Starting phenix.real_space_refine on Fri May 23 23:14:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8juy_36666/05_2025/8juy_36666_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8juy_36666/05_2025/8juy_36666.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8juy_36666/05_2025/8juy_36666.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8juy_36666/05_2025/8juy_36666.map" model { file = "/net/cci-nas-00/data/ceres_data/8juy_36666/05_2025/8juy_36666_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8juy_36666/05_2025/8juy_36666_neut.cif" } resolution = 4.34 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= 0.001 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 107 5.16 5 C 15675 2.51 5 N 4234 2.21 5 O 4521 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 59 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: 24554 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3472 Classifications: {'peptide': 442} Link IDs: {'CIS': 3, 'PCIS': 2, 'PTRANS': 30, 'TRANS': 406} Chain breaks: 3 Chain: "B" Number of atoms: 4197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4197 Classifications: {'peptide': 527} Link IDs: {'CIS': 3, 'PCIS': 2, 'PTRANS': 32, 'TRANS': 489} Chain breaks: 3 Chain: "C" Number of atoms: 4190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4190 Classifications: {'peptide': 527} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 492} Chain breaks: 3 Chain: "D" Number of atoms: 4206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4206 Classifications: {'peptide': 529} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 494} Chain breaks: 3 Chain: "E" Number of atoms: 4188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4188 Classifications: {'peptide': 526} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 32, 'TRANS': 489} Chain breaks: 3 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: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 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: 13.51, per 1000 atoms: 0.55 Number of scatterers: 24554 At special positions: 0 Unit cell: (141.9, 158.4, 139.7, 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 107 16.00 P 17 15.00 O 4521 8.00 N 4234 7.00 C 15675 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=11, symmetry=0 Number of additional bonds: simple=11, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.60 Conformation dependent library (CDL) restraints added in 3.1 seconds 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5850 Finding SS restraints... Secondary structure from input PDB file: 151 helices and 13 sheets defined 51.9% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.66 Creating SS restraints... Processing helix chain 'A' and resid 432 through 448 removed outlier: 3.579A pdb=" N LEU A 438 " --> pdb=" O HIS A 434 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU A 440 " --> pdb=" O ALA A 436 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N MET A 441 " --> pdb=" O ALA A 437 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A 442 " --> pdb=" O LEU A 438 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N PHE A 444 " --> pdb=" O GLU A 440 " (cutoff:3.500A) Proline residue: A 445 - end of helix Processing helix chain 'A' and resid 474 through 484 Processing helix chain 'A' and resid 507 through 524 removed outlier: 3.846A pdb=" N ARG A 524 " --> pdb=" O ALA A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 561 Processing helix chain 'A' and resid 600 through 611 removed outlier: 3.566A pdb=" N ARG A 604 " --> pdb=" O ASP A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 631 removed outlier: 3.728A pdb=" N LEU A 624 " --> pdb=" O LEU A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 655 removed outlier: 3.791A pdb=" N LEU A 648 " --> pdb=" O ALA A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 684 removed outlier: 3.674A pdb=" N ALA A 682 " --> pdb=" O ASP A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 720 removed outlier: 5.285A pdb=" N ASN A 711 " --> pdb=" O PRO A 707 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N THR A 712 " --> pdb=" O LEU A 708 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU A 717 " --> pdb=" O VAL A 713 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU A 718 " --> pdb=" O ASP A 714 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ALA A 719 " --> pdb=" O LYS A 715 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU A 720 " --> pdb=" O ILE A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 817 Processing helix chain 'A' and resid 826 through 831 removed outlier: 3.730A pdb=" N PHE A 831 " --> pdb=" O ILE A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 852 removed outlier: 3.651A pdb=" N THR A 841 " --> pdb=" O SER A 837 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA A 843 " --> pdb=" O GLU A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 868 removed outlier: 3.799A pdb=" N ILE A 868 " --> pdb=" O TRP A 865 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 880 Processing helix chain 'A' and resid 899 through 903 removed outlier: 3.783A pdb=" N ALA A 902 " --> pdb=" O PRO A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 909 removed outlier: 3.981A pdb=" N GLN A 908 " --> pdb=" O PRO A 904 " (cutoff:3.500A) 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 'B' and resid 432 through 448 removed outlier: 3.625A pdb=" N VAL B 442 " --> pdb=" O LEU B 438 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N PHE B 444 " --> pdb=" O GLU B 440 " (cutoff:3.500A) Proline residue: B 445 - end of helix Processing helix chain 'B' and resid 450 through 456 Processing helix chain 'B' and resid 472 through 485 removed outlier: 4.171A pdb=" N VAL B 476 " --> pdb=" O GLY B 472 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ALA B 477 " --> pdb=" O LYS B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 510 removed outlier: 4.288A pdb=" N GLU B 510 " --> pdb=" O VAL B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 523 removed outlier: 4.205A 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: 4.122A pdb=" N SER B 549 " --> pdb=" O ASP B 545 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET B 559 " --> pdb=" O LEU B 555 " (cutoff:3.500A) removed outlier: 4.344A 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 Processing helix chain 'B' and resid 620 through 629 Processing helix chain 'B' and resid 637 through 646 removed outlier: 3.624A pdb=" N ALA B 644 " --> pdb=" O LYS B 640 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA B 646 " --> pdb=" O ILE B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 655 removed outlier: 3.508A pdb=" N TYR B 655 " --> pdb=" O LEU B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 675 through 686 removed outlier: 4.269A pdb=" N PHE B 679 " --> pdb=" O SER B 675 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU B 680 " --> pdb=" O ALA B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 694 removed outlier: 4.392A pdb=" N ALA B 693 " --> pdb=" O ALA B 689 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL B 694 " --> pdb=" O SER B 690 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 689 through 694' Processing helix chain 'B' and resid 705 through 724 removed outlier: 5.735A pdb=" N ASN B 711 " --> pdb=" O PRO B 707 " (cutoff:3.500A) removed outlier: 5.871A 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 808 through 817 removed outlier: 3.882A pdb=" N ALA B 812 " --> pdb=" O HIS B 808 " (cutoff:3.500A) 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 removed outlier: 3.534A pdb=" N TRP B 865 " --> pdb=" O HIS B 861 " (cutoff:3.500A) 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 881 removed outlier: 3.878A pdb=" N LEU B 881 " --> pdb=" O PHE B 877 " (cutoff:3.500A) Processing helix chain 'B' and resid 899 through 903 Processing helix chain 'B' and resid 904 through 909 Processing helix chain 'B' and resid 912 through 916 Processing helix chain 'B' and resid 925 through 935 removed outlier: 4.026A pdb=" N ASP B 935 " --> pdb=" O LYS B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 1331 through 1344 removed outlier: 4.154A pdb=" N ASN B1335 " --> pdb=" O GLU B1331 " (cutoff:3.500A) Processing helix chain 'B' and resid 1348 through 1365 removed outlier: 3.888A pdb=" N TYR B1356 " --> pdb=" O LEU B1352 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ALA B1357 " --> pdb=" O GLU B1353 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL B1358 " --> pdb=" O ASN B1354 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE B1359 " --> pdb=" O LEU B1355 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER B1360 " --> pdb=" O TYR B1356 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N CYS B1362 " --> pdb=" O VAL B1358 " (cutoff:3.500A) Processing helix chain 'B' and resid 1375 through 1385 Processing helix chain 'C' and resid 432 through 443 removed outlier: 4.012A pdb=" N GLU C 440 " --> pdb=" O ALA C 436 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N MET C 441 " --> pdb=" O ALA C 437 " (cutoff:3.500A) removed outlier: 4.293A 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 448 through 453 removed outlier: 4.427A pdb=" N PHE C 452 " --> pdb=" O TYR C 448 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLU C 453 " --> pdb=" O PRO C 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 448 through 453' Processing helix chain 'C' and resid 473 through 486 removed outlier: 4.009A pdb=" N ALA C 477 " --> pdb=" O LYS C 473 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLN C 486 " --> pdb=" O ASN C 482 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 509 Processing helix chain 'C' and resid 510 through 523 removed outlier: 3.510A pdb=" N ARG C 514 " --> pdb=" O GLU C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 536 removed outlier: 3.629A pdb=" N GLY C 535 " --> pdb=" O GLN C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 560 removed outlier: 4.298A pdb=" N SER C 549 " --> pdb=" O ASP C 545 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASP C 560 " --> pdb=" O LEU C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 580 removed outlier: 3.617A pdb=" N SER C 579 " --> pdb=" O ARG C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 600 through 612 Processing helix chain 'C' and resid 620 through 630 removed outlier: 4.240A pdb=" N GLU C 629 " --> pdb=" O GLU C 625 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASN C 630 " --> pdb=" O GLU C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 655 removed outlier: 4.186A pdb=" N ALA C 647 " --> pdb=" O CYS C 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 661 removed outlier: 3.728A pdb=" N TYR C 659 " --> pdb=" O PRO C 656 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N THR C 661 " --> pdb=" O ILE C 658 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 686 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 removed outlier: 3.607A pdb=" N THR C 841 " --> pdb=" O SER C 837 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE C 846 " --> pdb=" O CYS C 842 " (cutoff:3.500A) Processing helix chain 'C' and resid 861 through 866 Processing helix chain 'C' and resid 870 through 881 removed outlier: 3.581A pdb=" N LEU C 881 " --> pdb=" O PHE C 877 " (cutoff:3.500A) Processing helix chain 'C' and resid 907 through 911 removed outlier: 3.537A pdb=" N PHE C 911 " --> pdb=" O GLN C 908 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 916 Processing helix chain 'C' and resid 925 through 939 removed outlier: 3.598A pdb=" N PHE C 933 " --> pdb=" O ARG C 929 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ASP C 935 " --> pdb=" O LYS C 931 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LEU C 936 " --> pdb=" O PHE C 932 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS C 939 " --> pdb=" O ASP C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 1331 through 1344 removed outlier: 3.928A pdb=" N ASN C1335 " --> pdb=" O GLU C1331 " (cutoff:3.500A) Processing helix chain 'C' and resid 1348 through 1366 removed outlier: 3.556A pdb=" N CYS C1362 " --> pdb=" O VAL C1358 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE C1363 " --> pdb=" O ILE C1359 " (cutoff:3.500A) Processing helix chain 'C' and resid 1374 through 1386 removed outlier: 4.207A pdb=" N LYS C1378 " --> pdb=" O SER C1374 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 440 removed outlier: 3.799A pdb=" N GLU D 440 " --> pdb=" O ALA D 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 443 through 448 Processing helix chain 'D' and resid 472 through 486 removed outlier: 3.677A pdb=" N ALA D 477 " --> pdb=" O LYS D 473 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN D 486 " --> pdb=" O ASN D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 507 through 523 removed outlier: 3.985A pdb=" N ARG D 511 " --> pdb=" O GLY D 507 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU D 513 " --> pdb=" O SER D 509 " (cutoff:3.500A) removed outlier: 3.649A 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 545 through 560 removed outlier: 4.379A pdb=" N SER D 549 " --> pdb=" O ASP D 545 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER D 553 " --> pdb=" O SER D 549 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU D 558 " --> pdb=" O THR D 554 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP D 560 " --> pdb=" O LEU D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 585 Processing helix chain 'D' and resid 600 through 612 removed outlier: 3.589A pdb=" N THR D 612 " --> pdb=" O LEU D 608 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 631 removed outlier: 3.886A pdb=" N ASN D 630 " --> pdb=" O GLU D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 637 through 655 removed outlier: 3.646A pdb=" N CYS D 643 " --> pdb=" O ILE D 639 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA D 644 " --> pdb=" O LYS D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 659 removed outlier: 3.550A pdb=" N TYR D 659 " --> pdb=" O PRO D 656 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 656 through 659' Processing helix chain 'D' and resid 677 through 685 removed outlier: 3.805A pdb=" N LYS D 685 " --> pdb=" O VAL D 681 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 693 removed outlier: 3.739A pdb=" N ARG D 692 " --> pdb=" O ALA D 689 " (cutoff:3.500A) removed outlier: 3.830A 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: 6.089A pdb=" N ASN D 711 " --> pdb=" O PRO D 707 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N THR D 712 " --> pdb=" O LEU D 708 " (cutoff:3.500A) Processing helix chain 'D' and resid 809 through 817 Processing helix chain 'D' and resid 826 through 831 Processing helix chain 'D' and resid 837 through 852 Processing helix chain 'D' and resid 861 through 869 removed outlier: 5.287A pdb=" N GLU D 867 " --> pdb=" O HIS D 863 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE D 868 " --> pdb=" O VAL D 864 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL D 869 " --> pdb=" O TRP D 865 " (cutoff:3.500A) Processing helix chain 'D' and resid 870 through 882 removed outlier: 4.051A 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 Processing helix chain 'D' and resid 912 through 916 Processing helix chain 'D' and resid 925 through 938 removed outlier: 4.561A pdb=" N ASP D 935 " --> pdb=" O LYS D 931 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N LEU D 936 " --> pdb=" O PHE D 932 " (cutoff:3.500A) Processing helix chain 'D' and resid 1332 through 1344 Processing helix chain 'D' and resid 1348 through 1366 removed outlier: 3.995A 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 448 removed outlier: 3.840A pdb=" N MET E 441 " --> pdb=" O ALA E 437 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N PHE E 444 " --> pdb=" O GLU E 440 " (cutoff:3.500A) Proline residue: E 445 - end of helix Processing helix chain 'E' and resid 450 through 455 removed outlier: 3.707A pdb=" N LYS E 454 " --> pdb=" O GLU E 450 " (cutoff:3.500A) removed outlier: 4.293A 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 505 through 523 removed outlier: 4.405A pdb=" N GLU E 510 " --> pdb=" O VAL E 506 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LEU E 513 " --> pdb=" O SER E 509 " (cutoff:3.500A) Processing helix chain 'E' and resid 532 through 536 Processing helix chain 'E' and resid 545 through 561 removed outlier: 3.972A pdb=" N SER E 549 " --> pdb=" O ASP E 545 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU E 558 " --> pdb=" O THR E 554 " (cutoff:3.500A) Processing helix chain 'E' and resid 562 through 565 Processing helix chain 'E' and resid 600 through 612 Processing helix chain 'E' and resid 620 through 631 removed outlier: 4.293A pdb=" N ASN E 630 " --> pdb=" O GLU E 626 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N CYS E 631 " --> pdb=" O LEU E 627 " (cutoff:3.500A) Processing helix chain 'E' and resid 635 through 655 removed outlier: 3.640A pdb=" N ALA E 644 " --> pdb=" O LYS E 640 " (cutoff:3.500A) Processing helix chain 'E' and resid 675 through 686 Processing helix chain 'E' and resid 705 through 723 removed outlier: 6.228A pdb=" N ASN E 711 " --> pdb=" O PRO E 707 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N THR E 712 " --> pdb=" O LEU E 708 " (cutoff:3.500A) Processing helix chain 'E' and resid 800 through 804 removed outlier: 4.108A 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: 3.558A pdb=" N THR E 841 " --> pdb=" O SER E 837 " (cutoff:3.500A) Processing helix chain 'E' and resid 861 through 866 Processing helix chain 'E' and resid 870 through 881 removed outlier: 3.523A pdb=" N LEU E 881 " --> pdb=" O PHE E 877 " (cutoff:3.500A) Processing helix chain 'E' and resid 904 through 909 removed outlier: 3.761A pdb=" N GLU E 909 " --> pdb=" O GLU E 905 " (cutoff:3.500A) Processing helix chain 'E' and resid 910 through 911 No H-bonds generated for 'chain 'E' and resid 910 through 911' Processing helix chain 'E' and resid 912 through 916 Processing helix chain 'E' and resid 925 through 935 removed outlier: 4.085A pdb=" N ASP E 935 " --> pdb=" O LYS E 931 " (cutoff:3.500A) Processing helix chain 'E' and resid 939 through 943 removed outlier: 3.837A pdb=" N LYS E 943 " --> pdb=" O GLN E 940 " (cutoff:3.500A) Processing helix chain 'E' and resid 1331 through 1344 Processing helix chain 'E' and resid 1348 through 1366 Processing helix chain 'E' and resid 1375 through 1385 Processing helix chain 'F' and resid 431 through 441 removed outlier: 3.527A pdb=" N ALA F 436 " --> pdb=" O SER F 432 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA F 437 " --> pdb=" O ASN F 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 472 through 485 Processing helix chain 'F' and resid 507 through 523 removed outlier: 4.042A pdb=" N MET F 523 " --> pdb=" O GLN F 519 " (cutoff:3.500A) Processing helix chain 'F' and resid 532 through 537 Processing helix chain 'F' and resid 545 through 559 Processing helix chain 'F' and resid 560 through 562 No H-bonds generated for 'chain 'F' and resid 560 through 562' Processing helix chain 'F' and resid 576 through 580 removed outlier: 3.759A pdb=" N ILE F 580 " --> pdb=" O LEU F 577 " (cutoff:3.500A) Processing helix chain 'F' and resid 602 through 612 removed outlier: 4.173A pdb=" N GLU F 606 " --> pdb=" O GLU F 602 " (cutoff:3.500A) Processing helix chain 'F' and resid 620 through 631 Processing helix chain 'F' and resid 637 through 654 Processing helix chain 'F' and resid 655 through 659 removed outlier: 3.762A pdb=" N ILE F 658 " --> pdb=" O TYR F 655 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N TYR F 659 " --> pdb=" O PRO F 656 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 655 through 659' Processing helix chain 'F' and resid 676 through 681 removed outlier: 3.584A pdb=" N GLU F 680 " --> pdb=" O ALA F 676 " (cutoff:3.500A) Processing helix chain 'F' and resid 682 through 686 removed outlier: 3.680A pdb=" N MET F 686 " --> pdb=" O MET F 683 " (cutoff:3.500A) Processing helix chain 'F' and resid 705 through 724 removed outlier: 3.864A pdb=" N LEU F 709 " --> pdb=" O VAL F 705 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ASN F 711 " --> pdb=" O PRO F 707 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N THR F 712 " --> pdb=" O LEU F 708 " (cutoff:3.500A) Processing helix chain 'F' and resid 808 through 816 removed outlier: 4.155A pdb=" N ALA F 812 " --> pdb=" O HIS F 808 " (cutoff:3.500A) Processing helix chain 'F' and resid 840 through 852 removed outlier: 4.040A pdb=" N GLN F 844 " --> pdb=" O GLU F 840 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE F 846 " --> pdb=" O CYS F 842 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR F 852 " --> pdb=" O GLU F 848 " (cutoff:3.500A) Processing helix chain 'F' and resid 861 through 866 Processing helix chain 'F' and resid 867 through 869 No H-bonds generated for 'chain 'F' and resid 867 through 869' Processing helix chain 'F' and resid 871 through 883 removed outlier: 3.679A pdb=" N ALA F 875 " --> pdb=" O PRO F 871 " (cutoff:3.500A) Processing helix chain 'F' and resid 899 through 903 removed outlier: 3.682A pdb=" N LEU F 903 " --> pdb=" O HIS F 900 " (cutoff:3.500A) Processing helix chain 'F' and resid 904 through 909 Processing helix chain 'F' and resid 925 through 934 Processing helix chain 'F' and resid 1332 through 1344 Processing helix chain 'F' and resid 1348 through 1366 removed outlier: 4.115A pdb=" N HIS F1366 " --> pdb=" O CYS F1362 " (cutoff:3.500A) Processing helix chain 'F' and resid 1374 through 1386 removed outlier: 3.513A pdb=" N GLU F1384 " --> pdb=" O GLU F1380 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 462 through 464 removed outlier: 7.469A pdb=" N CYS A 463 " --> pdb=" O GLY A 572 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 796 through 798 removed outlier: 3.979A pdb=" N PHE A 919 " --> pdb=" O LEU A 796 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 822 through 824 removed outlier: 3.729A pdb=" N TYR A 858 " --> pdb=" O TYR A 823 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL A 857 " --> pdb=" O LEU A 893 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 494 through 496 removed outlier: 3.543A pdb=" N ALA B 573 " --> pdb=" O PHE B 530 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N PHE B 594 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU B 464 " --> pdb=" O PHE B 594 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 821 through 824 removed outlier: 6.881A pdb=" N SER B 855 " --> pdb=" O LEU B 891 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N LEU B 893 " --> pdb=" O SER B 855 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL B 857 " --> pdb=" O LEU B 893 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N THR B 895 " --> pdb=" O VAL B 857 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N VAL B 859 " --> pdb=" O THR B 895 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER B 896 " --> pdb=" O ILE B 797 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLY B 799 " --> pdb=" O SER B 896 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 494 through 496 removed outlier: 3.630A pdb=" N ALA C 573 " --> pdb=" O PHE C 530 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR C 466 " --> pdb=" O PHE C 594 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 822 through 824 removed outlier: 6.532A pdb=" N TYR C 823 " --> pdb=" O TYR C 858 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU C 891 " --> pdb=" O SER C 855 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR C 895 " --> pdb=" O VAL C 859 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA C 894 " --> pdb=" O ILE C 795 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N PHE C 919 " --> pdb=" O ARG C 794 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU C 796 " --> pdb=" O PHE C 919 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 527 through 531 removed outlier: 3.564A pdb=" N ALA D 573 " --> pdb=" O PHE D 530 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N PHE D 594 " --> pdb=" O GLY D 462 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU D 464 " --> pdb=" O PHE D 594 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 821 through 824 removed outlier: 7.197A pdb=" N THR D 821 " --> pdb=" O ILE D 856 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N TYR D 858 " --> pdb=" O THR D 821 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N TYR D 823 " --> pdb=" O TYR D 858 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU D 891 " --> pdb=" O SER D 855 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR D 895 " --> pdb=" O VAL D 859 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE D 795 " --> pdb=" O ALA D 894 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N SER D 896 " --> pdb=" O ILE D 795 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE D 797 " --> pdb=" O SER D 896 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 492 through 495 removed outlier: 6.393A pdb=" N ALA E 492 " --> pdb=" O ILE E 527 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N PHE E 529 " --> pdb=" O ALA E 492 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N PHE E 494 " --> pdb=" O PHE E 529 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N VAL E 569 " --> pdb=" O SER E 526 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY E 572 " --> pdb=" O CYS E 463 " (cutoff:3.500A) removed outlier: 8.824A pdb=" N PHE E 594 " --> pdb=" O GLY E 462 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N LEU E 464 " --> pdb=" O PHE E 594 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 821 through 824 removed outlier: 3.667A pdb=" N THR E 895 " --> pdb=" O VAL E 859 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA E 894 " --> pdb=" O ILE E 795 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE E 919 " --> pdb=" O LEU E 796 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 570 through 573 removed outlier: 7.279A pdb=" N PHE F 594 " --> pdb=" O GLY F 462 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N LEU F 464 " --> pdb=" O PHE F 594 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 855 through 859 removed outlier: 6.774A pdb=" N SER F 855 " --> pdb=" O LEU F 891 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N LEU F 893 " --> pdb=" O SER F 855 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL F 857 " --> pdb=" O LEU F 893 " (cutoff:3.500A) removed outlier: 8.713A pdb=" N THR F 895 " --> pdb=" O VAL F 857 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL F 859 " --> pdb=" O THR F 895 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ILE F 797 " --> pdb=" O SER F 896 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N LEU F 796 " --> pdb=" O PHE F 919 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 940 hydrogen bonds defined for protein. 2694 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: 7.20 Time building geometry restraints manager: 7.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7828 1.34 - 1.46: 3872 1.46 - 1.58: 13223 1.58 - 1.70: 19 1.70 - 1.81: 155 Bond restraints: 25097 Sorted by residual: bond pdb=" CA ASP D 614 " pdb=" CB ASP D 614 " ideal model delta sigma weight residual 1.527 1.472 0.055 2.48e-02 1.63e+03 5.00e+00 bond pdb=" CG GLU B 626 " pdb=" CD GLU B 626 " ideal model delta sigma weight residual 1.516 1.470 0.046 2.50e-02 1.60e+03 3.46e+00 bond pdb=" CA ARG C 585 " pdb=" CB ARG C 585 " ideal model delta sigma weight residual 1.523 1.500 0.023 1.27e-02 6.20e+03 3.33e+00 bond pdb=" C LYS D 605 " pdb=" N GLU D 606 " ideal model delta sigma weight residual 1.334 1.308 0.026 1.43e-02 4.89e+03 3.27e+00 bond pdb=" O3B ATP C1401 " pdb=" PB ATP C1401 " ideal model delta sigma weight residual 1.592 1.539 0.053 3.00e-02 1.11e+03 3.14e+00 ... (remaining 25092 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 33264 2.49 - 4.98: 689 4.98 - 7.47: 63 7.47 - 9.97: 9 9.97 - 12.46: 3 Bond angle restraints: 34028 Sorted by residual: angle pdb=" N VAL C 907 " pdb=" CA VAL C 907 " pdb=" C VAL C 907 " ideal model delta sigma weight residual 111.90 107.88 4.02 8.10e-01 1.52e+00 2.47e+01 angle pdb=" N VAL B 864 " pdb=" CA VAL B 864 " pdb=" C VAL B 864 " ideal model delta sigma weight residual 113.42 108.12 5.30 1.17e+00 7.31e-01 2.05e+01 angle pdb=" N THR C1373 " pdb=" CA THR C1373 " pdb=" C THR C1373 " ideal model delta sigma weight residual 113.38 108.18 5.20 1.17e+00 7.31e-01 1.98e+01 angle pdb=" N LEU F 431 " pdb=" CA LEU F 431 " pdb=" C LEU F 431 " ideal model delta sigma weight residual 113.21 108.37 4.84 1.15e+00 7.56e-01 1.77e+01 angle pdb=" N THR E 474 " pdb=" CA THR E 474 " pdb=" C THR E 474 " ideal model delta sigma weight residual 113.18 107.65 5.53 1.33e+00 5.65e-01 1.73e+01 ... (remaining 34023 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.40: 14579 26.40 - 52.81: 759 52.81 - 79.21: 92 79.21 - 105.61: 14 105.61 - 132.02: 3 Dihedral angle restraints: 15447 sinusoidal: 6479 harmonic: 8968 Sorted by residual: dihedral pdb=" O2A ADP A1301 " pdb=" O3A ADP A1301 " pdb=" PA ADP A1301 " pdb=" PB ADP A1301 " ideal model delta sinusoidal sigma weight residual -60.00 72.02 -132.02 1 2.00e+01 2.50e-03 4.01e+01 dihedral pdb=" C5' ADP A1301 " pdb=" O5' ADP A1301 " pdb=" PA ADP A1301 " pdb=" O2A ADP A1301 " ideal model delta sinusoidal sigma weight residual -60.00 61.87 -121.87 1 2.00e+01 2.50e-03 3.67e+01 dihedral pdb=" O1B ADP A1301 " pdb=" O3A ADP A1301 " pdb=" PB ADP A1301 " pdb=" PA ADP A1301 " ideal model delta sinusoidal sigma weight residual -60.00 -176.58 116.58 1 2.00e+01 2.50e-03 3.47e+01 ... (remaining 15444 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2875 0.051 - 0.103: 801 0.103 - 0.154: 145 0.154 - 0.206: 11 0.206 - 0.257: 4 Chirality restraints: 3836 Sorted by residual: chirality pdb=" CA GLU B 625 " pdb=" N GLU B 625 " pdb=" C GLU B 625 " pdb=" CB GLU B 625 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CG LEU F 910 " pdb=" CB LEU F 910 " pdb=" CD1 LEU F 910 " pdb=" CD2 LEU F 910 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CB ILE A 912 " pdb=" CA ILE A 912 " pdb=" CG1 ILE A 912 " pdb=" CG2 ILE A 912 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 3833 not shown) Planarity restraints: 4361 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D 586 " 0.068 5.00e-02 4.00e+02 1.03e-01 1.69e+01 pdb=" N PRO D 587 " -0.178 5.00e-02 4.00e+02 pdb=" CA PRO D 587 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO D 587 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 524 " -0.055 5.00e-02 4.00e+02 8.45e-02 1.14e+01 pdb=" N PRO A 525 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO A 525 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 525 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 575 " 0.015 2.00e-02 2.50e+03 3.07e-02 9.45e+00 pdb=" CG ASN D 575 " -0.053 2.00e-02 2.50e+03 pdb=" OD1 ASN D 575 " 0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN D 575 " 0.018 2.00e-02 2.50e+03 ... (remaining 4358 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 550 2.66 - 3.22: 25041 3.22 - 3.78: 36913 3.78 - 4.34: 48747 4.34 - 4.90: 75769 Nonbonded interactions: 187020 Sorted by model distance: nonbonded pdb=" OD2 ASP C 668 " pdb=" OG SER C 670 " model vdw 2.100 3.040 nonbonded pdb=" OG SER E 690 " pdb=" OE1 GLN E 691 " model vdw 2.114 3.040 nonbonded pdb=" OE2 GLU E 440 " pdb=" OH TYR F 659 " model vdw 2.126 3.040 nonbonded pdb=" O ASP A 638 " pdb=" OG SER A 641 " model vdw 2.137 3.040 nonbonded pdb=" O GLU B1384 " pdb=" OG SER B1387 " model vdw 2.147 3.040 ... (remaining 187015 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 923)) selection = (chain 'F' and (resid 422 through 539 or resid 546 through 659 or resid 666 thro \ ugh 727 or resid 787 through 923)) } ncs_group { reference = (chain 'B' and (resid 422 through 690 or resid 692 through 693 or resid 697 thro \ ugh 727 or resid 786 through 945 or resid 1330 through 1389)) selection = (chain 'C' and (resid 422 through 693 or resid 697 through 1389)) selection = (chain 'D' and (resid 422 through 690 or resid 692 through 693 or resid 697 thro \ ugh 727 or resid 786 through 1389)) selection = (chain 'E' and (resid 422 through 690 or resid 692 through 693 or resid 697 thro \ ugh 727 or resid 786 through 1389)) } 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: 3.000 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: 0.000 Extract box with map and model: 0.560 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 51.760 Find NCS groups from input model: 1.890 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: 60.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6409 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 : 0.009 0.852 25108 Z= 0.784 Angle : 0.863 12.456 34028 Z= 0.477 Chirality : 0.048 0.257 3836 Planarity : 0.006 0.103 4361 Dihedral : 15.362 132.018 9597 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 19.63 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.71 % Favored : 91.16 % Rotamer: Outliers : 0.15 % Allowed : 0.71 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.03 % Cis-general : 0.35 % 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: -1.58 (0.15), residues: 3019 helix: -0.52 (0.14), residues: 1320 sheet: -0.54 (0.28), residues: 330 loop : -1.66 (0.17), residues: 1369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 865 HIS 0.009 0.002 HIS A 815 PHE 0.049 0.002 PHE F 877 TYR 0.018 0.002 TYR C 634 ARG 0.013 0.001 ARG F 913 Details of bonding type rmsd hydrogen bonds : bond 0.19504 ( 940) hydrogen bonds : angle 7.65249 ( 2694) covalent geometry : bond 0.00523 (25097) covalent geometry : angle 0.86317 (34028) Misc. bond : bond 0.35533 ( 11) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 2695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 542 time to evaluate : 2.824 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 523 MET cc_start: 0.2705 (tpp) cc_final: 0.0864 (mmt) REVERT: D 426 ASP cc_start: 0.8506 (p0) cc_final: 0.8237 (p0) REVERT: D 523 MET cc_start: 0.7300 (mpp) cc_final: 0.6979 (mtt) REVERT: D 530 PHE cc_start: 0.8345 (m-80) cc_final: 0.7980 (m-80) REVERT: D 559 MET cc_start: 0.7050 (ttm) cc_final: 0.6826 (mtp) REVERT: E 438 LEU cc_start: 0.8453 (pp) cc_final: 0.8250 (tt) REVERT: E 495 MET cc_start: 0.7396 (ppp) cc_final: 0.6865 (ppp) REVERT: F 615 TRP cc_start: 0.3799 (m-10) cc_final: 0.3314 (m-10) REVERT: F 721 GLN cc_start: 0.5393 (mp10) cc_final: 0.4722 (tp-100) REVERT: F 913 ARG cc_start: 0.0042 (tpt170) cc_final: -0.0184 (ptm-80) outliers start: 4 outliers final: 1 residues processed: 545 average time/residue: 0.4256 time to fit residues: 339.6293 Evaluate side-chains 259 residues out of total 2695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 258 time to evaluate : 2.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 255 optimal weight: 0.0670 chunk 229 optimal weight: 5.9990 chunk 127 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 154 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 237 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 144 optimal weight: 1.9990 chunk 176 optimal weight: 3.9990 chunk 275 optimal weight: 0.0010 overall best weight: 0.7928 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 434 HIS A 458 GLN A 512 GLN A 548 HIS A 908 GLN B 808 HIS C 512 GLN C1385 ASN D 691 GLN ** D 863 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 519 GLN E 815 HIS F 883 ASN F 922 GLN ** F1377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.146249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.110178 restraints weight = 96962.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.107748 restraints weight = 69505.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.108202 restraints weight = 63473.483| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 25108 Z= 0.151 Angle : 0.724 10.529 34028 Z= 0.366 Chirality : 0.046 0.275 3836 Planarity : 0.005 0.085 4361 Dihedral : 10.118 116.803 3486 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.15 % Favored : 92.71 % Rotamer: Outliers : 0.33 % Allowed : 5.31 % Favored : 94.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.03 % Cis-general : 0.35 % 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: -1.32 (0.15), residues: 3019 helix: -0.28 (0.14), residues: 1341 sheet: -0.25 (0.29), residues: 323 loop : -1.60 (0.17), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 505 HIS 0.011 0.001 HIS F 861 PHE 0.039 0.002 PHE F 877 TYR 0.021 0.001 TYR F 634 ARG 0.014 0.001 ARG F 654 Details of bonding type rmsd hydrogen bonds : bond 0.05377 ( 940) hydrogen bonds : angle 5.81069 ( 2694) covalent geometry : bond 0.00323 (25097) covalent geometry : angle 0.72364 (34028) Misc. bond : bond 0.00392 ( 11) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 383 time to evaluate : 2.596 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 441 MET cc_start: 0.5836 (OUTLIER) cc_final: 0.5060 (mmt) REVERT: A 523 MET cc_start: 0.3043 (tpp) cc_final: 0.1714 (mmt) REVERT: A 677 LYS cc_start: 0.5755 (tppt) cc_final: 0.5537 (tptp) REVERT: A 686 MET cc_start: -0.0958 (mtp) cc_final: -0.1709 (tpp) REVERT: B 488 ASP cc_start: 0.7379 (p0) cc_final: 0.6459 (t70) REVERT: B 808 HIS cc_start: 0.7332 (m90) cc_final: 0.7122 (m-70) REVERT: B 928 GLU cc_start: 0.7516 (mt-10) cc_final: 0.7306 (mt-10) REVERT: B 931 LYS cc_start: 0.7248 (mtpp) cc_final: 0.6891 (ptmt) REVERT: C 686 MET cc_start: 0.7783 (mmm) cc_final: 0.7157 (tpt) REVERT: C 1379 MET cc_start: 0.9114 (tpp) cc_final: 0.8903 (mmm) REVERT: D 559 MET cc_start: 0.7966 (ttm) cc_final: 0.7676 (mtp) REVERT: D 818 GLU cc_start: 0.7299 (pm20) cc_final: 0.6974 (pm20) REVERT: D 851 ARG cc_start: 0.8408 (ttp-110) cc_final: 0.7896 (ttp-110) REVERT: E 678 ASP cc_start: 0.7378 (m-30) cc_final: 0.6374 (t70) REVERT: E 680 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7682 (mp0) REVERT: E 1380 GLU cc_start: 0.8853 (OUTLIER) cc_final: 0.8471 (pp20) REVERT: F 559 MET cc_start: 0.5117 (tpt) cc_final: 0.3579 (ptt) REVERT: F 627 LEU cc_start: 0.8070 (tt) cc_final: 0.7660 (tt) REVERT: F 721 GLN cc_start: 0.7069 (mp10) cc_final: 0.5964 (tp-100) outliers start: 9 outliers final: 2 residues processed: 386 average time/residue: 0.3576 time to fit residues: 213.5770 Evaluate side-chains 257 residues out of total 2695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 252 time to evaluate : 2.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 23 optimal weight: 5.9990 chunk 172 optimal weight: 3.9990 chunk 283 optimal weight: 50.0000 chunk 75 optimal weight: 0.8980 chunk 1 optimal weight: 0.2980 chunk 302 optimal weight: 8.9990 chunk 79 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 281 optimal weight: 0.6980 chunk 214 optimal weight: 6.9990 chunk 192 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 GLN A 512 GLN A 908 GLN D 482 ASN D 691 GLN ** D 863 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 815 HIS F1351 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.145271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.110925 restraints weight = 98179.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.107326 restraints weight = 71886.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.107215 restraints weight = 68018.557| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25108 Z= 0.144 Angle : 0.688 10.371 34028 Z= 0.345 Chirality : 0.045 0.267 3836 Planarity : 0.005 0.083 4361 Dihedral : 9.666 106.920 3486 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.35 % Favored : 92.55 % Rotamer: Outliers : 0.11 % Allowed : 4.12 % Favored : 95.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.03 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.23 (0.15), residues: 3019 helix: -0.25 (0.14), residues: 1355 sheet: -0.23 (0.29), residues: 328 loop : -1.51 (0.18), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 865 HIS 0.009 0.001 HIS F 861 PHE 0.037 0.001 PHE F 877 TYR 0.013 0.001 TYR D 655 ARG 0.011 0.001 ARG B 604 Details of bonding type rmsd hydrogen bonds : bond 0.04508 ( 940) hydrogen bonds : angle 5.53696 ( 2694) covalent geometry : bond 0.00313 (25097) covalent geometry : angle 0.68807 (34028) Misc. bond : bond 0.00212 ( 11) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 331 time to evaluate : 2.631 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: A 441 MET cc_start: 0.6351 (mtt) cc_final: 0.5745 (mmt) REVERT: A 493 PHE cc_start: 0.4998 (m-10) cc_final: 0.4294 (m-10) REVERT: A 523 MET cc_start: 0.3395 (tpp) cc_final: 0.2071 (mmt) REVERT: A 677 LYS cc_start: 0.5719 (tppt) cc_final: 0.5505 (tptt) REVERT: A 686 MET cc_start: -0.0279 (mtp) cc_final: -0.1297 (tpp) REVERT: B 797 ILE cc_start: 0.8333 (mm) cc_final: 0.8122 (mm) REVERT: B 808 HIS cc_start: 0.7284 (m90) cc_final: 0.7041 (m-70) REVERT: B 878 THR cc_start: 0.8749 (m) cc_final: 0.8485 (p) REVERT: B 919 PHE cc_start: 0.7661 (t80) cc_final: 0.7184 (t80) REVERT: B 927 GLU cc_start: 0.7062 (tm-30) cc_final: 0.6749 (tm-30) REVERT: B 931 LYS cc_start: 0.7228 (mtpp) cc_final: 0.6871 (ptmt) REVERT: C 686 MET cc_start: 0.7687 (mmm) cc_final: 0.7043 (tpt) REVERT: C 1379 MET cc_start: 0.9135 (tpp) cc_final: 0.8915 (mmm) REVERT: D 559 MET cc_start: 0.7955 (ttm) cc_final: 0.7585 (mtp) REVERT: D 818 GLU cc_start: 0.7709 (pm20) cc_final: 0.7158 (pm20) REVERT: E 680 GLU cc_start: 0.8182 (mp0) cc_final: 0.7850 (mp0) REVERT: E 820 PHE cc_start: 0.7366 (m-80) cc_final: 0.7032 (m-80) REVERT: E 1384 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8204 (pp20) REVERT: F 442 VAL cc_start: 0.7001 (t) cc_final: 0.6795 (t) REVERT: F 559 MET cc_start: 0.4787 (tpt) cc_final: 0.3326 (ptt) REVERT: F 615 TRP cc_start: 0.2653 (m-10) cc_final: 0.2450 (m-10) REVERT: F 721 GLN cc_start: 0.6902 (mp10) cc_final: 0.5800 (tp-100) REVERT: F 911 PHE cc_start: 0.0986 (p90) cc_final: -0.0842 (p90) REVERT: F 913 ARG cc_start: 0.1958 (tpt170) cc_final: 0.0748 (mtm-85) outliers start: 3 outliers final: 0 residues processed: 333 average time/residue: 0.3570 time to fit residues: 185.1858 Evaluate side-chains 245 residues out of total 2695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 244 time to evaluate : 2.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 301 optimal weight: 0.0970 chunk 218 optimal weight: 4.9990 chunk 207 optimal weight: 0.0670 chunk 167 optimal weight: 0.6980 chunk 143 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 246 optimal weight: 1.9990 overall best weight: 1.1720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 GLN A 512 GLN B 616 ASN D 691 GLN ** D 863 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1330 HIS E 699 GLN E 815 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.144940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.110643 restraints weight = 99223.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.108074 restraints weight = 74953.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.108082 restraints weight = 67150.887| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25108 Z= 0.136 Angle : 0.671 11.733 34028 Z= 0.334 Chirality : 0.045 0.251 3836 Planarity : 0.005 0.078 4361 Dihedral : 9.306 95.044 3486 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.42 % Favored : 92.45 % Rotamer: Outliers : 0.11 % Allowed : 3.38 % Favored : 96.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.03 % Cis-general : 0.35 % 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: -1.08 (0.16), residues: 3019 helix: -0.11 (0.14), residues: 1350 sheet: -0.07 (0.29), residues: 332 loop : -1.47 (0.18), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 505 HIS 0.009 0.001 HIS F 861 PHE 0.031 0.001 PHE F 877 TYR 0.013 0.001 TYR D 915 ARG 0.006 0.000 ARG B1332 Details of bonding type rmsd hydrogen bonds : bond 0.04192 ( 940) hydrogen bonds : angle 5.25723 ( 2694) covalent geometry : bond 0.00301 (25097) covalent geometry : angle 0.67135 (34028) Misc. bond : bond 0.00262 ( 11) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 320 time to evaluate : 2.701 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 441 MET cc_start: 0.6663 (mtt) cc_final: 0.6211 (mmt) REVERT: A 493 PHE cc_start: 0.4835 (m-10) cc_final: 0.4400 (m-10) REVERT: A 523 MET cc_start: 0.4163 (tpp) cc_final: 0.2873 (mmt) REVERT: A 686 MET cc_start: -0.0014 (mtp) cc_final: -0.1229 (tpp) REVERT: B 878 THR cc_start: 0.8784 (m) cc_final: 0.8557 (p) REVERT: B 919 PHE cc_start: 0.7841 (t80) cc_final: 0.7130 (t80) REVERT: B 927 GLU cc_start: 0.7124 (tm-30) cc_final: 0.6843 (tm-30) REVERT: B 931 LYS cc_start: 0.7230 (mtpp) cc_final: 0.6909 (ptmt) REVERT: C 626 GLU cc_start: 0.7467 (tp30) cc_final: 0.7255 (tp30) REVERT: C 686 MET cc_start: 0.7514 (mmm) cc_final: 0.6918 (tpt) REVERT: C 851 ARG cc_start: 0.8578 (ttp-170) cc_final: 0.8337 (tmm-80) REVERT: D 559 MET cc_start: 0.8111 (ttm) cc_final: 0.7827 (mtp) REVERT: D 818 GLU cc_start: 0.7638 (pm20) cc_final: 0.7194 (pm20) REVERT: E 497 LYS cc_start: 0.7931 (mmtm) cc_final: 0.7558 (mmtm) REVERT: E 680 GLU cc_start: 0.7972 (mp0) cc_final: 0.7625 (mp0) REVERT: E 686 MET cc_start: 0.6285 (mmp) cc_final: 0.6035 (mmp) REVERT: F 460 PRO cc_start: 0.4018 (Cg_exo) cc_final: 0.3772 (Cg_endo) REVERT: F 497 LYS cc_start: 0.7160 (mppt) cc_final: 0.6803 (mmmm) REVERT: F 517 PHE cc_start: 0.6516 (m-10) cc_final: 0.6258 (m-10) REVERT: F 559 MET cc_start: 0.4686 (tpt) cc_final: 0.3359 (ptt) REVERT: F 615 TRP cc_start: 0.2483 (m-10) cc_final: 0.2248 (m-10) REVERT: F 721 GLN cc_start: 0.6829 (mp10) cc_final: 0.5741 (tp40) REVERT: F 808 HIS cc_start: 0.2082 (m170) cc_final: 0.0528 (m-70) REVERT: F 820 PHE cc_start: 0.4734 (m-80) cc_final: 0.4108 (m-80) outliers start: 3 outliers final: 0 residues processed: 323 average time/residue: 0.3668 time to fit residues: 182.4022 Evaluate side-chains 242 residues out of total 2695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 2.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 159 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 84 optimal weight: 7.9990 chunk 243 optimal weight: 7.9990 chunk 224 optimal weight: 5.9990 chunk 227 optimal weight: 0.6980 chunk 232 optimal weight: 9.9990 chunk 282 optimal weight: 20.0000 chunk 161 optimal weight: 0.9980 chunk 261 optimal weight: 9.9990 chunk 229 optimal weight: 2.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 GLN A 512 GLN D 548 HIS D 691 GLN ** D 863 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 726 HIS E 815 HIS ** E1381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 863 HIS ** 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 = 0.4246 r_free = 0.4246 target = 0.142803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.108239 restraints weight = 98237.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.103963 restraints weight = 80823.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.104156 restraints weight = 71486.411| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 25108 Z= 0.160 Angle : 0.693 10.122 34028 Z= 0.349 Chirality : 0.045 0.259 3836 Planarity : 0.005 0.068 4361 Dihedral : 9.119 88.304 3486 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.55 % Favored : 92.35 % Rotamer: Outliers : 0.15 % Allowed : 3.30 % Favored : 96.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.03 % Cis-general : 0.35 % 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: -1.14 (0.15), residues: 3019 helix: -0.12 (0.14), residues: 1358 sheet: -0.29 (0.30), residues: 325 loop : -1.48 (0.18), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 615 HIS 0.007 0.001 HIS F 861 PHE 0.037 0.002 PHE F 877 TYR 0.020 0.002 TYR A 521 ARG 0.012 0.001 ARG E 540 Details of bonding type rmsd hydrogen bonds : bond 0.04168 ( 940) hydrogen bonds : angle 5.19205 ( 2694) covalent geometry : bond 0.00355 (25097) covalent geometry : angle 0.69314 (34028) Misc. bond : bond 0.00448 ( 11) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 308 time to evaluate : 2.773 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: A 441 MET cc_start: 0.6416 (mtt) cc_final: 0.5886 (mmt) REVERT: A 458 GLN cc_start: -0.2395 (OUTLIER) cc_final: -0.2771 (tt0) REVERT: A 493 PHE cc_start: 0.5212 (m-10) cc_final: 0.4759 (m-10) REVERT: A 523 MET cc_start: 0.5012 (tpp) cc_final: 0.3681 (mmt) REVERT: A 686 MET cc_start: 0.0291 (mtp) cc_final: -0.0877 (tpp) REVERT: B 581 ASP cc_start: 0.8207 (t0) cc_final: 0.7941 (m-30) REVERT: B 919 PHE cc_start: 0.7811 (t80) cc_final: 0.7055 (t80) REVERT: C 626 GLU cc_start: 0.7899 (tp30) cc_final: 0.7552 (tp30) REVERT: C 686 MET cc_start: 0.7744 (mmm) cc_final: 0.6977 (tpt) REVERT: C 851 ARG cc_start: 0.8665 (ttp-170) cc_final: 0.8464 (tmm-80) REVERT: C 1367 ARG cc_start: 0.6449 (ptt180) cc_final: 0.5801 (ptp90) REVERT: D 515 LEU cc_start: 0.9186 (tp) cc_final: 0.8960 (tp) REVERT: D 818 GLU cc_start: 0.7691 (pm20) cc_final: 0.7368 (pm20) REVERT: E 497 LYS cc_start: 0.7885 (mmtm) cc_final: 0.7590 (mmtp) REVERT: E 789 MET cc_start: 0.6986 (tpp) cc_final: 0.6651 (tpp) REVERT: E 820 PHE cc_start: 0.7416 (m-80) cc_final: 0.6998 (m-80) REVERT: E 1380 GLU cc_start: 0.8977 (OUTLIER) cc_final: 0.8474 (pp20) REVERT: F 460 PRO cc_start: 0.3949 (Cg_exo) cc_final: 0.3741 (Cg_endo) REVERT: F 517 PHE cc_start: 0.6444 (m-10) cc_final: 0.6156 (m-10) REVERT: F 559 MET cc_start: 0.4887 (tpt) cc_final: 0.3491 (ptt) REVERT: F 615 TRP cc_start: 0.2912 (m-10) cc_final: 0.2666 (m-10) REVERT: F 721 GLN cc_start: 0.6774 (mp10) cc_final: 0.5649 (tp40) REVERT: F 808 HIS cc_start: 0.1785 (m170) cc_final: 0.0459 (m-70) outliers start: 4 outliers final: 2 residues processed: 312 average time/residue: 0.3607 time to fit residues: 174.7919 Evaluate side-chains 234 residues out of total 2695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 230 time to evaluate : 2.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 135 optimal weight: 0.0070 chunk 296 optimal weight: 7.9990 chunk 225 optimal weight: 0.8980 chunk 226 optimal weight: 3.9990 chunk 27 optimal weight: 20.0000 chunk 249 optimal weight: 0.7980 chunk 263 optimal weight: 6.9990 chunk 302 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 chunk 267 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 512 GLN B 844 GLN D 691 GLN D 863 HIS ** E1381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 863 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 882 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.143985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.110185 restraints weight = 97880.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.106771 restraints weight = 74255.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.107344 restraints weight = 69540.174| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25108 Z= 0.131 Angle : 0.674 9.960 34028 Z= 0.335 Chirality : 0.045 0.282 3836 Planarity : 0.005 0.070 4361 Dihedral : 8.852 85.744 3486 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.52 % Favored : 92.41 % Rotamer: Outliers : 0.04 % Allowed : 2.60 % Favored : 97.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.03 % Cis-general : 0.35 % 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: -0.95 (0.16), residues: 3019 helix: 0.03 (0.14), residues: 1345 sheet: -0.18 (0.30), residues: 320 loop : -1.37 (0.18), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 865 HIS 0.007 0.001 HIS F 611 PHE 0.038 0.001 PHE B 933 TYR 0.016 0.001 TYR B 823 ARG 0.011 0.000 ARG B 604 Details of bonding type rmsd hydrogen bonds : bond 0.03893 ( 940) hydrogen bonds : angle 5.06914 ( 2694) covalent geometry : bond 0.00290 (25097) covalent geometry : angle 0.67403 (34028) Misc. bond : bond 0.00397 ( 11) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 311 time to evaluate : 2.671 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: A 441 MET cc_start: 0.6405 (mtt) cc_final: 0.5823 (mmt) REVERT: A 493 PHE cc_start: 0.5262 (m-10) cc_final: 0.4900 (m-10) REVERT: A 523 MET cc_start: 0.4865 (tpp) cc_final: 0.3617 (mmt) REVERT: A 686 MET cc_start: 0.0216 (mtp) cc_final: -0.0965 (tpp) REVERT: A 789 MET cc_start: -0.0606 (ppp) cc_final: -0.1230 (mmt) REVERT: A 794 ARG cc_start: 0.6197 (mtm110) cc_final: 0.5490 (mmm-85) REVERT: B 919 PHE cc_start: 0.7841 (t80) cc_final: 0.7111 (t80) REVERT: C 686 MET cc_start: 0.7700 (mmm) cc_final: 0.7103 (tpt) REVERT: D 515 LEU cc_start: 0.9167 (tp) cc_final: 0.8957 (tp) REVERT: D 531 ASP cc_start: 0.8570 (t0) cc_final: 0.8271 (p0) REVERT: D 559 MET cc_start: 0.8318 (ttm) cc_final: 0.7817 (mtp) REVERT: D 818 GLU cc_start: 0.7533 (pm20) cc_final: 0.7163 (pm20) REVERT: E 576 ARG cc_start: 0.7230 (mtm110) cc_final: 0.6973 (ttm170) REVERT: E 680 GLU cc_start: 0.8025 (mp0) cc_final: 0.7443 (mp0) REVERT: E 789 MET cc_start: 0.6874 (tpp) cc_final: 0.6509 (tpp) REVERT: E 820 PHE cc_start: 0.7572 (m-80) cc_final: 0.7265 (m-80) REVERT: F 460 PRO cc_start: 0.4062 (Cg_exo) cc_final: 0.3810 (Cg_endo) REVERT: F 497 LYS cc_start: 0.7022 (mppt) cc_final: 0.6634 (mttt) REVERT: F 517 PHE cc_start: 0.6148 (m-10) cc_final: 0.5877 (m-10) REVERT: F 559 MET cc_start: 0.4827 (tpt) cc_final: 0.3464 (ptt) REVERT: F 615 TRP cc_start: 0.3082 (m-10) cc_final: 0.2832 (m-10) REVERT: F 808 HIS cc_start: 0.1869 (m170) cc_final: 0.0648 (m-70) outliers start: 1 outliers final: 0 residues processed: 312 average time/residue: 0.3577 time to fit residues: 173.5465 Evaluate side-chains 233 residues out of total 2695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 3.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 112 optimal weight: 0.9990 chunk 57 optimal weight: 10.0000 chunk 129 optimal weight: 4.9990 chunk 206 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 6 optimal weight: 8.9990 chunk 98 optimal weight: 0.7980 chunk 173 optimal weight: 0.9980 chunk 281 optimal weight: 9.9990 chunk 168 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 512 GLN B 657 GLN D 691 GLN F 882 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.144404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.120108 restraints weight = 109058.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.117277 restraints weight = 148750.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.117655 restraints weight = 109287.316| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.4596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25108 Z= 0.137 Angle : 0.675 11.344 34028 Z= 0.335 Chirality : 0.045 0.238 3836 Planarity : 0.005 0.071 4361 Dihedral : 8.614 83.570 3486 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.45 % Favored : 92.45 % Rotamer: Outliers : 0.04 % Allowed : 1.82 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.03 % Cis-general : 0.35 % 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 (0.16), residues: 3019 helix: 0.04 (0.14), residues: 1358 sheet: -0.24 (0.30), residues: 322 loop : -1.35 (0.18), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 865 HIS 0.007 0.001 HIS F 611 PHE 0.034 0.001 PHE F 877 TYR 0.024 0.001 TYR D 915 ARG 0.009 0.000 ARG E 496 Details of bonding type rmsd hydrogen bonds : bond 0.03880 ( 940) hydrogen bonds : angle 5.01782 ( 2694) covalent geometry : bond 0.00308 (25097) covalent geometry : angle 0.67547 (34028) Misc. bond : bond 0.00282 ( 11) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 307 time to evaluate : 2.577 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: A 441 MET cc_start: 0.6608 (mtt) cc_final: 0.5821 (mmt) REVERT: A 523 MET cc_start: 0.5302 (tpp) cc_final: 0.3534 (mmt) REVERT: A 789 MET cc_start: 0.0153 (ppp) cc_final: -0.2035 (mmt) REVERT: A 794 ARG cc_start: 0.6006 (mtm110) cc_final: 0.5759 (mmm-85) REVERT: A 831 PHE cc_start: 0.3878 (m-10) cc_final: 0.3585 (m-80) REVERT: B 808 HIS cc_start: 0.6803 (m90) cc_final: 0.6526 (m-70) REVERT: B 823 TYR cc_start: 0.6278 (m-80) cc_final: 0.5468 (m-80) REVERT: B 919 PHE cc_start: 0.7242 (t80) cc_final: 0.6625 (t80) REVERT: C 686 MET cc_start: 0.7514 (mmm) cc_final: 0.6968 (tpt) REVERT: D 515 LEU cc_start: 0.9159 (tp) cc_final: 0.8940 (tp) REVERT: E 497 LYS cc_start: 0.8555 (tptm) cc_final: 0.8312 (tptm) REVERT: F 460 PRO cc_start: 0.4066 (Cg_exo) cc_final: 0.3782 (Cg_endo) REVERT: F 497 LYS cc_start: 0.7299 (mppt) cc_final: 0.6842 (mttt) REVERT: F 517 PHE cc_start: 0.5826 (m-10) cc_final: 0.5507 (m-10) REVERT: F 559 MET cc_start: 0.5390 (tpt) cc_final: 0.3818 (ptt) REVERT: F 615 TRP cc_start: 0.3853 (m-10) cc_final: 0.3469 (m-10) REVERT: F 808 HIS cc_start: 0.1589 (m170) cc_final: 0.0302 (m-70) outliers start: 1 outliers final: 1 residues processed: 308 average time/residue: 0.3387 time to fit residues: 165.9455 Evaluate side-chains 224 residues out of total 2695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 223 time to evaluate : 2.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 159 optimal weight: 0.7980 chunk 282 optimal weight: 20.0000 chunk 68 optimal weight: 7.9990 chunk 158 optimal weight: 2.9990 chunk 208 optimal weight: 2.9990 chunk 201 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 92 optimal weight: 6.9990 chunk 273 optimal weight: 5.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 512 GLN ** C1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 611 HIS D 691 GLN ** F 863 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.140021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.105856 restraints weight = 99800.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.101067 restraints weight = 83679.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.101100 restraints weight = 77506.976| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.4962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 25108 Z= 0.212 Angle : 0.761 11.689 34028 Z= 0.382 Chirality : 0.047 0.210 3836 Planarity : 0.005 0.078 4361 Dihedral : 8.820 88.736 3486 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.02 % Favored : 91.88 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.03 % Cis-general : 0.35 % 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: -1.22 (0.15), residues: 3019 helix: -0.17 (0.14), residues: 1358 sheet: -0.58 (0.29), residues: 326 loop : -1.47 (0.18), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 865 HIS 0.007 0.001 HIS F 611 PHE 0.030 0.002 PHE F 877 TYR 0.017 0.002 TYR F1364 ARG 0.009 0.001 ARG F 913 Details of bonding type rmsd hydrogen bonds : bond 0.04467 ( 940) hydrogen bonds : angle 5.32550 ( 2694) covalent geometry : bond 0.00476 (25097) covalent geometry : angle 0.76101 (34028) Misc. bond : bond 0.00645 ( 11) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 2.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 493 PHE cc_start: 0.4523 (m-10) cc_final: 0.4038 (m-10) REVERT: A 523 MET cc_start: 0.4918 (tpp) cc_final: 0.3922 (mmt) REVERT: A 794 ARG cc_start: 0.6216 (mtm110) cc_final: 0.5408 (mmm-85) REVERT: B 823 TYR cc_start: 0.6308 (m-80) cc_final: 0.5366 (m-80) REVERT: B 919 PHE cc_start: 0.7771 (t80) cc_final: 0.7060 (t80) REVERT: C 686 MET cc_start: 0.7778 (mmm) cc_final: 0.7126 (tpt) REVERT: C 880 LEU cc_start: 0.9240 (tp) cc_final: 0.9031 (tp) REVERT: D 515 LEU cc_start: 0.9179 (tp) cc_final: 0.8954 (tp) REVERT: E 680 GLU cc_start: 0.7985 (mp0) cc_final: 0.7223 (mp0) REVERT: E 818 GLU cc_start: 0.7273 (pm20) cc_final: 0.6956 (pm20) REVERT: E 820 PHE cc_start: 0.7383 (m-80) cc_final: 0.7101 (m-80) REVERT: F 460 PRO cc_start: 0.3899 (Cg_exo) cc_final: 0.3655 (Cg_endo) REVERT: F 497 LYS cc_start: 0.6761 (mppt) cc_final: 0.6354 (mmtp) REVERT: F 559 MET cc_start: 0.5266 (tpt) cc_final: 0.4111 (ptt) REVERT: F 615 TRP cc_start: 0.3051 (m-10) cc_final: 0.2822 (m-10) REVERT: F 808 HIS cc_start: 0.1588 (m170) cc_final: 0.0488 (m-70) REVERT: F 920 ASN cc_start: 0.7771 (p0) cc_final: 0.7414 (m-40) outliers start: 0 outliers final: 0 residues processed: 286 average time/residue: 0.3297 time to fit residues: 151.8091 Evaluate side-chains 206 residues out of total 2695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 2.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 257 optimal weight: 5.9990 chunk 31 optimal weight: 20.0000 chunk 55 optimal weight: 2.9990 chunk 291 optimal weight: 0.6980 chunk 290 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 172 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 249 optimal weight: 0.8980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 861 HIS B1366 HIS C1366 HIS D 691 GLN E1370 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.141174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.108926 restraints weight = 98205.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.105766 restraints weight = 103821.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.106047 restraints weight = 73801.837| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.5160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25108 Z= 0.153 Angle : 0.715 11.652 34028 Z= 0.356 Chirality : 0.046 0.202 3836 Planarity : 0.005 0.068 4361 Dihedral : 8.539 87.795 3486 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.62 % Favored : 92.32 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.03 % Cis-general : 0.35 % 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: -1.16 (0.15), residues: 3019 helix: -0.13 (0.14), residues: 1358 sheet: -0.54 (0.29), residues: 325 loop : -1.45 (0.18), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 865 HIS 0.010 0.001 HIS D1366 PHE 0.032 0.001 PHE F 877 TYR 0.015 0.001 TYR D1364 ARG 0.011 0.001 ARG C 613 Details of bonding type rmsd hydrogen bonds : bond 0.04108 ( 940) hydrogen bonds : angle 5.24983 ( 2694) covalent geometry : bond 0.00339 (25097) covalent geometry : angle 0.71466 (34028) Misc. bond : bond 0.00388 ( 11) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 2.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 441 MET cc_start: 0.7189 (mtm) cc_final: 0.6948 (mmt) REVERT: A 523 MET cc_start: 0.5194 (tpp) cc_final: 0.3828 (mmt) REVERT: B 823 TYR cc_start: 0.6408 (m-80) cc_final: 0.5567 (m-80) REVERT: B 919 PHE cc_start: 0.7703 (t80) cc_final: 0.7020 (t80) REVERT: C 686 MET cc_start: 0.7733 (mmm) cc_final: 0.7118 (tpt) REVERT: C 880 LEU cc_start: 0.9147 (tp) cc_final: 0.8906 (tp) REVERT: D 515 LEU cc_start: 0.9191 (tp) cc_final: 0.8912 (tp) REVERT: E 497 LYS cc_start: 0.8450 (tptm) cc_final: 0.8037 (tppt) REVERT: E 680 GLU cc_start: 0.7882 (mp0) cc_final: 0.7215 (mp0) REVERT: E 818 GLU cc_start: 0.7072 (pm20) cc_final: 0.6786 (pm20) REVERT: E 820 PHE cc_start: 0.7238 (m-80) cc_final: 0.6967 (m-80) REVERT: F 460 PRO cc_start: 0.3860 (Cg_exo) cc_final: 0.3577 (Cg_endo) REVERT: F 497 LYS cc_start: 0.7050 (mppt) cc_final: 0.6615 (mmtp) REVERT: F 615 TRP cc_start: 0.3743 (m-10) cc_final: 0.3442 (m-10) REVERT: F 808 HIS cc_start: 0.1656 (m170) cc_final: 0.0470 (m-70) REVERT: F 851 ARG cc_start: 0.5682 (tpp-160) cc_final: 0.5425 (mmp80) REVERT: F 920 ASN cc_start: 0.7927 (p0) cc_final: 0.7616 (m-40) outliers start: 0 outliers final: 0 residues processed: 279 average time/residue: 0.3564 time to fit residues: 156.4163 Evaluate side-chains 213 residues out of total 2695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 2.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 86 optimal weight: 5.9990 chunk 300 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 chunk 141 optimal weight: 0.0030 chunk 193 optimal weight: 2.9990 chunk 229 optimal weight: 0.9980 chunk 139 optimal weight: 6.9990 chunk 105 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 52 optimal weight: 8.9990 overall best weight: 1.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 512 GLN ** B 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1366 HIS D 691 GLN F 882 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.142038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.108980 restraints weight = 99301.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.104823 restraints weight = 92003.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.104828 restraints weight = 79043.854| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.5334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25108 Z= 0.135 Angle : 0.707 11.566 34028 Z= 0.349 Chirality : 0.045 0.197 3836 Planarity : 0.005 0.067 4361 Dihedral : 8.296 82.980 3486 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.59 % Favored : 92.35 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.03 % Cis-general : 0.35 % 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: -1.04 (0.16), residues: 3019 helix: -0.02 (0.14), residues: 1357 sheet: -0.46 (0.29), residues: 327 loop : -1.39 (0.18), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 865 HIS 0.009 0.001 HIS F 611 PHE 0.031 0.001 PHE F 877 TYR 0.017 0.001 TYR E1356 ARG 0.009 0.001 ARG C 613 Details of bonding type rmsd hydrogen bonds : bond 0.03900 ( 940) hydrogen bonds : angle 5.16021 ( 2694) covalent geometry : bond 0.00302 (25097) covalent geometry : angle 0.70712 (34028) Misc. bond : bond 0.00268 ( 11) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 2.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 523 MET cc_start: 0.5107 (tpp) cc_final: 0.3920 (mmt) REVERT: B 823 TYR cc_start: 0.6334 (m-80) cc_final: 0.5461 (m-80) REVERT: B 912 ILE cc_start: 0.8407 (mm) cc_final: 0.8020 (tt) REVERT: B 919 PHE cc_start: 0.7874 (t80) cc_final: 0.7163 (t80) REVERT: C 686 MET cc_start: 0.7785 (mmm) cc_final: 0.7180 (tpt) REVERT: D 515 LEU cc_start: 0.9186 (tp) cc_final: 0.8963 (tp) REVERT: E 497 LYS cc_start: 0.8404 (tptm) cc_final: 0.7992 (tppt) REVERT: E 680 GLU cc_start: 0.7963 (mp0) cc_final: 0.7293 (mp0) REVERT: E 683 MET cc_start: 0.8836 (ptp) cc_final: 0.8631 (ptp) REVERT: E 789 MET cc_start: 0.6694 (tpt) cc_final: 0.6360 (tpt) REVERT: E 818 GLU cc_start: 0.7140 (pm20) cc_final: 0.6832 (pm20) REVERT: F 460 PRO cc_start: 0.3846 (Cg_exo) cc_final: 0.3603 (Cg_endo) REVERT: F 497 LYS cc_start: 0.6844 (mppt) cc_final: 0.6406 (mmtp) REVERT: F 615 TRP cc_start: 0.3256 (m-10) cc_final: 0.3006 (m-10) REVERT: F 808 HIS cc_start: 0.1758 (m170) cc_final: 0.0650 (m-70) REVERT: F 851 ARG cc_start: 0.5452 (tpp-160) cc_final: 0.5211 (mmp80) outliers start: 0 outliers final: 0 residues processed: 281 average time/residue: 0.3368 time to fit residues: 153.1163 Evaluate side-chains 205 residues out of total 2695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 2.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 42 optimal weight: 20.0000 chunk 194 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 288 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 171 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 chunk 236 optimal weight: 5.9990 chunk 15 optimal weight: 0.6980 chunk 64 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1366 HIS C1361 GLN D 691 GLN E1370 HIS F 882 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.139746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.104012 restraints weight = 97514.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.101263 restraints weight = 76854.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.101432 restraints weight = 63158.229| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.5660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 25108 Z= 0.180 Angle : 0.742 11.603 34028 Z= 0.371 Chirality : 0.046 0.197 3836 Planarity : 0.005 0.067 4361 Dihedral : 8.424 86.904 3486 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.25 % Favored : 91.65 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.03 % Cis-general : 0.35 % 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: -1.26 (0.15), residues: 3019 helix: -0.23 (0.14), residues: 1367 sheet: -0.59 (0.29), residues: 324 loop : -1.47 (0.18), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 865 HIS 0.008 0.001 HIS F 611 PHE 0.037 0.002 PHE B 933 TYR 0.018 0.002 TYR B1356 ARG 0.009 0.001 ARG B 929 Details of bonding type rmsd hydrogen bonds : bond 0.04316 ( 940) hydrogen bonds : angle 5.26036 ( 2694) covalent geometry : bond 0.00406 (25097) covalent geometry : angle 0.74230 (34028) Misc. bond : bond 0.00301 ( 11) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7342.99 seconds wall clock time: 129 minutes 54.32 seconds (7794.32 seconds total)