Starting phenix.real_space_refine on Mon Aug 25 02:48:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8juy_36666/08_2025/8juy_36666_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8juy_36666/08_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_36666/08_2025/8juy_36666.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8juy_36666/08_2025/8juy_36666.map" model { file = "/net/cci-nas-00/data/ceres_data/8juy_36666/08_2025/8juy_36666_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8juy_36666/08_2025/8juy_36666_neut.cif" } resolution = 4.34 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 5.20, per 1000 atoms: 0.21 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: 1.76 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.49 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: 2.90 Time building geometry restraints manager: 2.19 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: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 18.350 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.030 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.330 ------------------------------------------------------------------------------- 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 : 19.71 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.013 0.001 ARG F 913 TYR 0.018 0.002 TYR C 634 PHE 0.049 0.002 PHE F 877 TRP 0.022 0.002 TRP D 865 HIS 0.009 0.002 HIS A 815 Details of bonding type rmsd covalent geometry : bond 0.00523 (25097) covalent geometry : angle 0.86317 (34028) hydrogen bonds : bond 0.19504 ( 940) hydrogen bonds : angle 7.65249 ( 2694) 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 : 0.717 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: 0.1687 time to fit residues: 135.8880 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 : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.0370 chunk 298 optimal weight: 5.9990 overall best weight: 0.8660 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.146146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.110874 restraints weight = 97846.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.107761 restraints weight = 72721.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.107874 restraints weight = 60369.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.107991 restraints weight = 53908.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.108241 restraints weight = 47142.551| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 25108 Z= 0.156 Angle : 0.732 10.518 34028 Z= 0.372 Chirality : 0.047 0.285 3836 Planarity : 0.005 0.085 4361 Dihedral : 10.147 117.570 3486 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.12 % Favored : 92.75 % Rotamer: Outliers : 0.33 % Allowed : 5.38 % Favored : 94.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.03 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.34 (0.15), residues: 3019 helix: -0.29 (0.14), residues: 1340 sheet: -0.26 (0.29), residues: 323 loop : -1.60 (0.17), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 654 TYR 0.020 0.002 TYR F 634 PHE 0.039 0.002 PHE F 877 TRP 0.017 0.002 TRP A 505 HIS 0.011 0.001 HIS F 861 Details of bonding type rmsd covalent geometry : bond 0.00336 (25097) covalent geometry : angle 0.73234 (34028) hydrogen bonds : bond 0.05293 ( 940) hydrogen bonds : angle 5.82837 ( 2694) Misc. bond : bond 0.00327 ( 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 390 residues out of total 2695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 381 time to evaluate : 0.931 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: 0.5736 (OUTLIER) cc_final: 0.4889 (mmt) REVERT: A 523 MET cc_start: 0.3024 (tpp) cc_final: 0.1708 (mmt) REVERT: A 677 LYS cc_start: 0.5722 (tppt) cc_final: 0.5502 (tptp) REVERT: A 686 MET cc_start: -0.1005 (mtp) cc_final: -0.1735 (tpp) REVERT: B 488 ASP cc_start: 0.7357 (p0) cc_final: 0.6470 (t70) REVERT: B 927 GLU cc_start: 0.6548 (tm-30) cc_final: 0.6181 (tm-30) REVERT: B 931 LYS cc_start: 0.7308 (mtpp) cc_final: 0.6946 (ptmt) REVERT: C 1379 MET cc_start: 0.9134 (tpp) cc_final: 0.8925 (mmm) REVERT: D 559 MET cc_start: 0.7863 (ttm) cc_final: 0.7534 (mtp) REVERT: D 818 GLU cc_start: 0.7610 (pm20) cc_final: 0.7074 (pm20) REVERT: E 497 LYS cc_start: 0.7794 (mmtm) cc_final: 0.7566 (mmtp) REVERT: E 678 ASP cc_start: 0.7347 (m-30) cc_final: 0.6368 (t70) REVERT: F 559 MET cc_start: 0.5147 (tpt) cc_final: 0.3624 (ptt) REVERT: F 627 LEU cc_start: 0.8067 (tt) cc_final: 0.7646 (tt) REVERT: F 721 GLN cc_start: 0.7070 (mp10) cc_final: 0.5964 (tp-100) outliers start: 9 outliers final: 2 residues processed: 384 average time/residue: 0.1516 time to fit residues: 91.0503 Evaluate side-chains 250 residues out of total 2695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 247 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 73 optimal weight: 10.0000 chunk 251 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 205 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 chunk 261 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 294 optimal weight: 3.9990 chunk 177 optimal weight: 2.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 B 808 HIS ** C 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 482 ASN D 691 GLN D 808 HIS ** D 863 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1330 HIS E 815 HIS F1351 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.145221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.111132 restraints weight = 98616.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.107463 restraints weight = 78213.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.107346 restraints weight = 71735.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.107898 restraints weight = 58202.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.107955 restraints weight = 50550.487| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.3204 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= 0.142 Angle : 0.687 10.652 34028 Z= 0.344 Chirality : 0.045 0.260 3836 Planarity : 0.005 0.082 4361 Dihedral : 9.669 106.760 3486 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.35 % Favored : 92.55 % Rotamer: Outliers : 0.19 % Allowed : 4.04 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.23 (0.15), residues: 3019 helix: -0.24 (0.14), residues: 1355 sheet: -0.28 (0.29), residues: 330 loop : -1.50 (0.18), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 604 TYR 0.014 0.001 TYR F1347 PHE 0.037 0.002 PHE F 877 TRP 0.013 0.001 TRP F 615 HIS 0.009 0.001 HIS F 861 Details of bonding type rmsd covalent geometry : bond 0.00314 (25097) covalent geometry : angle 0.68748 (34028) hydrogen bonds : bond 0.04518 ( 940) hydrogen bonds : angle 5.50490 ( 2694) Misc. bond : bond 0.00243 ( 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 340 residues out of total 2695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 335 time to evaluate : 0.699 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 414 VAL cc_start: 0.5727 (m) cc_final: 0.5376 (m) REVERT: A 441 MET cc_start: 0.6503 (mtt) cc_final: 0.5898 (mmt) REVERT: A 493 PHE cc_start: 0.4987 (m-10) cc_final: 0.4413 (m-10) REVERT: A 523 MET cc_start: 0.3411 (tpp) cc_final: 0.2055 (mmt) REVERT: A 677 LYS cc_start: 0.5763 (tppt) cc_final: 0.5521 (tptt) REVERT: A 686 MET cc_start: -0.0292 (mtp) cc_final: -0.1321 (tpp) REVERT: B 808 HIS cc_start: 0.7327 (m90) cc_final: 0.7061 (m-70) REVERT: B 878 THR cc_start: 0.8755 (m) cc_final: 0.8502 (p) REVERT: B 931 LYS cc_start: 0.7124 (mtpp) cc_final: 0.6821 (ptmt) REVERT: C 686 MET cc_start: 0.7674 (mmm) cc_final: 0.7004 (tpt) REVERT: D 818 GLU cc_start: 0.7488 (pm20) cc_final: 0.7094 (pm20) REVERT: D 935 ASP cc_start: 0.7625 (t0) cc_final: 0.7222 (t0) REVERT: E 497 LYS cc_start: 0.7859 (mmtm) cc_final: 0.7542 (mmtp) REVERT: E 820 PHE cc_start: 0.7478 (m-80) cc_final: 0.7139 (m-80) REVERT: E 1384 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8127 (pp20) REVERT: F 559 MET cc_start: 0.4962 (tpt) cc_final: 0.3489 (ptt) REVERT: F 615 TRP cc_start: 0.2626 (m-10) cc_final: 0.2385 (m-10) REVERT: F 721 GLN cc_start: 0.6866 (mp10) cc_final: 0.5760 (tp-100) REVERT: F 911 PHE cc_start: 0.0943 (p90) cc_final: -0.0787 (p90) REVERT: F 913 ARG cc_start: 0.2021 (tpt170) cc_final: 0.0779 (mtm-85) outliers start: 5 outliers final: 1 residues processed: 338 average time/residue: 0.1449 time to fit residues: 76.9527 Evaluate side-chains 247 residues out of total 2695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 245 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 133 optimal weight: 0.9990 chunk 299 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 302 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 130 optimal weight: 0.9980 chunk 214 optimal weight: 10.0000 chunk 205 optimal weight: 6.9990 chunk 290 optimal weight: 20.0000 chunk 259 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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** E 699 GLN E 815 HIS ** 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 = 0.4261 r_free = 0.4261 target = 0.144544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.110064 restraints weight = 98817.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.107836 restraints weight = 73399.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.107609 restraints weight = 63795.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.107814 restraints weight = 58805.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.108448 restraints weight = 48766.045| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.3657 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= 0.140 Angle : 0.674 10.169 34028 Z= 0.337 Chirality : 0.045 0.247 3836 Planarity : 0.005 0.078 4361 Dihedral : 9.284 92.460 3486 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.35 % Favored : 92.51 % Rotamer: Outliers : 0.15 % Allowed : 3.45 % Favored : 96.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.03 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.16), residues: 3019 helix: -0.12 (0.14), residues: 1351 sheet: -0.14 (0.29), residues: 330 loop : -1.46 (0.18), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1332 TYR 0.012 0.001 TYR D 915 PHE 0.034 0.001 PHE F 877 TRP 0.010 0.001 TRP E 866 HIS 0.009 0.001 HIS F 861 Details of bonding type rmsd covalent geometry : bond 0.00308 (25097) covalent geometry : angle 0.67448 (34028) hydrogen bonds : bond 0.04172 ( 940) hydrogen bonds : angle 5.23973 ( 2694) Misc. bond : bond 0.00551 ( 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 320 residues out of total 2695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 316 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 441 MET cc_start: 0.6583 (mtt) cc_final: 0.6115 (mmt) REVERT: A 458 GLN cc_start: -0.2807 (OUTLIER) cc_final: -0.3198 (tt0) REVERT: A 493 PHE cc_start: 0.4600 (m-10) cc_final: 0.4166 (m-10) REVERT: A 523 MET cc_start: 0.4134 (tpp) cc_final: 0.2854 (mmt) REVERT: A 686 MET cc_start: 0.0030 (mtp) cc_final: -0.1161 (tpp) REVERT: B 919 PHE cc_start: 0.7787 (t80) cc_final: 0.7098 (t80) REVERT: B 931 LYS cc_start: 0.7304 (mtpp) cc_final: 0.6816 (ptmt) REVERT: C 626 GLU cc_start: 0.7601 (tp30) cc_final: 0.7401 (tp30) REVERT: C 686 MET cc_start: 0.7536 (mmm) cc_final: 0.6855 (tpt) REVERT: D 818 GLU cc_start: 0.7578 (pm20) cc_final: 0.7120 (pm20) REVERT: E 933 PHE cc_start: 0.7899 (t80) cc_final: 0.7580 (t80) REVERT: F 442 VAL cc_start: 0.6962 (t) cc_final: 0.6667 (t) REVERT: F 460 PRO cc_start: 0.4018 (Cg_exo) cc_final: 0.3767 (Cg_endo) REVERT: F 497 LYS cc_start: 0.7123 (mppt) cc_final: 0.6776 (mmmm) REVERT: F 517 PHE cc_start: 0.6519 (m-10) cc_final: 0.6257 (m-10) REVERT: F 529 PHE cc_start: 0.4279 (t80) cc_final: 0.3664 (t80) REVERT: F 559 MET cc_start: 0.4633 (tpt) cc_final: 0.3306 (ptt) REVERT: F 615 TRP cc_start: 0.2553 (m-10) cc_final: 0.2349 (m-10) REVERT: F 721 GLN cc_start: 0.6879 (mp10) cc_final: 0.5780 (tp40) REVERT: F 808 HIS cc_start: 0.2104 (m170) cc_final: 0.0588 (m-70) REVERT: F 820 PHE cc_start: 0.4941 (m-80) cc_final: 0.4317 (m-10) outliers start: 4 outliers final: 0 residues processed: 320 average time/residue: 0.1620 time to fit residues: 81.8736 Evaluate side-chains 242 residues out of total 2695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 241 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 50 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 80 optimal weight: 10.0000 chunk 127 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 chunk 299 optimal weight: 7.9990 chunk 277 optimal weight: 5.9990 chunk 148 optimal weight: 0.0060 chunk 262 optimal weight: 0.7980 chunk 169 optimal weight: 4.9990 chunk 6 optimal weight: 20.0000 overall best weight: 2.5602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 512 GLN B 861 HIS D 544 GLN D 691 GLN ** D 863 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.141364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.106657 restraints weight = 99079.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.103190 restraints weight = 74320.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.103547 restraints weight = 68661.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.103760 restraints weight = 54489.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.103879 restraints weight = 49023.803| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.4205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 25108 Z= 0.197 Angle : 0.732 11.500 34028 Z= 0.369 Chirality : 0.046 0.262 3836 Planarity : 0.006 0.092 4361 Dihedral : 9.207 86.222 3486 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.92 % Favored : 91.98 % Rotamer: Outliers : 0.11 % Allowed : 3.41 % Favored : 96.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.03 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.25 (0.15), residues: 3019 helix: -0.22 (0.14), residues: 1358 sheet: -0.49 (0.29), residues: 327 loop : -1.49 (0.18), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 540 TYR 0.039 0.002 TYR A 521 PHE 0.036 0.002 PHE F 877 TRP 0.013 0.002 TRP E 615 HIS 0.007 0.001 HIS E 726 Details of bonding type rmsd covalent geometry : bond 0.00437 (25097) covalent geometry : angle 0.73154 (34028) hydrogen bonds : bond 0.04485 ( 940) hydrogen bonds : angle 5.26102 ( 2694) Misc. bond : bond 0.00271 ( 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 306 residues out of total 2695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 303 time to evaluate : 0.857 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: 0.6471 (mtt) cc_final: 0.5949 (mmt) REVERT: A 493 PHE cc_start: 0.4523 (m-10) cc_final: 0.4136 (m-10) REVERT: A 523 MET cc_start: 0.4748 (tpp) cc_final: 0.3580 (mmt) REVERT: A 686 MET cc_start: 0.0284 (mtp) cc_final: -0.0881 (tpp) REVERT: A 794 ARG cc_start: 0.6350 (mtm110) cc_final: 0.5438 (mmm-85) REVERT: B 919 PHE cc_start: 0.7870 (t80) cc_final: 0.7119 (t80) REVERT: B 931 LYS cc_start: 0.7112 (mtpp) cc_final: 0.6887 (ptmt) REVERT: C 686 MET cc_start: 0.7633 (mmm) cc_final: 0.6984 (tpt) REVERT: C 880 LEU cc_start: 0.9281 (tp) cc_final: 0.8986 (tp) REVERT: D 515 LEU cc_start: 0.9177 (tp) cc_final: 0.8937 (tp) REVERT: D 544 GLN cc_start: 0.7947 (OUTLIER) cc_final: 0.7381 (pp30) REVERT: D 818 GLU cc_start: 0.7542 (pm20) cc_final: 0.7120 (pm20) REVERT: E 497 LYS cc_start: 0.8597 (tptm) cc_final: 0.8381 (tptp) REVERT: E 789 MET cc_start: 0.6890 (tpp) cc_final: 0.6545 (tpp) REVERT: E 820 PHE cc_start: 0.7599 (m-80) cc_final: 0.7217 (m-80) REVERT: F 497 LYS cc_start: 0.7000 (mppt) cc_final: 0.6628 (mmmt) REVERT: F 517 PHE cc_start: 0.6519 (m-10) cc_final: 0.6218 (m-10) REVERT: F 559 MET cc_start: 0.4782 (tpt) cc_final: 0.3444 (ptt) REVERT: F 615 TRP cc_start: 0.2785 (m-10) cc_final: 0.2470 (m-10) REVERT: F 721 GLN cc_start: 0.6887 (mp10) cc_final: 0.5824 (tp40) REVERT: F 808 HIS cc_start: 0.1698 (m170) cc_final: 0.0499 (m-70) outliers start: 3 outliers final: 1 residues processed: 306 average time/residue: 0.1487 time to fit residues: 71.6644 Evaluate side-chains 215 residues out of total 2695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 213 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 262 optimal weight: 3.9990 chunk 142 optimal weight: 9.9990 chunk 242 optimal weight: 4.9990 chunk 145 optimal weight: 3.9990 chunk 290 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 144 optimal weight: 0.8980 chunk 29 optimal weight: 0.0870 chunk 271 optimal weight: 7.9990 chunk 116 optimal weight: 0.9980 chunk 202 optimal weight: 10.0000 overall best weight: 1.9962 ------------------------------------------------------------------------------- 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 C 721 GLN C1366 HIS ** D 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 691 GLN ** D 863 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 726 HIS ** F 863 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 882 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.141834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.108828 restraints weight = 99976.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.105391 restraints weight = 81155.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.105238 restraints weight = 77099.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.105825 restraints weight = 63138.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.105871 restraints weight = 52664.006| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.4558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25108 Z= 0.161 Angle : 0.707 9.875 34028 Z= 0.354 Chirality : 0.046 0.244 3836 Planarity : 0.005 0.071 4361 Dihedral : 8.881 81.048 3486 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.95 % Favored : 91.95 % Rotamer: Outliers : 0.04 % Allowed : 2.71 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.03 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.18 (0.15), residues: 3019 helix: -0.15 (0.14), residues: 1350 sheet: -0.44 (0.29), residues: 322 loop : -1.47 (0.18), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 929 TYR 0.018 0.002 TYR A 521 PHE 0.033 0.002 PHE F 877 TRP 0.019 0.002 TRP B 865 HIS 0.007 0.001 HIS F 611 Details of bonding type rmsd covalent geometry : bond 0.00363 (25097) covalent geometry : angle 0.70657 (34028) hydrogen bonds : bond 0.04171 ( 940) hydrogen bonds : angle 5.21382 ( 2694) Misc. bond : bond 0.00247 ( 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 301 residues out of total 2695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 300 time to evaluate : 1.009 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: 0.5279 (tpp) cc_final: 0.4030 (mmt) REVERT: A 794 ARG cc_start: 0.6129 (mtm110) cc_final: 0.5443 (mmm-85) REVERT: B 808 HIS cc_start: 0.7104 (m90) cc_final: 0.6691 (m-70) REVERT: B 823 TYR cc_start: 0.6611 (m-80) cc_final: 0.6181 (m-80) REVERT: B 919 PHE cc_start: 0.7887 (t80) cc_final: 0.7160 (t80) REVERT: C 686 MET cc_start: 0.7668 (mmm) cc_final: 0.7035 (tpt) REVERT: D 515 LEU cc_start: 0.9120 (tp) cc_final: 0.8886 (tp) REVERT: D 818 GLU cc_start: 0.7460 (pm20) cc_final: 0.7036 (pm20) REVERT: E 680 GLU cc_start: 0.8036 (mp0) cc_final: 0.7488 (mp0) REVERT: E 789 MET cc_start: 0.6915 (tpp) cc_final: 0.6453 (tpp) REVERT: E 820 PHE cc_start: 0.7538 (m-80) cc_final: 0.7281 (m-80) REVERT: F 497 LYS cc_start: 0.7038 (mppt) cc_final: 0.6599 (tppp) REVERT: F 517 PHE cc_start: 0.6130 (m-10) cc_final: 0.5869 (m-10) REVERT: F 559 MET cc_start: 0.4625 (tpt) cc_final: 0.3430 (ptt) REVERT: F 615 TRP cc_start: 0.2997 (m-10) cc_final: 0.2705 (m-10) REVERT: F 808 HIS cc_start: 0.1556 (m170) cc_final: 0.0370 (m-70) REVERT: F 920 ASN cc_start: 0.7746 (p0) cc_final: 0.7432 (m-40) outliers start: 1 outliers final: 0 residues processed: 301 average time/residue: 0.1465 time to fit residues: 70.1315 Evaluate side-chains 219 residues out of total 2695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 22 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 250 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 271 optimal weight: 9.9990 chunk 232 optimal weight: 0.9990 chunk 76 optimal weight: 9.9990 chunk 125 optimal weight: 0.9980 chunk 167 optimal weight: 1.9990 chunk 262 optimal weight: 0.9990 chunk 243 optimal weight: 0.6980 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 844 GLN C 721 GLN D 544 GLN D 691 GLN ** D 863 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.142327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.107931 restraints weight = 98964.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.105206 restraints weight = 76248.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.105683 restraints weight = 67678.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.105912 restraints weight = 55939.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.105891 restraints weight = 49059.724| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.4802 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= 0.130 Angle : 0.683 12.078 34028 Z= 0.336 Chirality : 0.045 0.236 3836 Planarity : 0.005 0.072 4361 Dihedral : 8.660 82.355 3486 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.52 % Favored : 92.38 % Rotamer: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.03 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.16), residues: 3019 helix: -0.04 (0.14), residues: 1352 sheet: -0.42 (0.29), residues: 322 loop : -1.42 (0.18), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 613 TYR 0.029 0.001 TYR B 823 PHE 0.034 0.001 PHE F 877 TRP 0.014 0.001 TRP B 865 HIS 0.009 0.001 HIS A 611 Details of bonding type rmsd covalent geometry : bond 0.00290 (25097) covalent geometry : angle 0.68323 (34028) hydrogen bonds : bond 0.03856 ( 940) hydrogen bonds : angle 5.01242 ( 2694) Misc. bond : bond 0.00300 ( 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 295 residues out of total 2695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 time to evaluate : 0.969 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 516 LEU cc_start: 0.4623 (mt) cc_final: 0.4340 (pp) REVERT: A 523 MET cc_start: 0.5071 (tpp) cc_final: 0.3917 (mmt) REVERT: A 686 MET cc_start: 0.0053 (tmm) cc_final: -0.2281 (mtt) REVERT: B 808 HIS cc_start: 0.7116 (m90) cc_final: 0.6744 (m-70) REVERT: B 919 PHE cc_start: 0.7895 (t80) cc_final: 0.7157 (t80) REVERT: C 686 MET cc_start: 0.7600 (mmm) cc_final: 0.6968 (tpt) REVERT: D 515 LEU cc_start: 0.9099 (tp) cc_final: 0.8849 (tp) REVERT: D 818 GLU cc_start: 0.7417 (pm20) cc_final: 0.7014 (pm20) REVERT: E 497 LYS cc_start: 0.8365 (tptm) cc_final: 0.8049 (tppt) REVERT: E 789 MET cc_start: 0.6506 (tpp) cc_final: 0.6161 (tpp) REVERT: F 615 TRP cc_start: 0.3054 (m-10) cc_final: 0.2736 (m-10) REVERT: F 808 HIS cc_start: 0.1533 (m170) cc_final: 0.0448 (m-70) outliers start: 0 outliers final: 0 residues processed: 295 average time/residue: 0.1458 time to fit residues: 68.9238 Evaluate side-chains 221 residues out of total 2695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 269 optimal weight: 0.9990 chunk 127 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 7 optimal weight: 0.9980 chunk 208 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 chunk 237 optimal weight: 6.9990 chunk 83 optimal weight: 0.6980 chunk 228 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 512 GLN C 548 HIS C 721 GLN ** D 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 691 GLN ** D 863 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1370 HIS ** E1381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.141820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.106987 restraints weight = 98425.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.104920 restraints weight = 84084.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.104921 restraints weight = 65749.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.105082 restraints weight = 55804.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.105110 restraints weight = 51902.398| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.5022 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= 0.147 Angle : 0.704 11.817 34028 Z= 0.349 Chirality : 0.045 0.227 3836 Planarity : 0.005 0.072 4361 Dihedral : 8.540 85.291 3486 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.72 % Favored : 92.15 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.03 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.16), residues: 3019 helix: -0.05 (0.14), residues: 1351 sheet: -0.44 (0.29), residues: 322 loop : -1.38 (0.18), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 613 TYR 0.027 0.001 TYR B1356 PHE 0.034 0.001 PHE F 877 TRP 0.019 0.001 TRP B 865 HIS 0.008 0.001 HIS F 611 Details of bonding type rmsd covalent geometry : bond 0.00329 (25097) covalent geometry : angle 0.70380 (34028) hydrogen bonds : bond 0.03989 ( 940) hydrogen bonds : angle 5.12746 ( 2694) Misc. bond : bond 0.00268 ( 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 284 residues out of total 2695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 523 MET cc_start: 0.5142 (tpp) cc_final: 0.3941 (mmt) REVERT: A 686 MET cc_start: 0.0122 (tmm) cc_final: -0.1682 (mtm) REVERT: B 878 THR cc_start: 0.8697 (m) cc_final: 0.8453 (p) REVERT: B 919 PHE cc_start: 0.7832 (t80) cc_final: 0.7131 (t80) REVERT: C 686 MET cc_start: 0.7640 (mmm) cc_final: 0.7019 (tpt) REVERT: D 515 LEU cc_start: 0.9153 (tp) cc_final: 0.8943 (tp) REVERT: E 497 LYS cc_start: 0.8438 (tptm) cc_final: 0.7934 (tptt) REVERT: E 680 GLU cc_start: 0.7913 (mp0) cc_final: 0.7292 (mp0) REVERT: E 789 MET cc_start: 0.6754 (tpp) cc_final: 0.6392 (tpp) REVERT: E 820 PHE cc_start: 0.7386 (m-80) cc_final: 0.6892 (m-80) REVERT: F 497 LYS cc_start: 0.6956 (mppt) cc_final: 0.6560 (mmtp) REVERT: F 615 TRP cc_start: 0.3382 (m-10) cc_final: 0.3048 (m-10) REVERT: F 808 HIS cc_start: 0.1731 (m170) cc_final: 0.0541 (m-70) outliers start: 0 outliers final: 0 residues processed: 284 average time/residue: 0.1482 time to fit residues: 67.6535 Evaluate side-chains 210 residues out of total 2695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 86 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 281 optimal weight: 10.0000 chunk 172 optimal weight: 4.9990 chunk 299 optimal weight: 0.8980 chunk 177 optimal weight: 2.9990 chunk 230 optimal weight: 1.9990 chunk 218 optimal weight: 1.9990 chunk 300 optimal weight: 3.9990 chunk 21 optimal weight: 7.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 512 GLN C 721 GLN ** D 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 691 GLN ** D 863 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1381 GLN ** 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 = 0.4211 r_free = 0.4211 target = 0.141154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.109482 restraints weight = 99139.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.105442 restraints weight = 100455.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.105781 restraints weight = 83684.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.106005 restraints weight = 64390.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.106300 restraints weight = 53596.050| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.5254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 25108 Z= 0.163 Angle : 0.721 11.714 34028 Z= 0.359 Chirality : 0.046 0.215 3836 Planarity : 0.005 0.070 4361 Dihedral : 8.468 84.503 3486 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.78 % Favored : 92.15 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.03 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.15), residues: 3019 helix: -0.11 (0.14), residues: 1364 sheet: -0.54 (0.29), residues: 325 loop : -1.46 (0.18), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 929 TYR 0.016 0.001 TYR B1356 PHE 0.033 0.002 PHE F 877 TRP 0.019 0.001 TRP B 865 HIS 0.008 0.001 HIS F 611 Details of bonding type rmsd covalent geometry : bond 0.00367 (25097) covalent geometry : angle 0.72076 (34028) hydrogen bonds : bond 0.04176 ( 940) hydrogen bonds : angle 5.24788 ( 2694) Misc. bond : bond 0.00282 ( 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 273 residues out of total 2695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 523 MET cc_start: 0.5286 (tpp) cc_final: 0.3931 (mmt) REVERT: A 794 ARG cc_start: 0.6391 (ptp-170) cc_final: 0.6004 (ptp-170) REVERT: B 878 THR cc_start: 0.8711 (m) cc_final: 0.8458 (p) REVERT: B 919 PHE cc_start: 0.7584 (t80) cc_final: 0.6900 (t80) REVERT: C 626 GLU cc_start: 0.7925 (tp30) cc_final: 0.7698 (tp30) REVERT: C 686 MET cc_start: 0.7716 (mmm) cc_final: 0.7138 (tpt) REVERT: D 515 LEU cc_start: 0.9184 (tp) cc_final: 0.8960 (tp) REVERT: E 497 LYS cc_start: 0.8426 (tptm) cc_final: 0.7883 (tptt) REVERT: E 680 GLU cc_start: 0.7947 (mp0) cc_final: 0.7249 (mp0) REVERT: E 789 MET cc_start: 0.6669 (tpp) cc_final: 0.6326 (tpp) REVERT: E 820 PHE cc_start: 0.7499 (m-80) cc_final: 0.7159 (m-80) REVERT: F 497 LYS cc_start: 0.7161 (mppt) cc_final: 0.6769 (mmtp) REVERT: F 615 TRP cc_start: 0.3773 (m-10) cc_final: 0.3420 (m-10) REVERT: F 808 HIS cc_start: 0.1478 (m170) cc_final: 0.0363 (m-70) REVERT: F 851 ARG cc_start: 0.5617 (tpp-160) cc_final: 0.3888 (ptm-80) outliers start: 0 outliers final: 0 residues processed: 273 average time/residue: 0.1348 time to fit residues: 59.0187 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 : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 74 optimal weight: 9.9990 chunk 157 optimal weight: 0.8980 chunk 134 optimal weight: 0.2980 chunk 218 optimal weight: 0.6980 chunk 163 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 289 optimal weight: 5.9990 chunk 225 optimal weight: 7.9990 chunk 187 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 C 721 GLN ** D 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 691 GLN ** D 863 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1370 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.142333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.109381 restraints weight = 98541.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.106681 restraints weight = 81948.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.106778 restraints weight = 68652.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.106935 restraints weight = 53601.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.106989 restraints weight = 49711.723| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.5389 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= 0.130 Angle : 0.699 11.518 34028 Z= 0.346 Chirality : 0.045 0.193 3836 Planarity : 0.005 0.099 4361 Dihedral : 8.146 83.043 3486 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.29 % Favored : 92.68 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.03 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.16), residues: 3019 helix: -0.06 (0.14), residues: 1363 sheet: -0.40 (0.29), residues: 325 loop : -1.34 (0.18), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 652 TYR 0.017 0.001 TYR E1356 PHE 0.034 0.001 PHE F 877 TRP 0.011 0.001 TRP B 865 HIS 0.009 0.001 HIS F 611 Details of bonding type rmsd covalent geometry : bond 0.00287 (25097) covalent geometry : angle 0.69893 (34028) hydrogen bonds : bond 0.03792 ( 940) hydrogen bonds : angle 5.13061 ( 2694) 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 286 residues out of total 2695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 523 MET cc_start: 0.4809 (tpp) cc_final: 0.3697 (mmt) REVERT: A 794 ARG cc_start: 0.6284 (ptp-170) cc_final: 0.5585 (ptp90) REVERT: B 878 THR cc_start: 0.8684 (m) cc_final: 0.8437 (p) REVERT: B 912 ILE cc_start: 0.8418 (mm) cc_final: 0.8039 (tt) REVERT: B 919 PHE cc_start: 0.7808 (t80) cc_final: 0.7144 (t80) REVERT: C 686 MET cc_start: 0.7667 (mmm) cc_final: 0.7078 (tpt) REVERT: C 847 ARG cc_start: 0.7974 (ttm110) cc_final: 0.7753 (ttm110) REVERT: E 497 LYS cc_start: 0.8336 (tptm) cc_final: 0.7812 (tptt) REVERT: E 540 ARG cc_start: 0.8038 (tmm160) cc_final: 0.7321 (mmm160) REVERT: E 680 GLU cc_start: 0.7834 (mp0) cc_final: 0.7243 (mp0) REVERT: E 789 MET cc_start: 0.6535 (tpp) cc_final: 0.6164 (tpp) REVERT: E 820 PHE cc_start: 0.7451 (m-80) cc_final: 0.7100 (m-80) REVERT: F 497 LYS cc_start: 0.7104 (mppt) cc_final: 0.6678 (mmtp) REVERT: F 615 TRP cc_start: 0.3404 (m-10) cc_final: 0.3151 (m-10) REVERT: F 808 HIS cc_start: 0.1741 (m170) cc_final: 0.0581 (m-70) REVERT: F 851 ARG cc_start: 0.5674 (tpp-160) cc_final: 0.4020 (ptm160) outliers start: 0 outliers final: 0 residues processed: 286 average time/residue: 0.1312 time to fit residues: 60.2687 Evaluate side-chains 211 residues out of total 2695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 172 optimal weight: 5.9990 chunk 268 optimal weight: 20.0000 chunk 244 optimal weight: 0.0070 chunk 200 optimal weight: 9.9990 chunk 60 optimal weight: 0.9980 chunk 213 optimal weight: 4.9990 chunk 199 optimal weight: 0.3980 chunk 0 optimal weight: 20.0000 chunk 96 optimal weight: 0.9990 chunk 277 optimal weight: 1.9990 chunk 260 optimal weight: 8.9990 overall best weight: 0.8802 ------------------------------------------------------------------------------- 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 C 721 GLN ** D 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 691 GLN ** D 863 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.142555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.109068 restraints weight = 98475.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.106001 restraints weight = 86050.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.106077 restraints weight = 69296.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.106218 restraints weight = 57594.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.106414 restraints weight = 50837.115| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.5506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 25108 Z= 0.128 Angle : 0.696 11.419 34028 Z= 0.343 Chirality : 0.045 0.204 3836 Planarity : 0.005 0.097 4361 Dihedral : 8.002 84.137 3486 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.45 % Favored : 92.48 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.16), residues: 3019 helix: 0.01 (0.14), residues: 1359 sheet: -0.30 (0.29), residues: 326 loop : -1.34 (0.18), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D 851 TYR 0.018 0.001 TYR D 915 PHE 0.035 0.001 PHE F 877 TRP 0.012 0.001 TRP B 865 HIS 0.008 0.001 HIS F 611 Details of bonding type rmsd covalent geometry : bond 0.00287 (25097) covalent geometry : angle 0.69585 (34028) hydrogen bonds : bond 0.03678 ( 940) hydrogen bonds : angle 5.04408 ( 2694) Misc. bond : bond 0.00262 ( 11) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3548.39 seconds wall clock time: 62 minutes 16.78 seconds (3736.78 seconds total)