cc_start: 0.3865 (t-100) cc_final: 0.2640 (t-100) REVERT: F 893 LEU cc_start: 0.6572 (mt) cc_final: 0.6106 (pp) outliers start: 2 outliers final: 0 residues processed: 283 average time/residue: 0.3357 time to fit residues: 154.9761 Evaluate side-chains 200 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 2.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 27 optimal weight: 10.0000 chunk 265 optimal weight: 9.9990 chunk 228 optimal weight: 6.9990 chunk 251 optimal weight: 5.9990 chunk 271 optimal weight: 6.9990 chunk 211 optimal weight: 0.9980 chunk 26 optimal weight: 7.9990 chunk 15 optimal weight: 20.0000 chunk 176 optimal weight: 0.0010 chunk 89 optimal weight: 5.9990 chunk 11 optimal weight: 20.0000 overall best weight: 3.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 611 HIS B 611 HIS ** B 699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 844 GLN B 861 HIS B1366 HIS ** B1381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 611 HIS ** C 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 922 GLN ** C1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 691 GLN E 787 GLN ** E 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 900 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 548 HIS F 630 ASN ** F 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.123561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.097798 restraints weight = 117309.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.095393 restraints weight = 104478.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.095424 restraints weight = 101828.056| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.8483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 25831 Z= 0.291 Angle : 0.928 13.118 35014 Z= 0.470 Chirality : 0.052 0.285 3948 Planarity : 0.007 0.122 4488 Dihedral : 9.385 102.501 3581 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.52 % Favored : 91.35 % Rotamer: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.15), residues: 3109 helix: -0.06 (0.13), residues: 1443 sheet: -0.13 (0.27), residues: 377 loop : -1.32 (0.18), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP A 615 HIS 0.019 0.002 HIS B1366 PHE 0.038 0.003 PHE B 530 TYR 0.057 0.003 TYR F 915 ARG 0.017 0.001 ARG E 565 Details of bonding type rmsd hydrogen bonds : bond 0.05726 ( 1008) hydrogen bonds : angle 5.43910 ( 2883) covalent geometry : bond 0.00649 (25829) covalent geometry : angle 0.92850 (35014) Misc. bond : bond 0.00218 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 2.724 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 639 ILE cc_start: 0.6671 (mm) cc_final: 0.6449 (mm) REVERT: A 683 MET cc_start: -0.3798 (mmt) cc_final: -0.4023 (mtm) REVERT: A 789 MET cc_start: 0.1261 (ttp) cc_final: 0.0292 (mmm) REVERT: A 1379 MET cc_start: -0.4647 (mmt) cc_final: -0.4956 (mmp) REVERT: B 495 MET cc_start: 0.7506 (tmm) cc_final: 0.7240 (tmm) REVERT: B 545 ASP cc_start: 0.8202 (m-30) cc_final: 0.7965 (m-30) REVERT: B 827 ILE cc_start: 0.8845 (mm) cc_final: 0.8574 (mm) REVERT: B 932 PHE cc_start: 0.7682 (t80) cc_final: 0.7175 (t80) REVERT: C 525 PRO cc_start: 0.9208 (Cg_exo) cc_final: 0.8394 (Cg_endo) REVERT: C 595 LEU cc_start: 0.9206 (tp) cc_final: 0.8941 (tt) REVERT: C 848 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8459 (tm-30) REVERT: C 1379 MET cc_start: 0.8071 (mmt) cc_final: 0.7665 (mmp) REVERT: D 523 MET cc_start: 0.6349 (tpt) cc_final: 0.6072 (ptp) REVERT: D 631 CYS cc_start: 0.7176 (p) cc_final: 0.6782 (p) REVERT: E 435 ILE cc_start: 0.8854 (mt) cc_final: 0.8537 (tt) REVERT: E 638 ASP cc_start: 0.9099 (m-30) cc_final: 0.8536 (m-30) REVERT: E 648 LEU cc_start: 0.9117 (mp) cc_final: 0.8847 (tt) REVERT: E 792 ARG cc_start: 0.7114 (mtt180) cc_final: 0.6618 (mtt180) REVERT: E 1379 MET cc_start: 0.8630 (mpp) cc_final: 0.8025 (mpp) REVERT: F 626 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7666 (tm-30) REVERT: F 825 LEU cc_start: 0.8405 (tp) cc_final: 0.8087 (tp) REVERT: F 893 LEU cc_start: 0.6838 (mt) cc_final: 0.6485 (mt) outliers start: 0 outliers final: 0 residues processed: 269 average time/residue: 0.3504 time to fit residues: 153.4950 Evaluate side-chains 190 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 2.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 161 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 147 optimal weight: 5.9990 chunk 289 optimal weight: 0.9980 chunk 126 optimal weight: 2.9990 chunk 174 optimal weight: 4.9990 chunk 163 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 223 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 691 GLN ** C1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 458 GLN D 482 ASN ** D 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 815 HIS F 548 HIS ** F 940 GLN ** 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 = 0.4185 r_free = 0.4185 target = 0.125854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.094992 restraints weight = 112822.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.095042 restraints weight = 83029.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.096088 restraints weight = 65330.443| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.8646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25831 Z= 0.142 Angle : 0.700 10.872 35014 Z= 0.346 Chirality : 0.045 0.287 3948 Planarity : 0.005 0.074 4488 Dihedral : 8.711 101.751 3581 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.75 % Favored : 93.18 % Rotamer: Outliers : 0.04 % Allowed : 1.08 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.16), residues: 3109 helix: 0.40 (0.14), residues: 1443 sheet: 0.08 (0.27), residues: 373 loop : -1.17 (0.19), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 615 HIS 0.005 0.001 HIS A 611 PHE 0.023 0.001 PHE C 517 TYR 0.018 0.002 TYR B 521 ARG 0.011 0.001 ARG B 490 Details of bonding type rmsd hydrogen bonds : bond 0.04082 ( 1008) hydrogen bonds : angle 4.91602 ( 2883) covalent geometry : bond 0.00317 (25829) covalent geometry : angle 0.70035 (35014) Misc. bond : bond 0.00224 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 272 time to evaluate : 2.704 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 639 ILE cc_start: 0.5900 (mm) cc_final: 0.5661 (mm) REVERT: A 683 MET cc_start: -0.1972 (mmt) cc_final: -0.2437 (mtm) REVERT: A 789 MET cc_start: 0.0958 (ttp) cc_final: -0.0424 (mtp) REVERT: A 1379 MET cc_start: -0.3396 (mmt) cc_final: -0.3839 (mmp) REVERT: B 495 MET cc_start: 0.7529 (tmm) cc_final: 0.7281 (tmm) REVERT: B 545 ASP cc_start: 0.8101 (m-30) cc_final: 0.7714 (m-30) REVERT: B 827 ILE cc_start: 0.8820 (mm) cc_final: 0.8548 (mm) REVERT: B 842 CYS cc_start: 0.9084 (t) cc_final: 0.8837 (t) REVERT: B 932 PHE cc_start: 0.7558 (t80) cc_final: 0.7040 (t80) REVERT: C 548 HIS cc_start: 0.7232 (m90) cc_final: 0.6870 (m90) REVERT: C 595 LEU cc_start: 0.9201 (tp) cc_final: 0.8906 (tt) REVERT: C 691 GLN cc_start: 0.7736 (OUTLIER) cc_final: 0.7364 (pp30) REVERT: C 1379 MET cc_start: 0.7988 (mmt) cc_final: 0.7497 (mmp) REVERT: E 435 ILE cc_start: 0.8861 (mt) cc_final: 0.8533 (tt) REVERT: E 592 ARG cc_start: 0.6785 (mmm160) cc_final: 0.6156 (mmm160) REVERT: E 638 ASP cc_start: 0.8996 (m-30) cc_final: 0.8513 (m-30) REVERT: E 792 ARG cc_start: 0.6973 (mtt180) cc_final: 0.6626 (mtt180) REVERT: E 1379 MET cc_start: 0.8393 (mpp) cc_final: 0.8069 (mpp) REVERT: F 531 ASP cc_start: 0.8428 (t0) cc_final: 0.7973 (p0) REVERT: F 556 LEU cc_start: 0.8299 (pp) cc_final: 0.7930 (tp) REVERT: F 626 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7029 (tm-30) REVERT: F 627 LEU cc_start: 0.8316 (mt) cc_final: 0.8027 (mt) REVERT: F 825 LEU cc_start: 0.8199 (tp) cc_final: 0.7732 (tp) REVERT: F 893 LEU cc_start: 0.6689 (mt) cc_final: 0.6336 (mt) outliers start: 1 outliers final: 0 residues processed: 273 average time/residue: 0.3475 time to fit residues: 149.8008 Evaluate side-chains 191 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 190 time to evaluate : 2.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 6.9990 chunk 112 optimal weight: 0.9980 chunk 87 optimal weight: 6.9990 chunk 127 optimal weight: 0.0010 chunk 241 optimal weight: 0.1980 chunk 121 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 309 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 229 optimal weight: 1.9990 chunk 221 optimal weight: 0.0570 overall best weight: 0.4304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 548 HIS ** F 940 GLN ** 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 = 0.4216 r_free = 0.4216 target = 0.127708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.096778 restraints weight = 112634.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.097019 restraints weight = 82033.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.098008 restraints weight = 64644.017| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.8681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25831 Z= 0.123 Angle : 0.676 10.142 35014 Z= 0.330 Chirality : 0.044 0.233 3948 Planarity : 0.005 0.075 4488 Dihedral : 8.216 101.368 3581 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.50 % Favored : 93.44 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.16), residues: 3109 helix: 0.62 (0.14), residues: 1445 sheet: 0.23 (0.28), residues: 367 loop : -1.08 (0.19), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 615 HIS 0.004 0.001 HIS A 900 PHE 0.032 0.001 PHE F 877 TYR 0.021 0.001 TYR F 858 ARG 0.014 0.001 ARG E 565 Details of bonding type rmsd hydrogen bonds : bond 0.03446 ( 1008) hydrogen bonds : angle 4.69395 ( 2883) covalent geometry : bond 0.00258 (25829) covalent geometry : angle 0.67623 (35014) Misc. bond : bond 0.00245 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 2.830 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 639 ILE cc_start: 0.5975 (mm) cc_final: 0.5711 (mm) REVERT: A 683 MET cc_start: -0.2318 (mmt) cc_final: -0.2865 (mtp) REVERT: A 789 MET cc_start: 0.0232 (ttp) cc_final: -0.0521 (mtp) REVERT: A 1379 MET cc_start: -0.3559 (mmt) cc_final: -0.4014 (mmp) REVERT: B 495 MET cc_start: 0.7579 (tmm) cc_final: 0.7368 (tmm) REVERT: B 545 ASP cc_start: 0.8204 (m-30) cc_final: 0.7826 (m-30) REVERT: B 842 CYS cc_start: 0.9050 (t) cc_final: 0.8805 (t) REVERT: B 932 PHE cc_start: 0.7587 (t80) cc_final: 0.7046 (t80) REVERT: C 514 ARG cc_start: 0.8181 (mtt-85) cc_final: 0.7971 (ttm110) REVERT: C 548 HIS cc_start: 0.7055 (m90) cc_final: 0.6661 (m90) REVERT: C 631 CYS cc_start: 0.6593 (p) cc_final: 0.6239 (p) REVERT: C 1379 MET cc_start: 0.8005 (mmt) cc_final: 0.7650 (mmp) REVERT: D 595 LEU cc_start: 0.9272 (tt) cc_final: 0.9069 (pp) REVERT: D 631 CYS cc_start: 0.7158 (p) cc_final: 0.6952 (p) REVERT: E 523 MET cc_start: 0.5522 (tpt) cc_final: 0.5277 (tpp) REVERT: E 592 ARG cc_start: 0.6880 (mmm160) cc_final: 0.5464 (mmm160) REVERT: E 638 ASP cc_start: 0.8970 (m-30) cc_final: 0.8511 (m-30) REVERT: E 683 MET cc_start: 0.8441 (tmm) cc_final: 0.8133 (tmm) REVERT: E 792 ARG cc_start: 0.6925 (mtt180) cc_final: 0.6675 (mtt180) REVERT: E 1379 MET cc_start: 0.8192 (mpp) cc_final: 0.7925 (mpp) REVERT: F 531 ASP cc_start: 0.8370 (t0) cc_final: 0.7920 (p0) REVERT: F 556 LEU cc_start: 0.8286 (pp) cc_final: 0.7993 (tp) REVERT: F 626 GLU cc_start: 0.7658 (tm-30) cc_final: 0.7338 (tm-30) REVERT: F 825 LEU cc_start: 0.7982 (tp) cc_final: 0.7718 (tp) REVERT: F 858 TYR cc_start: 0.5785 (t80) cc_final: 0.5382 (t80) REVERT: F 893 LEU cc_start: 0.6058 (mt) cc_final: 0.5637 (mt) outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 0.3488 time to fit residues: 148.1226 Evaluate side-chains 188 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 3.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 26 optimal weight: 10.0000 chunk 258 optimal weight: 3.9990 chunk 86 optimal weight: 8.9990 chunk 68 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 133 optimal weight: 0.6980 chunk 227 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 chunk 32 optimal weight: 0.7980 chunk 229 optimal weight: 3.9990 chunk 308 optimal weight: 6.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 900 HIS ** B 699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 458 GLN ** C 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 900 HIS F 548 HIS ** F 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.125380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.095583 restraints weight = 113078.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.096211 restraints weight = 86519.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.096486 restraints weight = 66985.420| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.9000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25831 Z= 0.136 Angle : 0.687 11.232 35014 Z= 0.337 Chirality : 0.045 0.233 3948 Planarity : 0.005 0.073 4488 Dihedral : 8.125 101.730 3581 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.85 % Favored : 93.08 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.16), residues: 3109 helix: 0.70 (0.14), residues: 1441 sheet: 0.23 (0.27), residues: 374 loop : -1.02 (0.19), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 615 HIS 0.003 0.001 HIS C 863 PHE 0.023 0.001 PHE F 517 TYR 0.021 0.001 TYR F 448 ARG 0.010 0.000 ARG F 652 Details of bonding type rmsd hydrogen bonds : bond 0.03661 ( 1008) hydrogen bonds : angle 4.79922 ( 2883) covalent geometry : bond 0.00308 (25829) covalent geometry : angle 0.68659 (35014) Misc. bond : bond 0.00265 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 2.673 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 639 ILE cc_start: 0.5976 (mm) cc_final: 0.5770 (mm) REVERT: A 683 MET cc_start: -0.2855 (mmt) cc_final: -0.3358 (mtp) REVERT: A 789 MET cc_start: 0.0180 (ttp) cc_final: -0.0429 (mtp) REVERT: A 1379 MET cc_start: -0.3679 (mmt) cc_final: -0.4109 (mmp) REVERT: B 545 ASP cc_start: 0.8161 (m-30) cc_final: 0.7743 (m-30) REVERT: B 591 ASP cc_start: 0.8402 (p0) cc_final: 0.8117 (p0) REVERT: B 827 ILE cc_start: 0.8845 (mm) cc_final: 0.8602 (mm) REVERT: B 842 CYS cc_start: 0.9099 (t) cc_final: 0.8844 (t) REVERT: B 932 PHE cc_start: 0.7690 (t80) cc_final: 0.7141 (t80) REVERT: C 631 CYS cc_start: 0.6468 (p) cc_final: 0.6192 (p) REVERT: C 1379 MET cc_start: 0.7878 (mmt) cc_final: 0.7370 (mmp) REVERT: E 592 ARG cc_start: 0.7117 (mmm160) cc_final: 0.5691 (mmm160) REVERT: E 638 ASP cc_start: 0.9083 (m-30) cc_final: 0.8657 (m-30) REVERT: E 661 THR cc_start: 0.7822 (p) cc_final: 0.7593 (t) REVERT: E 683 MET cc_start: 0.8375 (tmm) cc_final: 0.8093 (tmm) REVERT: E 792 ARG cc_start: 0.6933 (mtt180) cc_final: 0.6659 (mtt180) REVERT: E 1379 MET cc_start: 0.8194 (mpp) cc_final: 0.7934 (mpp) REVERT: F 531 ASP cc_start: 0.8471 (t0) cc_final: 0.7991 (p0) REVERT: F 556 LEU cc_start: 0.8290 (pp) cc_final: 0.7973 (tp) REVERT: F 626 GLU cc_start: 0.7638 (tm-30) cc_final: 0.7297 (tm-30) REVERT: F 825 LEU cc_start: 0.8001 (tp) cc_final: 0.7644 (tp) REVERT: F 893 LEU cc_start: 0.6551 (mt) cc_final: 0.6193 (mt) REVERT: F 1379 MET cc_start: 0.8731 (mpp) cc_final: 0.8052 (mpp) outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.3410 time to fit residues: 139.1109 Evaluate side-chains 178 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 2.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 52 optimal weight: 8.9990 chunk 303 optimal weight: 0.7980 chunk 297 optimal weight: 4.9990 chunk 183 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 185 optimal weight: 5.9990 chunk 227 optimal weight: 3.9990 chunk 146 optimal weight: 7.9990 chunk 98 optimal weight: 8.9990 chunk 143 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 548 HIS F 808 HIS ** F 940 GLN ** 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 = 0.4176 r_free = 0.4176 target = 0.125066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.095074 restraints weight = 113355.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.095988 restraints weight = 85306.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.097642 restraints weight = 63689.992| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.9267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25831 Z= 0.127 Angle : 0.678 12.847 35014 Z= 0.330 Chirality : 0.044 0.234 3948 Planarity : 0.005 0.071 4488 Dihedral : 8.025 102.211 3581 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.75 % Favored : 93.21 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.16), residues: 3109 helix: 0.72 (0.14), residues: 1442 sheet: 0.31 (0.27), residues: 387 loop : -1.03 (0.19), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 615 HIS 0.007 0.001 HIS F 808 PHE 0.022 0.001 PHE F 517 TYR 0.020 0.001 TYR B 858 ARG 0.009 0.000 ARG F 652 Details of bonding type rmsd hydrogen bonds : bond 0.03493 ( 1008) hydrogen bonds : angle 4.71869 ( 2883) covalent geometry : bond 0.00287 (25829) covalent geometry : angle 0.67763 (35014) Misc. bond : bond 0.00217 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8077.39 seconds wall clock time: 142 minutes 10.93 seconds (8530.93 seconds total)