Starting phenix.real_space_refine on Mon Aug 25 04:59:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8juw_36665/08_2025/8juw_36665_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8juw_36665/08_2025/8juw_36665.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8juw_36665/08_2025/8juw_36665.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8juw_36665/08_2025/8juw_36665.map" model { file = "/net/cci-nas-00/data/ceres_data/8juw_36665/08_2025/8juw_36665_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8juw_36665/08_2025/8juw_36665_neut.cif" } resolution = 3.79 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 17 5.49 5 S 110 5.16 5 C 16134 2.51 5 N 4362 2.21 5 O 4659 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.01s 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: 25282 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 4157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4157 Classifications: {'peptide': 523} Link IDs: {'CIS': 3, 'PCIS': 2, 'PTRANS': 30, 'TRANS': 487} Chain breaks: 5 Chain: "B" Number of atoms: 4210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4210 Classifications: {'peptide': 529} Link IDs: {'CIS': 3, 'PCIS': 2, 'PTRANS': 32, 'TRANS': 491} Chain breaks: 2 Chain: "C" Number of atoms: 4199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4199 Classifications: {'peptide': 528} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 493} Chain breaks: 2 Chain: "D" Number of atoms: 4213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4213 Classifications: {'peptide': 530} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 495} Chain breaks: 2 Chain: "E" Number of atoms: 4202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4202 Classifications: {'peptide': 528} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 32, 'TRANS': 491} Chain breaks: 2 Chain: "F" Number of atoms: 4119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 4119 Classifications: {'peptide': 518} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 30, 'TRANS': 483} Chain breaks: 4 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 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: 5.76, per 1000 atoms: 0.23 Number of scatterers: 25282 At special positions: 0 Unit cell: (125.4, 165, 149.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 110 16.00 P 17 15.00 O 4659 8.00 N 4362 7.00 C 16134 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=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.95 Conformation dependent library (CDL) restraints added in 759.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 6220 Ramachandran restraints generated. 3110 Oldfield, 0 Emsley, 3110 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6024 Finding SS restraints... Secondary structure from input PDB file: 154 helices and 12 sheets defined 52.4% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 432 through 448 removed outlier: 4.789A pdb=" N GLU A 440 " --> pdb=" O ALA A 436 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N MET A 441 " --> pdb=" O ALA A 437 " (cutoff:3.500A) removed outlier: 5.128A 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 485 Processing helix chain 'A' and resid 507 through 524 removed outlier: 4.146A pdb=" N ARG A 511 " --> pdb=" O GLY A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 536 Processing helix chain 'A' and resid 548 through 561 Processing helix chain 'A' and resid 576 through 580 removed outlier: 4.046A pdb=" N SER A 579 " --> pdb=" O ARG A 576 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE A 580 " --> pdb=" O LEU A 577 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 576 through 580' Processing helix chain 'A' and resid 600 through 612 Processing helix chain 'A' and resid 620 through 631 Processing helix chain 'A' and resid 636 through 655 removed outlier: 3.860A pdb=" N ALA A 647 " --> pdb=" O CYS A 643 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU A 648 " --> pdb=" O ALA A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 685 removed outlier: 3.912A pdb=" N VAL A 681 " --> pdb=" O LYS A 677 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS A 685 " --> pdb=" O VAL A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 721 removed outlier: 6.337A pdb=" N ASN A 711 " --> pdb=" O PRO A 707 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N THR A 712 " --> pdb=" O LEU A 708 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN A 721 " --> pdb=" O LEU A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 729 removed outlier: 4.023A pdb=" N GLU A 728 " --> pdb=" O PRO A 725 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE A 729 " --> pdb=" O HIS A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 817 Processing helix chain 'A' and resid 826 through 831 Processing helix chain 'A' and resid 837 through 852 removed outlier: 4.373A pdb=" N THR A 841 " --> pdb=" O SER A 837 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N CYS A 842 " --> pdb=" O PRO A 838 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ALA A 843 " --> pdb=" O GLU A 839 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR A 852 " --> pdb=" O GLU A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 866 Processing helix chain 'A' and resid 870 through 881 Processing helix chain 'A' and resid 899 through 903 Processing helix chain 'A' and resid 904 through 909 Processing helix chain 'A' and resid 910 through 911 No H-bonds generated for 'chain 'A' and resid 910 through 911' Processing helix chain 'A' and resid 912 through 916 Processing helix chain 'A' and resid 926 through 938 removed outlier: 4.746A pdb=" N ASP A 935 " --> pdb=" O LYS A 931 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N LEU A 936 " --> pdb=" O PHE A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 943 removed outlier: 3.944A pdb=" N LYS A 943 " --> pdb=" O GLN A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1344 removed outlier: 4.050A pdb=" N ASN A1335 " --> pdb=" O GLU A1331 " (cutoff:3.500A) Processing helix chain 'A' and resid 1348 through 1365 removed outlier: 3.904A pdb=" N TYR A1356 " --> pdb=" O LEU A1352 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA A1357 " --> pdb=" O GLU A1353 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN A1361 " --> pdb=" O ALA A1357 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS A1362 " --> pdb=" O VAL A1358 " (cutoff:3.500A) Processing helix chain 'A' and resid 1375 through 1386 removed outlier: 4.814A pdb=" N GLU A1384 " --> pdb=" O GLU A1380 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 443 removed outlier: 3.732A pdb=" N MET B 441 " --> pdb=" O ALA B 437 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL B 442 " --> pdb=" O LEU B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 447 Processing helix chain 'B' and resid 450 through 456 removed outlier: 3.511A pdb=" N PHE B 455 " --> pdb=" O VAL B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 485 removed outlier: 3.967A pdb=" N VAL B 476 " --> pdb=" O GLY B 472 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ALA B 477 " --> pdb=" O LYS B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 523 removed outlier: 4.296A pdb=" N LEU B 513 " --> pdb=" O SER B 509 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ARG B 514 " --> pdb=" O GLU B 510 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N MET B 523 " --> pdb=" O GLN B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 536 removed outlier: 3.571A pdb=" N GLY B 535 " --> pdb=" O GLN B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 560 removed outlier: 4.035A pdb=" N SER B 549 " --> pdb=" O ASP B 545 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ASP B 560 " --> pdb=" O LEU B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 580 removed outlier: 3.664A pdb=" N SER B 579 " --> pdb=" O ARG B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 612 removed outlier: 3.677A pdb=" N ARG B 604 " --> pdb=" O ASP B 600 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS B 605 " --> pdb=" O LYS B 601 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU B 606 " --> pdb=" O GLU B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 630 removed outlier: 3.682A pdb=" N ASN B 630 " --> pdb=" O GLU B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 646 removed outlier: 3.781A pdb=" N ALA B 644 " --> pdb=" O LYS B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 655 Processing helix chain 'B' and resid 656 through 659 removed outlier: 4.601A pdb=" N TYR B 659 " --> pdb=" O PRO B 656 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 656 through 659' Processing helix chain 'B' and resid 675 through 686 removed outlier: 3.851A pdb=" N PHE B 679 " --> pdb=" O SER B 675 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU B 680 " --> pdb=" O ALA B 676 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL B 681 " --> pdb=" O LYS B 677 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA B 682 " --> pdb=" O ASP B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 724 removed outlier: 7.465A pdb=" N ASN B 711 " --> pdb=" O PRO B 707 " (cutoff:3.500A) removed outlier: 5.765A 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 Processing helix chain 'B' and resid 826 through 831 Processing helix chain 'B' and resid 837 through 852 Processing helix chain 'B' and resid 861 through 866 Processing helix chain 'B' and resid 867 through 869 No H-bonds generated for 'chain 'B' and resid 867 through 869' Processing helix chain 'B' and resid 870 through 882 removed outlier: 3.504A pdb=" N GLN B 882 " --> pdb=" O THR B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 899 through 903 removed outlier: 3.553A pdb=" N LEU B 903 " --> pdb=" O HIS B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 904 through 909 Processing helix chain 'B' and resid 910 through 911 No H-bonds generated for 'chain 'B' and resid 910 through 911' Processing helix chain 'B' and resid 912 through 916 Processing helix chain 'B' and resid 925 through 935 removed outlier: 4.467A pdb=" N ASP B 935 " --> pdb=" O LYS B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 1331 through 1344 removed outlier: 4.070A pdb=" N ASN B1335 " --> pdb=" O GLU B1331 " (cutoff:3.500A) Processing helix chain 'B' and resid 1348 through 1365 removed outlier: 3.754A pdb=" N ALA B1357 " --> pdb=" O GLU B1353 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE B1359 " --> pdb=" O LEU B1355 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N CYS B1362 " --> pdb=" O VAL B1358 " (cutoff:3.500A) Processing helix chain 'B' and resid 1375 through 1386 removed outlier: 3.533A pdb=" N GLU B1384 " --> pdb=" O GLU B1380 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 443 removed outlier: 4.108A pdb=" N GLU C 440 " --> pdb=" O ALA C 436 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N MET C 441 " --> pdb=" O ALA C 437 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL C 442 " --> pdb=" O LEU C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 448 Processing helix chain 'C' and resid 451 through 456 removed outlier: 4.190A pdb=" N PHE C 455 " --> pdb=" O VAL C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 486 removed outlier: 3.813A pdb=" N ALA C 477 " --> pdb=" O LYS C 473 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLN C 486 " --> pdb=" O ASN C 482 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 523 removed outlier: 3.809A pdb=" N ARG C 514 " --> pdb=" O GLU C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 536 Processing helix chain 'C' and resid 546 through 559 Processing helix chain 'C' and resid 576 through 580 removed outlier: 3.559A pdb=" N SER C 579 " --> pdb=" O ARG C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 585 Processing helix chain 'C' and resid 600 through 612 removed outlier: 3.800A pdb=" N LYS C 605 " --> pdb=" O LYS C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 631 removed outlier: 3.840A pdb=" N GLU C 626 " --> pdb=" O THR C 622 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLU C 629 " --> pdb=" O GLU C 625 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASN C 630 " --> pdb=" O GLU C 626 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N CYS C 631 " --> pdb=" O LEU C 627 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 655 removed outlier: 3.596A pdb=" N ALA C 644 " --> pdb=" O LYS C 640 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ALA C 647 " --> pdb=" O CYS C 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 685 removed outlier: 3.588A pdb=" N PHE C 679 " --> pdb=" O SER C 675 " (cutoff:3.500A) Processing helix chain 'C' and resid 705 through 724 removed outlier: 4.041A pdb=" N LEU C 709 " --> pdb=" O VAL C 705 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN C 710 " --> pdb=" O LYS C 706 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N ASN C 711 " --> pdb=" O PRO C 707 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N THR C 712 " --> pdb=" O LEU C 708 " (cutoff:3.500A) 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: 3.612A pdb=" N THR C 841 " --> pdb=" O SER C 837 " (cutoff:3.500A) removed outlier: 3.881A 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: 3.583A pdb=" N LEU C 881 " --> pdb=" O PHE C 877 " (cutoff:3.500A) Processing helix chain 'C' and resid 899 through 903 Processing helix chain 'C' and resid 912 through 916 Processing helix chain 'C' and resid 925 through 939 removed outlier: 3.608A pdb=" N PHE C 933 " --> pdb=" O ARG C 929 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ASP C 935 " --> pdb=" O LYS C 931 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N LEU C 936 " --> pdb=" O PHE C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 1331 through 1344 removed outlier: 3.955A pdb=" N ASN C1335 " --> pdb=" O GLU C1331 " (cutoff:3.500A) Processing helix chain 'C' and resid 1348 through 1366 removed outlier: 4.044A pdb=" N CYS C1362 " --> pdb=" O VAL C1358 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE C1363 " --> pdb=" O ILE C1359 " (cutoff:3.500A) Processing helix chain 'C' and resid 1375 through 1385 Processing helix chain 'D' and resid 432 through 443 removed outlier: 3.833A pdb=" N ALA D 436 " --> pdb=" O SER D 432 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA D 437 " --> pdb=" O ASN D 433 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU D 440 " --> pdb=" O ALA D 436 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N MET D 441 " --> pdb=" O ALA D 437 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL D 442 " --> pdb=" O LEU D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 443 through 448 Processing helix chain 'D' and resid 451 through 456 removed outlier: 4.386A pdb=" N PHE D 455 " --> pdb=" O VAL D 451 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 486 removed outlier: 3.781A pdb=" N ALA D 477 " --> pdb=" O LYS D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 507 through 523 removed outlier: 3.729A pdb=" N ARG D 511 " --> pdb=" O GLY D 507 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU D 513 " --> pdb=" O SER D 509 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG D 514 " --> pdb=" O GLU D 510 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR D 521 " --> pdb=" O PHE D 517 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 536 Processing helix chain 'D' and resid 546 through 560 removed outlier: 3.966A pdb=" N SER D 553 " --> pdb=" O SER D 549 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU D 558 " --> pdb=" O THR D 554 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ASP D 560 " --> pdb=" O LEU D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 612 removed outlier: 5.504A pdb=" N LYS D 609 " --> pdb=" O LYS D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 631 removed outlier: 3.871A pdb=" N ASN D 630 " --> pdb=" O GLU D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 655 removed outlier: 3.865A pdb=" N LYS D 640 " --> pdb=" O GLY D 636 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N CYS D 643 " --> pdb=" O ILE D 639 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ALA D 644 " --> pdb=" O LYS D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 659 removed outlier: 4.224A 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: 3.543A pdb=" N VAL D 681 " --> pdb=" O LYS D 677 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN D 684 " --> pdb=" O GLU D 680 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS D 685 " --> pdb=" O VAL D 681 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 693 removed outlier: 3.688A pdb=" N ARG D 692 " --> pdb=" O ALA D 689 " (cutoff:3.500A) removed outlier: 4.437A 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: 6.024A pdb=" N ASN D 711 " --> pdb=" O PRO D 707 " (cutoff:3.500A) removed outlier: 5.739A 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 removed outlier: 4.022A pdb=" N THR D 841 " --> pdb=" O SER D 837 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE D 846 " --> pdb=" O CYS D 842 " (cutoff:3.500A) Processing helix chain 'D' and resid 861 through 866 Processing helix chain 'D' and resid 870 through 881 removed outlier: 3.709A pdb=" N LEU D 881 " --> pdb=" O PHE D 877 " (cutoff:3.500A) Processing helix chain 'D' and resid 904 through 910 removed outlier: 3.972A pdb=" N LEU D 910 " --> pdb=" O GLU D 906 " (cutoff:3.500A) Processing helix chain 'D' and resid 912 through 916 Processing helix chain 'D' and resid 925 through 938 removed outlier: 3.650A pdb=" N ARG D 929 " --> pdb=" O ASP D 925 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ASP D 935 " --> pdb=" O LYS D 931 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N LEU D 936 " --> pdb=" O PHE D 932 " (cutoff:3.500A) Processing helix chain 'D' and resid 1331 through 1344 removed outlier: 4.188A pdb=" N ASN D1335 " --> pdb=" O GLU D1331 " (cutoff:3.500A) Processing helix chain 'D' and resid 1348 through 1366 removed outlier: 3.530A pdb=" N CYS D1362 " --> pdb=" O VAL D1358 " (cutoff:3.500A) removed outlier: 3.652A 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 435 through 443 removed outlier: 3.748A pdb=" N MET E 441 " --> pdb=" O ALA E 437 " (cutoff:3.500A) Processing helix chain 'E' and resid 443 through 448 Processing helix chain 'E' and resid 450 through 455 removed outlier: 3.948A pdb=" N LYS E 454 " --> pdb=" O GLU E 450 " (cutoff:3.500A) removed outlier: 4.375A 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 507 through 523 removed outlier: 4.744A pdb=" N LEU E 513 " --> pdb=" O SER E 509 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ARG E 514 " --> pdb=" O GLU E 510 " (cutoff:3.500A) Processing helix chain 'E' and resid 533 through 536 Processing helix chain 'E' and resid 545 through 561 removed outlier: 3.892A pdb=" N SER E 549 " --> pdb=" O ASP E 545 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU E 558 " --> pdb=" O THR E 554 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY E 561 " --> pdb=" O ALA E 557 " (cutoff:3.500A) Processing helix chain 'E' and resid 600 through 612 Processing helix chain 'E' and resid 620 through 631 removed outlier: 4.091A pdb=" N ASN E 630 " --> pdb=" O GLU E 626 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N CYS E 631 " --> pdb=" O LEU E 627 " (cutoff:3.500A) Processing helix chain 'E' and resid 635 through 655 removed outlier: 3.861A pdb=" N CYS E 643 " --> pdb=" O ILE E 639 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA E 644 " --> pdb=" O LYS E 640 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA E 647 " --> pdb=" O CYS E 643 " (cutoff:3.500A) Processing helix chain 'E' and resid 675 through 686 removed outlier: 3.508A pdb=" N LYS E 685 " --> pdb=" O VAL E 681 " (cutoff:3.500A) Processing helix chain 'E' and resid 705 through 724 removed outlier: 6.940A pdb=" N ASN E 711 " --> pdb=" O PRO E 707 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N THR E 712 " --> pdb=" O LEU E 708 " (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: 3.521A pdb=" N THR E 841 " --> pdb=" O SER E 837 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR E 852 " --> pdb=" O GLU E 848 " (cutoff:3.500A) Processing helix chain 'E' and resid 861 through 866 removed outlier: 3.548A pdb=" N TRP E 866 " --> pdb=" O ILE E 862 " (cutoff:3.500A) Processing helix chain 'E' and resid 870 through 881 removed outlier: 3.571A pdb=" N LEU E 881 " --> pdb=" O PHE E 877 " (cutoff:3.500A) Processing helix chain 'E' and resid 904 through 909 removed outlier: 3.782A 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 933 Processing helix chain 'E' and resid 1331 through 1344 Processing helix chain 'E' and resid 1348 through 1366 removed outlier: 3.641A pdb=" N HIS E1366 " --> pdb=" O CYS E1362 " (cutoff:3.500A) Processing helix chain 'E' and resid 1375 through 1386 Processing helix chain 'F' and resid 431 through 442 removed outlier: 3.643A pdb=" N ILE F 435 " --> pdb=" O LEU F 431 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA F 436 " --> pdb=" O SER F 432 " (cutoff:3.500A) Processing helix chain 'F' and resid 442 through 448 Processing helix chain 'F' and resid 472 through 486 removed outlier: 4.037A pdb=" N VAL F 476 " --> pdb=" O GLY F 472 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA F 477 " --> pdb=" O LYS F 473 " (cutoff:3.500A) Processing helix chain 'F' and resid 510 through 523 removed outlier: 4.022A pdb=" N ARG F 514 " --> pdb=" O GLU F 510 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR F 521 " --> pdb=" O PHE F 517 " (cutoff:3.500A) Processing helix chain 'F' and resid 532 through 537 removed outlier: 4.452A pdb=" N LEU F 536 " --> pdb=" O GLN F 532 " (cutoff:3.500A) Processing helix chain 'F' and resid 545 through 562 Processing helix chain 'F' and resid 602 through 612 removed outlier: 4.181A pdb=" N GLU F 606 " --> pdb=" O GLU F 602 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR F 612 " --> pdb=" O LEU F 608 " (cutoff:3.500A) Processing helix chain 'F' and resid 620 through 631 Processing helix chain 'F' and resid 636 through 654 removed outlier: 3.591A pdb=" N CYS F 643 " --> pdb=" O ILE F 639 " (cutoff:3.500A) Processing helix chain 'F' and resid 655 through 659 removed outlier: 3.827A pdb=" N TYR F 659 " --> pdb=" O PRO F 656 " (cutoff:3.500A) Processing helix chain 'F' and resid 675 through 684 removed outlier: 4.250A pdb=" N PHE F 679 " --> pdb=" O SER F 675 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLU F 680 " --> pdb=" O ALA F 676 " (cutoff:3.500A) Processing helix chain 'F' and resid 705 through 724 removed outlier: 6.467A pdb=" N ASN F 711 " --> pdb=" O PRO F 707 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N THR F 712 " --> pdb=" O LEU F 708 " (cutoff:3.500A) Processing helix chain 'F' and resid 808 through 817 removed outlier: 3.670A pdb=" N ALA F 812 " --> pdb=" O HIS F 808 " (cutoff:3.500A) Processing helix chain 'F' and resid 826 through 831 Processing helix chain 'F' and resid 837 through 852 removed outlier: 3.540A pdb=" N THR F 841 " --> pdb=" O SER F 837 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA F 843 " --> pdb=" O GLU F 839 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLN F 844 " --> pdb=" O GLU F 840 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE F 846 " --> pdb=" O CYS F 842 " (cutoff:3.500A) Processing helix chain 'F' and resid 861 through 866 Processing helix chain 'F' and resid 870 through 883 removed outlier: 3.618A pdb=" N LYS F 874 " --> pdb=" O GLY F 870 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA F 875 " --> pdb=" O PRO F 871 " (cutoff:3.500A) Processing helix chain 'F' and resid 899 through 903 removed outlier: 3.602A 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 932 Processing helix chain 'F' and resid 1332 through 1344 Processing helix chain 'F' and resid 1345 through 1347 No H-bonds generated for 'chain 'F' and resid 1345 through 1347' Processing helix chain 'F' and resid 1348 through 1366 removed outlier: 3.792A pdb=" N CYS F1362 " --> pdb=" O VAL F1358 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE F1363 " --> pdb=" O ILE F1359 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR F1364 " --> pdb=" O SER F1360 " (cutoff:3.500A) Processing helix chain 'F' and resid 1374 through 1386 removed outlier: 3.522A pdb=" N GLU F1384 " --> pdb=" O GLU F1380 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 492 through 497 removed outlier: 6.809A pdb=" N ALA A 492 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N PHE A 529 " --> pdb=" O ALA A 492 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N PHE A 494 " --> pdb=" O PHE A 529 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ASP A 531 " --> pdb=" O PHE A 494 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ARG A 496 " --> pdb=" O ASP A 531 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N SER A 526 " --> pdb=" O VAL A 569 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N ILE A 571 " --> pdb=" O SER A 526 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE A 528 " --> pdb=" O ILE A 571 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N ALA A 573 " --> pdb=" O ILE A 528 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N PHE A 530 " --> pdb=" O ALA A 573 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N GLY A 462 " --> pdb=" O ARG A 592 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N PHE A 594 " --> pdb=" O GLY A 462 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU A 464 " --> pdb=" O PHE A 594 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 821 through 824 removed outlier: 6.561A pdb=" N THR A 821 " --> pdb=" O ILE A 856 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N TYR A 858 " --> pdb=" O THR A 821 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TYR A 823 " --> pdb=" O TYR A 858 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N THR A 895 " --> pdb=" O VAL A 859 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE A 795 " --> pdb=" O ALA A 894 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N SER A 896 " --> pdb=" O ILE A 795 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE A 797 " --> pdb=" O SER A 896 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 494 through 496 removed outlier: 6.761A pdb=" N PHE B 494 " --> pdb=" O PHE B 529 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA B 573 " --> pdb=" O PHE B 530 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N PHE B 594 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU B 464 " --> pdb=" O PHE B 594 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 822 through 824 removed outlier: 3.738A pdb=" N THR B 895 " --> pdb=" O VAL B 859 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 494 through 496 removed outlier: 3.699A pdb=" N VAL C 569 " --> pdb=" O SER C 526 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY C 572 " --> pdb=" O CYS C 463 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR C 574 " --> pdb=" O PHE C 465 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLY C 462 " --> pdb=" O ARG C 592 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N PHE C 594 " --> pdb=" O GLY C 462 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU C 464 " --> pdb=" O PHE C 594 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 821 through 824 removed outlier: 3.627A pdb=" N TYR C 858 " --> pdb=" O TYR C 823 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N SER C 855 " --> pdb=" O LEU C 891 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N LEU C 893 " --> pdb=" O SER C 855 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N VAL C 857 " --> pdb=" O LEU C 893 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N THR C 895 " --> pdb=" O VAL C 857 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N VAL C 859 " --> pdb=" O THR C 895 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU C 796 " --> pdb=" O PHE C 919 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 492 through 496 removed outlier: 6.633A pdb=" N ALA D 492 " --> pdb=" O ILE D 527 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N PHE D 529 " --> pdb=" O ALA D 492 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N PHE D 494 " --> pdb=" O PHE D 529 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ASP D 531 " --> pdb=" O PHE D 494 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ARG D 496 " --> pdb=" O ASP D 531 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY D 572 " --> pdb=" O CYS D 463 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N PHE D 594 " --> pdb=" O GLY D 462 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU D 464 " --> pdb=" O PHE D 594 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 821 through 824 removed outlier: 6.660A pdb=" N SER D 855 " --> pdb=" O LEU D 891 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N LEU D 893 " --> pdb=" O SER D 855 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N VAL D 857 " --> pdb=" O LEU D 893 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N THR D 895 " --> pdb=" O VAL D 857 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N PHE D 919 " --> pdb=" O ARG D 794 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LEU D 796 " --> pdb=" O PHE D 919 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 492 through 495 removed outlier: 6.514A pdb=" N ALA E 492 " --> pdb=" O ILE E 527 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N PHE E 529 " --> pdb=" O ALA E 492 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N PHE E 494 " --> pdb=" O PHE E 529 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N ASP E 531 " --> pdb=" O PHE E 494 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N VAL E 569 " --> pdb=" O SER E 526 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS E 463 " --> pdb=" O VAL E 570 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 822 through 824 removed outlier: 3.686A pdb=" N THR E 895 " --> pdb=" O VAL E 859 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA E 894 " --> pdb=" O ILE E 795 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE E 919 " --> pdb=" O LEU E 796 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 492 through 497 removed outlier: 6.837A pdb=" N ALA F 492 " --> pdb=" O ILE F 527 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N PHE F 529 " --> pdb=" O ALA F 492 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N PHE F 494 " --> pdb=" O PHE F 529 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N ASP F 531 " --> pdb=" O PHE F 494 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ARG F 496 " --> pdb=" O ASP F 531 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N SER F 526 " --> pdb=" O VAL F 569 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ILE F 571 " --> pdb=" O SER F 526 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N ILE F 528 " --> pdb=" O ILE F 571 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N ALA F 573 " --> pdb=" O ILE F 528 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N PHE F 530 " --> pdb=" O ALA F 573 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 821 through 824 removed outlier: 6.361A pdb=" N THR F 821 " --> pdb=" O ILE F 856 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N TYR F 858 " --> pdb=" O THR F 821 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N TYR F 823 " --> pdb=" O TYR F 858 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR F 895 " --> pdb=" O VAL F 859 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA F 894 " --> pdb=" O ILE F 795 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N PHE F 919 " --> pdb=" O ARG F 794 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU F 796 " --> pdb=" O PHE F 919 " (cutoff:3.500A) 983 hydrogen bonds defined for protein. 2844 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: 3.36 Time building geometry restraints manager: 2.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8223 1.34 - 1.46: 4703 1.46 - 1.58: 12733 1.58 - 1.70: 19 1.70 - 1.82: 159 Bond restraints: 25837 Sorted by residual: bond pdb=" CG GLU A 934 " pdb=" CD GLU A 934 " ideal model delta sigma weight residual 1.516 1.465 0.051 2.50e-02 1.60e+03 4.18e+00 bond pdb=" C LEU B 938 " pdb=" N LYS B 939 " ideal model delta sigma weight residual 1.332 1.305 0.027 1.40e-02 5.10e+03 3.74e+00 bond pdb=" CA THR D 574 " pdb=" CB THR D 574 " ideal model delta sigma weight residual 1.534 1.506 0.028 1.60e-02 3.91e+03 3.11e+00 bond pdb=" CG GLU E1382 " pdb=" CD GLU E1382 " ideal model delta sigma weight residual 1.516 1.476 0.040 2.50e-02 1.60e+03 2.59e+00 bond pdb=" C LYS E 473 " pdb=" N THR E 474 " ideal model delta sigma weight residual 1.332 1.312 0.021 1.40e-02 5.10e+03 2.21e+00 ... (remaining 25832 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 34377 2.50 - 5.00: 572 5.00 - 7.49: 65 7.49 - 9.99: 8 9.99 - 12.49: 3 Bond angle restraints: 35025 Sorted by residual: angle pdb=" N ILE F 672 " pdb=" CA ILE F 672 " pdb=" C ILE F 672 " ideal model delta sigma weight residual 111.91 105.77 6.14 8.90e-01 1.26e+00 4.76e+01 angle pdb=" N ILE B 868 " pdb=" CA ILE B 868 " pdb=" C ILE B 868 " ideal model delta sigma weight residual 113.71 108.22 5.49 9.50e-01 1.11e+00 3.33e+01 angle pdb=" C LEU E 624 " pdb=" N GLU E 625 " pdb=" CA GLU E 625 " ideal model delta sigma weight residual 121.14 112.56 8.58 1.75e+00 3.27e-01 2.40e+01 angle pdb=" N VAL A 414 " pdb=" CA VAL A 414 " pdb=" C VAL A 414 " ideal model delta sigma weight residual 113.10 108.99 4.11 9.70e-01 1.06e+00 1.79e+01 angle pdb=" C LYS C 473 " pdb=" N THR C 474 " pdb=" CA THR C 474 " ideal model delta sigma weight residual 121.14 115.03 6.11 1.75e+00 3.27e-01 1.22e+01 ... (remaining 35020 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.33: 15386 32.33 - 64.66: 467 64.66 - 96.99: 55 96.99 - 129.33: 0 129.33 - 161.66: 3 Dihedral angle restraints: 15911 sinusoidal: 6677 harmonic: 9234 Sorted by residual: dihedral pdb=" O2A ADP A1401 " pdb=" O3A ADP A1401 " pdb=" PA ADP A1401 " pdb=" PB ADP A1401 " ideal model delta sinusoidal sigma weight residual -60.00 101.66 -161.66 1 2.00e+01 2.50e-03 4.68e+01 dihedral pdb=" C5' ADP A1401 " pdb=" O5' ADP A1401 " pdb=" PA ADP A1401 " pdb=" O2A ADP A1401 " ideal model delta sinusoidal sigma weight residual -60.00 80.71 -140.71 1 2.00e+01 2.50e-03 4.26e+01 dihedral pdb=" O1B ADP A1401 " pdb=" O3A ADP A1401 " pdb=" PB ADP A1401 " pdb=" PA ADP A1401 " ideal model delta sinusoidal sigma weight residual -60.00 79.88 -139.89 1 2.00e+01 2.50e-03 4.24e+01 ... (remaining 15908 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2808 0.048 - 0.097: 924 0.097 - 0.145: 201 0.145 - 0.193: 12 0.193 - 0.242: 4 Chirality restraints: 3949 Sorted by residual: chirality pdb=" CG LEU F 558 " pdb=" CB LEU F 558 " pdb=" CD1 LEU F 558 " pdb=" CD2 LEU F 558 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA ASN A 616 " pdb=" N ASN A 616 " pdb=" C ASN A 616 " pdb=" CB ASN A 616 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CG LEU E 938 " pdb=" CB LEU E 938 " pdb=" CD1 LEU E 938 " pdb=" CD2 LEU E 938 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 3946 not shown) Planarity restraints: 4490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN E 787 " -0.062 5.00e-02 4.00e+02 9.25e-02 1.37e+01 pdb=" N PRO E 788 " 0.160 5.00e-02 4.00e+02 pdb=" CA PRO E 788 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO E 788 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 468 " -0.050 5.00e-02 4.00e+02 7.61e-02 9.28e+00 pdb=" N PRO D 469 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO D 469 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO D 469 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 944 " -0.050 5.00e-02 4.00e+02 7.47e-02 8.94e+00 pdb=" N PRO C 945 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO C 945 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 945 " -0.046 5.00e-02 4.00e+02 ... (remaining 4487 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 392 2.66 - 3.22: 24341 3.22 - 3.78: 35578 3.78 - 4.34: 46804 4.34 - 4.90: 77539 Nonbonded interactions: 184654 Sorted by model distance: nonbonded pdb=" O GLN F 657 " pdb=" OG1 THR F 661 " model vdw 2.105 3.040 nonbonded pdb=" OH TYR D 655 " pdb=" OD1 ASP D 668 " model vdw 2.107 3.040 nonbonded pdb=" OH TYR F 655 " pdb=" O ASP F 668 " model vdw 2.124 3.040 nonbonded pdb=" NH1 ARG D 604 " pdb=" O CYS D 631 " model vdw 2.156 3.120 nonbonded pdb=" OD2 ASP C 668 " pdb=" OG SER C 670 " model vdw 2.174 3.040 ... (remaining 184649 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 422 through 598 or resid 601 through 688 or resid 696 thro \ ugh 727 or resid 787 through 943 or resid 1331 through 1388)) selection = (chain 'B' and (resid 422 through 539 or resid 546 through 598 or resid 601 thro \ ugh 659 or resid 666 through 688 or resid 696 through 727 or resid 787 through 9 \ 23 or resid 925 through 943 or resid 1331 through 1388)) selection = (chain 'C' and (resid 422 through 539 or resid 546 through 598 or resid 601 thro \ ugh 659 or resid 666 through 688 or resid 696 through 727 or resid 787 through 9 \ 23 or resid 925 through 943 or resid 1331 through 1388)) selection = (chain 'D' and (resid 422 through 539 or resid 546 through 598 or resid 601 thro \ ugh 659 or resid 666 through 688 or resid 696 through 727 or resid 787 through 9 \ 23 or resid 925 through 943 or resid 1331 through 1388)) selection = (chain 'E' and (resid 422 through 539 or resid 546 through 598 or resid 601 thro \ ugh 659 or resid 666 through 688 or resid 696 through 727 or resid 787 through 9 \ 23 or resid 925 through 943 or resid 1331 through 1388)) selection = (chain 'F' and (resid 422 through 539 or resid 546 through 659 or resid 666 thro \ ugh 727 or resid 787 through 923 or resid 925 through 943 or resid 1331 through \ 1388)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 20.160 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 25845 Z= 0.262 Angle : 0.801 12.492 35025 Z= 0.422 Chirality : 0.048 0.242 3949 Planarity : 0.006 0.093 4490 Dihedral : 15.487 161.658 9887 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.46 % Favored : 91.38 % Rotamer: Outliers : 0.04 % Allowed : 0.61 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3110 helix: -0.12 (0.14), residues: 1399 sheet: 0.03 (0.28), residues: 375 loop : -1.65 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 794 TYR 0.019 0.002 TYR F 823 PHE 0.027 0.002 PHE B 831 TRP 0.026 0.002 TRP A 505 HIS 0.008 0.001 HIS E 726 Details of bonding type rmsd covalent geometry : bond 0.00619 (25837) covalent geometry : angle 0.80121 (35025) hydrogen bonds : bond 0.21389 ( 983) hydrogen bonds : angle 7.00296 ( 2844) Misc. bond : bond 0.00597 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6220 Ramachandran restraints generated. 3110 Oldfield, 0 Emsley, 3110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6220 Ramachandran restraints generated. 3110 Oldfield, 0 Emsley, 3110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 409 time to evaluate : 0.951 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 495 MET cc_start: 0.7105 (tpt) cc_final: 0.6422 (tpp) REVERT: A 615 TRP cc_start: 0.4783 (m-10) cc_final: 0.4033 (m100) REVERT: A 686 MET cc_start: 0.2623 (pmm) cc_final: 0.2033 (pmm) REVERT: A 839 GLU cc_start: 0.6998 (mm-30) cc_final: 0.6724 (tp30) REVERT: B 523 MET cc_start: 0.7638 (mpp) cc_final: 0.7097 (mtt) REVERT: F 441 MET cc_start: 0.5417 (ptm) cc_final: 0.4710 (ptt) REVERT: F 457 ILE cc_start: 0.7061 (mm) cc_final: 0.6824 (pt) REVERT: F 638 ASP cc_start: 0.4924 (p0) cc_final: 0.4397 (m-30) REVERT: F 686 MET cc_start: -0.0267 (pmm) cc_final: -0.1900 (ptm) outliers start: 1 outliers final: 0 residues processed: 410 average time/residue: 0.1771 time to fit residues: 107.9956 Evaluate side-chains 186 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.3980 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.5980 chunk 298 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1335 ASN B 434 HIS ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 611 HIS B 882 GLN B1330 HIS C1366 HIS C1385 ASN D 691 GLN D1330 HIS E 611 HIS E 922 GLN F1377 GLN F1381 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.108247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.074261 restraints weight = 87308.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.076138 restraints weight = 47439.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.077282 restraints weight = 32502.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.078117 restraints weight = 25812.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.078545 restraints weight = 22552.826| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25845 Z= 0.152 Angle : 0.692 11.107 35025 Z= 0.349 Chirality : 0.044 0.173 3949 Planarity : 0.005 0.057 4490 Dihedral : 9.401 175.774 3582 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.11 % Favored : 93.79 % Rotamer: Outliers : 1.22 % Allowed : 8.60 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % 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: -0.67 (0.15), residues: 3110 helix: 0.36 (0.14), residues: 1409 sheet: 0.23 (0.28), residues: 373 loop : -1.52 (0.17), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 496 TYR 0.017 0.002 TYR A 858 PHE 0.019 0.001 PHE F 465 TRP 0.015 0.001 TRP F 865 HIS 0.005 0.001 HIS B 611 Details of bonding type rmsd covalent geometry : bond 0.00336 (25837) covalent geometry : angle 0.69191 (35025) hydrogen bonds : bond 0.05273 ( 983) hydrogen bonds : angle 5.11148 ( 2844) Misc. bond : bond 0.00350 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6220 Ramachandran restraints generated. 3110 Oldfield, 0 Emsley, 3110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6220 Ramachandran restraints generated. 3110 Oldfield, 0 Emsley, 3110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 229 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 560 ASP cc_start: 0.7392 (t0) cc_final: 0.7171 (t70) REVERT: A 615 TRP cc_start: 0.4656 (m-10) cc_final: 0.3589 (m100) REVERT: A 686 MET cc_start: 0.5141 (pmm) cc_final: 0.4483 (pmm) REVERT: A 848 GLU cc_start: 0.7598 (tp30) cc_final: 0.7273 (tp30) REVERT: E 523 MET cc_start: 0.7500 (tpt) cc_final: 0.7247 (tpp) REVERT: E 559 MET cc_start: 0.8672 (mmm) cc_final: 0.8465 (mmm) REVERT: F 441 MET cc_start: 0.5306 (ptm) cc_final: 0.4941 (ptt) REVERT: F 457 ILE cc_start: 0.6149 (mm) cc_final: 0.5713 (pt) REVERT: F 565 ARG cc_start: 0.3640 (pmt170) cc_final: 0.3397 (mpt180) REVERT: F 686 MET cc_start: 0.3516 (pmm) cc_final: 0.3046 (ptm) outliers start: 34 outliers final: 16 residues processed: 246 average time/residue: 0.1592 time to fit residues: 61.6461 Evaluate side-chains 207 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 191 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain B residue 484 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 880 LEU Chi-restraints excluded: chain C residue 937 ILE Chi-restraints excluded: chain D residue 630 ASN Chi-restraints excluded: chain D residue 631 CYS Chi-restraints excluded: chain D residue 848 GLU Chi-restraints excluded: chain D residue 862 ILE Chi-restraints excluded: chain E residue 648 LEU Chi-restraints excluded: chain E residue 712 THR Chi-restraints excluded: chain E residue 720 LEU Chi-restraints excluded: chain E residue 846 ILE Chi-restraints excluded: chain F residue 641 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 160 optimal weight: 6.9990 chunk 82 optimal weight: 6.9990 chunk 52 optimal weight: 0.0980 chunk 305 optimal weight: 10.0000 chunk 309 optimal weight: 9.9990 chunk 227 optimal weight: 7.9990 chunk 79 optimal weight: 4.9990 chunk 236 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 220 optimal weight: 10.0000 chunk 292 optimal weight: 5.9990 overall best weight: 4.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 GLN ** A 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1381 GLN ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 684 GLN F1381 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.102740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.071365 restraints weight = 88052.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.072616 restraints weight = 57393.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.072359 restraints weight = 35336.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.072747 restraints weight = 35315.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.072850 restraints weight = 30946.232| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 25845 Z= 0.312 Angle : 0.785 11.070 35025 Z= 0.397 Chirality : 0.047 0.174 3949 Planarity : 0.006 0.073 4490 Dihedral : 9.417 174.013 3582 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.97 % Favored : 91.93 % Rotamer: Outliers : 2.45 % Allowed : 11.84 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.84 (0.15), residues: 3110 helix: 0.27 (0.14), residues: 1413 sheet: 0.03 (0.28), residues: 374 loop : -1.63 (0.17), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C1367 TYR 0.031 0.002 TYR F 448 PHE 0.042 0.002 PHE F 452 TRP 0.013 0.002 TRP D 865 HIS 0.008 0.001 HIS D 434 Details of bonding type rmsd covalent geometry : bond 0.00731 (25837) covalent geometry : angle 0.78545 (35025) hydrogen bonds : bond 0.05788 ( 983) hydrogen bonds : angle 5.20153 ( 2844) Misc. bond : bond 0.00527 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6220 Ramachandran restraints generated. 3110 Oldfield, 0 Emsley, 3110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6220 Ramachandran restraints generated. 3110 Oldfield, 0 Emsley, 3110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 183 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 615 TRP cc_start: 0.5398 (m-10) cc_final: 0.4111 (m100) REVERT: A 686 MET cc_start: 0.5104 (pmm) cc_final: 0.4084 (pmm) REVERT: A 848 GLU cc_start: 0.7693 (tp30) cc_final: 0.7384 (tp30) REVERT: B 1379 MET cc_start: 0.8276 (mmt) cc_final: 0.7939 (mmt) REVERT: C 873 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.9044 (tt) REVERT: D 556 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.9024 (tt) REVERT: D 717 LEU cc_start: 0.9508 (OUTLIER) cc_final: 0.9022 (mm) REVERT: E 523 MET cc_start: 0.7443 (tpt) cc_final: 0.7229 (tpp) REVERT: E 559 MET cc_start: 0.8921 (mmm) cc_final: 0.8712 (mmm) REVERT: E 686 MET cc_start: 0.8369 (tpp) cc_final: 0.8008 (tpp) REVERT: E 1352 LEU cc_start: 0.9631 (OUTLIER) cc_final: 0.9413 (mm) REVERT: F 441 MET cc_start: 0.4879 (ptm) cc_final: 0.4335 (ptp) REVERT: F 451 VAL cc_start: 0.6217 (t) cc_final: 0.5707 (t) REVERT: F 457 ILE cc_start: 0.6996 (mm) cc_final: 0.6567 (pt) REVERT: F 565 ARG cc_start: 0.2918 (pmt170) cc_final: 0.2015 (mtt180) REVERT: F 686 MET cc_start: 0.2211 (pmm) cc_final: 0.0720 (ptm) outliers start: 68 outliers final: 33 residues processed: 233 average time/residue: 0.1614 time to fit residues: 59.9995 Evaluate side-chains 197 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 160 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 455 PHE Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 786 TYR Chi-restraints excluded: chain C residue 827 ILE Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 923 LEU Chi-restraints excluded: chain C residue 937 ILE Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 630 ASN Chi-restraints excluded: chain D residue 631 CYS Chi-restraints excluded: chain D residue 694 VAL Chi-restraints excluded: chain D residue 717 LEU Chi-restraints excluded: chain D residue 845 VAL Chi-restraints excluded: chain D residue 862 ILE Chi-restraints excluded: chain D residue 880 LEU Chi-restraints excluded: chain E residue 428 VAL Chi-restraints excluded: chain E residue 476 VAL Chi-restraints excluded: chain E residue 484 CYS Chi-restraints excluded: chain E residue 493 PHE Chi-restraints excluded: chain E residue 517 PHE Chi-restraints excluded: chain E residue 648 LEU Chi-restraints excluded: chain E residue 712 THR Chi-restraints excluded: chain E residue 720 LEU Chi-restraints excluded: chain E residue 1352 LEU Chi-restraints excluded: chain E residue 1382 GLU Chi-restraints excluded: chain F residue 444 PHE Chi-restraints excluded: chain F residue 476 VAL Chi-restraints excluded: chain F residue 641 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 10 optimal weight: 0.9980 chunk 293 optimal weight: 8.9990 chunk 109 optimal weight: 0.9990 chunk 233 optimal weight: 5.9990 chunk 200 optimal weight: 2.9990 chunk 245 optimal weight: 9.9990 chunk 273 optimal weight: 5.9990 chunk 301 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 148 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.104874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.073687 restraints weight = 87935.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.074705 restraints weight = 50783.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.075081 restraints weight = 37679.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.075638 restraints weight = 29401.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.075738 restraints weight = 25415.426| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25845 Z= 0.146 Angle : 0.628 10.417 35025 Z= 0.313 Chirality : 0.043 0.160 3949 Planarity : 0.005 0.053 4490 Dihedral : 8.990 178.932 3582 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.17 % Favored : 93.70 % Rotamer: Outliers : 1.91 % Allowed : 13.93 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % 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: -0.52 (0.16), residues: 3110 helix: 0.58 (0.14), residues: 1419 sheet: 0.16 (0.28), residues: 374 loop : -1.51 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 543 TYR 0.023 0.001 TYR A 858 PHE 0.025 0.001 PHE F 452 TRP 0.010 0.001 TRP D 865 HIS 0.004 0.001 HIS A 815 Details of bonding type rmsd covalent geometry : bond 0.00340 (25837) covalent geometry : angle 0.62793 (35025) hydrogen bonds : bond 0.04333 ( 983) hydrogen bonds : angle 4.63841 ( 2844) Misc. bond : bond 0.00352 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6220 Ramachandran restraints generated. 3110 Oldfield, 0 Emsley, 3110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6220 Ramachandran restraints generated. 3110 Oldfield, 0 Emsley, 3110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 187 time to evaluate : 0.684 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 556 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8403 (pp) REVERT: A 686 MET cc_start: 0.5297 (pmm) cc_final: 0.4385 (pmm) REVERT: A 826 ASP cc_start: 0.8707 (t70) cc_final: 0.8462 (t70) REVERT: A 848 GLU cc_start: 0.7725 (tp30) cc_final: 0.7385 (tp30) REVERT: B 1379 MET cc_start: 0.8233 (mmt) cc_final: 0.7802 (mmt) REVERT: D 717 LEU cc_start: 0.9460 (OUTLIER) cc_final: 0.9014 (mm) REVERT: E 423 VAL cc_start: 0.8194 (OUTLIER) cc_final: 0.7856 (t) REVERT: E 523 MET cc_start: 0.7434 (tpt) cc_final: 0.7223 (tpp) REVERT: E 530 PHE cc_start: 0.7440 (m-80) cc_final: 0.6683 (m-10) REVERT: E 649 CYS cc_start: 0.9303 (t) cc_final: 0.9090 (t) REVERT: E 819 LYS cc_start: 0.6231 (OUTLIER) cc_final: 0.6015 (pttm) REVERT: F 441 MET cc_start: 0.4673 (ptm) cc_final: 0.4265 (ptm) REVERT: F 457 ILE cc_start: 0.6933 (mm) cc_final: 0.6517 (pt) REVERT: F 565 ARG cc_start: 0.2713 (pmt170) cc_final: 0.1927 (mpt180) REVERT: F 686 MET cc_start: 0.2620 (pmm) cc_final: 0.1143 (ptm) REVERT: F 893 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7373 (mt) REVERT: F 1365 ARG cc_start: 0.7454 (mmp80) cc_final: 0.7109 (mmp80) outliers start: 53 outliers final: 29 residues processed: 227 average time/residue: 0.1398 time to fit residues: 51.6869 Evaluate side-chains 201 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 167 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 455 PHE Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 1344 SER Chi-restraints excluded: chain C residue 484 CYS Chi-restraints excluded: chain C residue 786 TYR Chi-restraints excluded: chain C residue 827 ILE Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 937 ILE Chi-restraints excluded: chain D residue 471 THR Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 630 ASN Chi-restraints excluded: chain D residue 694 VAL Chi-restraints excluded: chain D residue 717 LEU Chi-restraints excluded: chain D residue 862 ILE Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain E residue 493 PHE Chi-restraints excluded: chain E residue 517 PHE Chi-restraints excluded: chain E residue 648 LEU Chi-restraints excluded: chain E residue 712 THR Chi-restraints excluded: chain E residue 720 LEU Chi-restraints excluded: chain E residue 819 LYS Chi-restraints excluded: chain E residue 846 ILE Chi-restraints excluded: chain E residue 938 LEU Chi-restraints excluded: chain E residue 1382 GLU Chi-restraints excluded: chain F residue 444 PHE Chi-restraints excluded: chain F residue 476 VAL Chi-restraints excluded: chain F residue 836 THR Chi-restraints excluded: chain F residue 893 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 225 optimal weight: 8.9990 chunk 270 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 183 optimal weight: 0.9990 chunk 138 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 208 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 140 optimal weight: 0.8980 chunk 200 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.105190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.073772 restraints weight = 87222.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.075133 restraints weight = 51381.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.075267 restraints weight = 38585.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.075954 restraints weight = 27836.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.075991 restraints weight = 23023.301| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25845 Z= 0.129 Angle : 0.606 10.062 35025 Z= 0.299 Chirality : 0.042 0.234 3949 Planarity : 0.004 0.052 4490 Dihedral : 8.637 178.288 3582 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.04 % Favored : 92.89 % Rotamer: Outliers : 1.98 % Allowed : 14.83 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % 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: -0.28 (0.16), residues: 3110 helix: 0.79 (0.14), residues: 1418 sheet: 0.36 (0.28), residues: 372 loop : -1.43 (0.18), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 576 TYR 0.020 0.001 TYR A 858 PHE 0.021 0.001 PHE F 452 TRP 0.010 0.001 TRP D 865 HIS 0.003 0.001 HIS A 815 Details of bonding type rmsd covalent geometry : bond 0.00299 (25837) covalent geometry : angle 0.60609 (35025) hydrogen bonds : bond 0.03842 ( 983) hydrogen bonds : angle 4.40183 ( 2844) Misc. bond : bond 0.00320 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6220 Ramachandran restraints generated. 3110 Oldfield, 0 Emsley, 3110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6220 Ramachandran restraints generated. 3110 Oldfield, 0 Emsley, 3110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 181 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 556 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8281 (pp) REVERT: A 686 MET cc_start: 0.5308 (pmm) cc_final: 0.4550 (pmm) REVERT: A 699 GLN cc_start: 0.7913 (tm-30) cc_final: 0.7658 (tm-30) REVERT: A 848 GLU cc_start: 0.7724 (tp30) cc_final: 0.7344 (tp30) REVERT: A 1379 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7576 (mtm) REVERT: B 1379 MET cc_start: 0.8198 (mmt) cc_final: 0.7732 (mmt) REVERT: D 717 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.8992 (mm) REVERT: E 530 PHE cc_start: 0.7392 (m-80) cc_final: 0.6610 (m-10) REVERT: E 686 MET cc_start: 0.8269 (tpp) cc_final: 0.7923 (tpp) REVERT: E 819 LYS cc_start: 0.6245 (OUTLIER) cc_final: 0.6012 (pttm) REVERT: F 441 MET cc_start: 0.4645 (ptm) cc_final: 0.4296 (ptm) REVERT: F 457 ILE cc_start: 0.6893 (mm) cc_final: 0.6483 (pt) REVERT: F 564 SER cc_start: 0.1014 (t) cc_final: 0.0717 (m) REVERT: F 565 ARG cc_start: 0.2630 (pmt170) cc_final: 0.1883 (mpt180) REVERT: F 686 MET cc_start: 0.2833 (pmm) cc_final: 0.1462 (ptm) REVERT: F 893 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7268 (mt) REVERT: F 1365 ARG cc_start: 0.7548 (mmp80) cc_final: 0.7243 (mmp80) outliers start: 55 outliers final: 34 residues processed: 223 average time/residue: 0.1344 time to fit residues: 49.2487 Evaluate side-chains 204 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 165 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 455 PHE Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 1379 MET Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 1344 SER Chi-restraints excluded: chain C residue 786 TYR Chi-restraints excluded: chain C residue 827 ILE Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 881 LEU Chi-restraints excluded: chain D residue 471 THR Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 630 ASN Chi-restraints excluded: chain D residue 694 VAL Chi-restraints excluded: chain D residue 717 LEU Chi-restraints excluded: chain D residue 798 VAL Chi-restraints excluded: chain D residue 818 GLU Chi-restraints excluded: chain D residue 880 LEU Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain E residue 428 VAL Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 493 PHE Chi-restraints excluded: chain E residue 648 LEU Chi-restraints excluded: chain E residue 667 LEU Chi-restraints excluded: chain E residue 712 THR Chi-restraints excluded: chain E residue 720 LEU Chi-restraints excluded: chain E residue 819 LYS Chi-restraints excluded: chain E residue 846 ILE Chi-restraints excluded: chain E residue 938 LEU Chi-restraints excluded: chain E residue 1382 GLU Chi-restraints excluded: chain F residue 476 VAL Chi-restraints excluded: chain F residue 598 LEU Chi-restraints excluded: chain F residue 641 SER Chi-restraints excluded: chain F residue 681 VAL Chi-restraints excluded: chain F residue 893 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 43 optimal weight: 4.9990 chunk 212 optimal weight: 0.1980 chunk 111 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 267 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 197 optimal weight: 0.2980 chunk 27 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.105530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.074671 restraints weight = 87929.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.075376 restraints weight = 54315.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.075852 restraints weight = 38728.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.076293 restraints weight = 31523.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.076329 restraints weight = 25423.910| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 25845 Z= 0.116 Angle : 0.595 10.825 35025 Z= 0.291 Chirality : 0.042 0.190 3949 Planarity : 0.004 0.082 4490 Dihedral : 8.291 179.341 3582 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.46 % Favored : 93.47 % Rotamer: Outliers : 2.16 % Allowed : 15.01 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % 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: -0.08 (0.16), residues: 3110 helix: 0.97 (0.15), residues: 1417 sheet: 0.55 (0.28), residues: 365 loop : -1.37 (0.18), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 543 TYR 0.018 0.001 TYR A 448 PHE 0.019 0.001 PHE F 452 TRP 0.011 0.001 TRP F 615 HIS 0.003 0.000 HIS A 815 Details of bonding type rmsd covalent geometry : bond 0.00266 (25837) covalent geometry : angle 0.59459 (35025) hydrogen bonds : bond 0.03461 ( 983) hydrogen bonds : angle 4.22052 ( 2844) Misc. bond : bond 0.00291 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6220 Ramachandran restraints generated. 3110 Oldfield, 0 Emsley, 3110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6220 Ramachandran restraints generated. 3110 Oldfield, 0 Emsley, 3110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 186 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 556 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8228 (pp) REVERT: A 576 ARG cc_start: 0.8029 (ttp-110) cc_final: 0.7441 (mtm110) REVERT: A 686 MET cc_start: 0.5252 (pmm) cc_final: 0.4482 (pmm) REVERT: A 699 GLN cc_start: 0.7919 (tm-30) cc_final: 0.7686 (tm-30) REVERT: A 848 GLU cc_start: 0.7756 (tp30) cc_final: 0.7284 (tp30) REVERT: A 1379 MET cc_start: 0.8027 (OUTLIER) cc_final: 0.7472 (mtm) REVERT: B 1379 MET cc_start: 0.8220 (mmt) cc_final: 0.7800 (mmt) REVERT: C 873 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.8953 (tt) REVERT: D 705 VAL cc_start: 0.8907 (OUTLIER) cc_final: 0.8673 (t) REVERT: D 717 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9047 (mm) REVERT: E 517 PHE cc_start: 0.7441 (t80) cc_final: 0.7114 (m-80) REVERT: E 559 MET cc_start: 0.8711 (mmm) cc_final: 0.8459 (mmm) REVERT: E 686 MET cc_start: 0.8262 (tpp) cc_final: 0.7923 (tpp) REVERT: E 819 LYS cc_start: 0.6164 (OUTLIER) cc_final: 0.5874 (pttm) REVERT: F 441 MET cc_start: 0.4638 (ptm) cc_final: 0.4260 (ptm) REVERT: F 457 ILE cc_start: 0.6882 (mm) cc_final: 0.6482 (pt) REVERT: F 564 SER cc_start: 0.1063 (t) cc_final: 0.0758 (m) REVERT: F 565 ARG cc_start: 0.2446 (pmt170) cc_final: 0.1722 (mpt180) REVERT: F 686 MET cc_start: 0.2719 (pmm) cc_final: 0.1169 (ptm) REVERT: F 893 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.7215 (mt) REVERT: F 1365 ARG cc_start: 0.7679 (mmp80) cc_final: 0.7438 (mmp80) outliers start: 60 outliers final: 37 residues processed: 231 average time/residue: 0.1447 time to fit residues: 54.6369 Evaluate side-chains 212 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 168 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 455 PHE Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 1379 MET Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 1344 SER Chi-restraints excluded: chain C residue 786 TYR Chi-restraints excluded: chain C residue 827 ILE Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 881 LEU Chi-restraints excluded: chain D residue 471 THR Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 630 ASN Chi-restraints excluded: chain D residue 694 VAL Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain D residue 709 LEU Chi-restraints excluded: chain D residue 717 LEU Chi-restraints excluded: chain D residue 786 TYR Chi-restraints excluded: chain D residue 798 VAL Chi-restraints excluded: chain D residue 818 GLU Chi-restraints excluded: chain E residue 428 VAL Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 493 PHE Chi-restraints excluded: chain E residue 648 LEU Chi-restraints excluded: chain E residue 649 CYS Chi-restraints excluded: chain E residue 712 THR Chi-restraints excluded: chain E residue 720 LEU Chi-restraints excluded: chain E residue 819 LYS Chi-restraints excluded: chain E residue 846 ILE Chi-restraints excluded: chain E residue 1382 GLU Chi-restraints excluded: chain F residue 444 PHE Chi-restraints excluded: chain F residue 598 LEU Chi-restraints excluded: chain F residue 641 SER Chi-restraints excluded: chain F residue 681 VAL Chi-restraints excluded: chain F residue 703 THR Chi-restraints excluded: chain F residue 833 VAL Chi-restraints excluded: chain F residue 836 THR Chi-restraints excluded: chain F residue 893 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 164 optimal weight: 4.9990 chunk 104 optimal weight: 0.5980 chunk 73 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 227 optimal weight: 6.9990 chunk 152 optimal weight: 0.3980 chunk 303 optimal weight: 5.9990 chunk 172 optimal weight: 2.9990 chunk 288 optimal weight: 0.9990 chunk 145 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 434 HIS ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1385 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.104901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.073819 restraints weight = 87843.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.075011 restraints weight = 53503.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.075438 restraints weight = 35609.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.075937 restraints weight = 28908.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.075966 restraints weight = 24676.428| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25845 Z= 0.135 Angle : 0.608 16.768 35025 Z= 0.297 Chirality : 0.042 0.162 3949 Planarity : 0.004 0.082 4490 Dihedral : 8.083 178.227 3582 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.69 % Favored : 93.25 % Rotamer: Outliers : 2.27 % Allowed : 15.58 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % 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: -0.03 (0.16), residues: 3110 helix: 0.99 (0.15), residues: 1420 sheet: 0.56 (0.28), residues: 367 loop : -1.31 (0.18), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 576 TYR 0.025 0.001 TYR F 823 PHE 0.015 0.001 PHE F 452 TRP 0.012 0.001 TRP F 615 HIS 0.004 0.001 HIS F 863 Details of bonding type rmsd covalent geometry : bond 0.00316 (25837) covalent geometry : angle 0.60786 (35025) hydrogen bonds : bond 0.03619 ( 983) hydrogen bonds : angle 4.22381 ( 2844) Misc. bond : bond 0.00333 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6220 Ramachandran restraints generated. 3110 Oldfield, 0 Emsley, 3110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6220 Ramachandran restraints generated. 3110 Oldfield, 0 Emsley, 3110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 171 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 556 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8280 (pp) REVERT: A 686 MET cc_start: 0.5207 (pmm) cc_final: 0.4742 (pmm) REVERT: A 699 GLN cc_start: 0.8001 (tm-30) cc_final: 0.7711 (tm-30) REVERT: A 848 GLU cc_start: 0.7866 (tp30) cc_final: 0.7445 (tp30) REVERT: A 1379 MET cc_start: 0.7855 (OUTLIER) cc_final: 0.7294 (mtm) REVERT: B 789 MET cc_start: 0.7918 (ttp) cc_final: 0.7700 (tmm) REVERT: B 1379 MET cc_start: 0.8277 (mmt) cc_final: 0.7900 (mmt) REVERT: C 873 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.8987 (tt) REVERT: D 705 VAL cc_start: 0.8935 (OUTLIER) cc_final: 0.8706 (t) REVERT: D 717 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.9053 (mm) REVERT: E 686 MET cc_start: 0.8279 (tpp) cc_final: 0.7910 (tpp) REVERT: E 720 LEU cc_start: 0.7293 (OUTLIER) cc_final: 0.6971 (pp) REVERT: E 819 LYS cc_start: 0.6151 (OUTLIER) cc_final: 0.5928 (pttm) REVERT: F 441 MET cc_start: 0.4762 (OUTLIER) cc_final: 0.4367 (ptp) REVERT: F 457 ILE cc_start: 0.6784 (mm) cc_final: 0.6392 (pt) REVERT: F 893 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.7312 (mt) REVERT: F 1365 ARG cc_start: 0.7688 (mmp80) cc_final: 0.7480 (mmp80) outliers start: 63 outliers final: 41 residues processed: 217 average time/residue: 0.1407 time to fit residues: 50.7017 Evaluate side-chains 217 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 167 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 455 PHE Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 1379 MET Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain C residue 695 THR Chi-restraints excluded: chain C residue 714 ASP Chi-restraints excluded: chain C residue 786 TYR Chi-restraints excluded: chain C residue 827 ILE Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 881 LEU Chi-restraints excluded: chain D residue 471 THR Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 630 ASN Chi-restraints excluded: chain D residue 694 VAL Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain D residue 709 LEU Chi-restraints excluded: chain D residue 717 LEU Chi-restraints excluded: chain D residue 786 TYR Chi-restraints excluded: chain D residue 798 VAL Chi-restraints excluded: chain D residue 818 GLU Chi-restraints excluded: chain D residue 880 LEU Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain E residue 428 VAL Chi-restraints excluded: chain E residue 493 PHE Chi-restraints excluded: chain E residue 517 PHE Chi-restraints excluded: chain E residue 648 LEU Chi-restraints excluded: chain E residue 712 THR Chi-restraints excluded: chain E residue 720 LEU Chi-restraints excluded: chain E residue 819 LYS Chi-restraints excluded: chain E residue 846 ILE Chi-restraints excluded: chain E residue 1382 GLU Chi-restraints excluded: chain F residue 441 MET Chi-restraints excluded: chain F residue 444 PHE Chi-restraints excluded: chain F residue 476 VAL Chi-restraints excluded: chain F residue 495 MET Chi-restraints excluded: chain F residue 598 LEU Chi-restraints excluded: chain F residue 641 SER Chi-restraints excluded: chain F residue 681 VAL Chi-restraints excluded: chain F residue 703 THR Chi-restraints excluded: chain F residue 833 VAL Chi-restraints excluded: chain F residue 836 THR Chi-restraints excluded: chain F residue 893 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 68 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 chunk 285 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 197 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 212 optimal weight: 2.9990 chunk 278 optimal weight: 5.9990 chunk 181 optimal weight: 3.9990 chunk 246 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.103823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.072599 restraints weight = 87534.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.073440 restraints weight = 51777.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.073868 restraints weight = 40897.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.074672 restraints weight = 29938.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.074718 restraints weight = 23653.662| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 25845 Z= 0.153 Angle : 0.627 14.739 35025 Z= 0.307 Chirality : 0.042 0.143 3949 Planarity : 0.005 0.072 4490 Dihedral : 7.932 173.743 3582 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.82 % Favored : 93.12 % Rotamer: Outliers : 2.37 % Allowed : 15.98 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % 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: -0.03 (0.16), residues: 3110 helix: 0.98 (0.14), residues: 1428 sheet: 0.49 (0.28), residues: 377 loop : -1.30 (0.18), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 543 TYR 0.017 0.001 TYR F 448 PHE 0.014 0.001 PHE F 465 TRP 0.010 0.001 TRP F 865 HIS 0.003 0.001 HIS F 863 Details of bonding type rmsd covalent geometry : bond 0.00359 (25837) covalent geometry : angle 0.62704 (35025) hydrogen bonds : bond 0.03799 ( 983) hydrogen bonds : angle 4.24659 ( 2844) Misc. bond : bond 0.00402 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6220 Ramachandran restraints generated. 3110 Oldfield, 0 Emsley, 3110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6220 Ramachandran restraints generated. 3110 Oldfield, 0 Emsley, 3110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 171 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 526 SER cc_start: 0.8419 (m) cc_final: 0.8186 (m) REVERT: A 556 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8122 (pp) REVERT: A 576 ARG cc_start: 0.8113 (ttp-110) cc_final: 0.7492 (mtm110) REVERT: A 686 MET cc_start: 0.5217 (pmm) cc_final: 0.4728 (pmm) REVERT: A 699 GLN cc_start: 0.8026 (tm-30) cc_final: 0.7703 (tm-30) REVERT: A 848 GLU cc_start: 0.7831 (tp30) cc_final: 0.7434 (tp30) REVERT: A 1379 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.7387 (mtm) REVERT: B 686 MET cc_start: 0.7763 (tmm) cc_final: 0.7473 (tmm) REVERT: B 1379 MET cc_start: 0.8252 (mmt) cc_final: 0.7879 (mmt) REVERT: C 591 ASP cc_start: 0.7700 (m-30) cc_final: 0.7491 (m-30) REVERT: C 708 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.9081 (tt) REVERT: D 705 VAL cc_start: 0.8977 (OUTLIER) cc_final: 0.8760 (t) REVERT: D 717 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.9049 (mm) REVERT: E 559 MET cc_start: 0.8671 (mmm) cc_final: 0.8436 (mmp) REVERT: E 686 MET cc_start: 0.8344 (tpp) cc_final: 0.8003 (tpp) REVERT: E 720 LEU cc_start: 0.7310 (OUTLIER) cc_final: 0.6990 (pp) REVERT: E 819 LYS cc_start: 0.6162 (OUTLIER) cc_final: 0.5926 (pttm) REVERT: F 441 MET cc_start: 0.4415 (ptm) cc_final: 0.4068 (ptp) REVERT: F 457 ILE cc_start: 0.6742 (mm) cc_final: 0.6366 (pt) REVERT: F 567 GLU cc_start: 0.6779 (mp0) cc_final: 0.6250 (mt-10) REVERT: F 686 MET cc_start: 0.2977 (pmm) cc_final: 0.1309 (ptm) REVERT: F 893 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.7211 (mt) outliers start: 66 outliers final: 42 residues processed: 219 average time/residue: 0.1534 time to fit residues: 55.5506 Evaluate side-chains 208 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 158 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 455 PHE Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 1379 MET Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 845 VAL Chi-restraints excluded: chain C residue 695 THR Chi-restraints excluded: chain C residue 708 LEU Chi-restraints excluded: chain C residue 714 ASP Chi-restraints excluded: chain C residue 786 TYR Chi-restraints excluded: chain C residue 827 ILE Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 881 LEU Chi-restraints excluded: chain C residue 923 LEU Chi-restraints excluded: chain D residue 471 THR Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 630 ASN Chi-restraints excluded: chain D residue 694 VAL Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain D residue 709 LEU Chi-restraints excluded: chain D residue 717 LEU Chi-restraints excluded: chain D residue 786 TYR Chi-restraints excluded: chain D residue 798 VAL Chi-restraints excluded: chain D residue 818 GLU Chi-restraints excluded: chain D residue 880 LEU Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain E residue 428 VAL Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 493 PHE Chi-restraints excluded: chain E residue 648 LEU Chi-restraints excluded: chain E residue 712 THR Chi-restraints excluded: chain E residue 720 LEU Chi-restraints excluded: chain E residue 819 LYS Chi-restraints excluded: chain E residue 846 ILE Chi-restraints excluded: chain E residue 938 LEU Chi-restraints excluded: chain E residue 1382 GLU Chi-restraints excluded: chain F residue 444 PHE Chi-restraints excluded: chain F residue 476 VAL Chi-restraints excluded: chain F residue 495 MET Chi-restraints excluded: chain F residue 598 LEU Chi-restraints excluded: chain F residue 681 VAL Chi-restraints excluded: chain F residue 703 THR Chi-restraints excluded: chain F residue 789 MET Chi-restraints excluded: chain F residue 893 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 54 optimal weight: 0.7980 chunk 85 optimal weight: 0.5980 chunk 171 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 266 optimal weight: 8.9990 chunk 206 optimal weight: 3.9990 chunk 254 optimal weight: 2.9990 chunk 174 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E1366 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.104976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.073685 restraints weight = 86858.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.074810 restraints weight = 49902.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.075214 restraints weight = 37009.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.075935 restraints weight = 26678.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.075986 restraints weight = 22370.111| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25845 Z= 0.111 Angle : 0.610 14.988 35025 Z= 0.294 Chirality : 0.041 0.152 3949 Planarity : 0.004 0.072 4490 Dihedral : 7.681 168.721 3582 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.40 % Favored : 93.54 % Rotamer: Outliers : 1.66 % Allowed : 16.73 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % 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: 0.14 (0.16), residues: 3110 helix: 1.14 (0.15), residues: 1421 sheet: 0.73 (0.29), residues: 361 loop : -1.26 (0.18), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 543 TYR 0.020 0.001 TYR F 659 PHE 0.012 0.001 PHE F 452 TRP 0.010 0.001 TRP F 615 HIS 0.004 0.000 HIS F 863 Details of bonding type rmsd covalent geometry : bond 0.00254 (25837) covalent geometry : angle 0.60991 (35025) hydrogen bonds : bond 0.03243 ( 983) hydrogen bonds : angle 4.04414 ( 2844) Misc. bond : bond 0.00290 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6220 Ramachandran restraints generated. 3110 Oldfield, 0 Emsley, 3110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6220 Ramachandran restraints generated. 3110 Oldfield, 0 Emsley, 3110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 181 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 556 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8070 (pp) REVERT: A 686 MET cc_start: 0.5314 (pmm) cc_final: 0.4827 (pmm) REVERT: A 699 GLN cc_start: 0.8032 (tm-30) cc_final: 0.7686 (tm-30) REVERT: A 848 GLU cc_start: 0.7870 (tp30) cc_final: 0.7466 (tp30) REVERT: A 1379 MET cc_start: 0.7896 (OUTLIER) cc_final: 0.7364 (mtm) REVERT: B 686 MET cc_start: 0.7717 (tmm) cc_final: 0.7422 (tmm) REVERT: B 1379 MET cc_start: 0.8325 (mmt) cc_final: 0.7941 (mmt) REVERT: C 591 ASP cc_start: 0.8122 (m-30) cc_final: 0.7920 (m-30) REVERT: C 708 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9046 (tt) REVERT: D 705 VAL cc_start: 0.8915 (OUTLIER) cc_final: 0.8684 (t) REVERT: D 848 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8589 (mp0) REVERT: E 686 MET cc_start: 0.8297 (tpp) cc_final: 0.7873 (tpp) REVERT: E 720 LEU cc_start: 0.7376 (OUTLIER) cc_final: 0.6988 (pp) REVERT: E 819 LYS cc_start: 0.6268 (OUTLIER) cc_final: 0.6027 (pttm) REVERT: E 858 TYR cc_start: 0.8415 (t80) cc_final: 0.7970 (t80) REVERT: F 441 MET cc_start: 0.4469 (OUTLIER) cc_final: 0.4097 (ptp) REVERT: F 457 ILE cc_start: 0.6620 (mm) cc_final: 0.6257 (pt) REVERT: F 686 MET cc_start: 0.3131 (pmm) cc_final: 0.1689 (ptm) REVERT: F 718 GLU cc_start: 0.9119 (tm-30) cc_final: 0.8869 (mt-10) REVERT: F 893 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7302 (mt) outliers start: 46 outliers final: 36 residues processed: 213 average time/residue: 0.1356 time to fit residues: 47.4414 Evaluate side-chains 210 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 166 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 455 PHE Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 1379 MET Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain C residue 695 THR Chi-restraints excluded: chain C residue 708 LEU Chi-restraints excluded: chain C residue 786 TYR Chi-restraints excluded: chain C residue 827 ILE Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain D residue 471 THR Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 630 ASN Chi-restraints excluded: chain D residue 694 VAL Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain D residue 709 LEU Chi-restraints excluded: chain D residue 786 TYR Chi-restraints excluded: chain D residue 798 VAL Chi-restraints excluded: chain D residue 818 GLU Chi-restraints excluded: chain D residue 880 LEU Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 493 PHE Chi-restraints excluded: chain E residue 648 LEU Chi-restraints excluded: chain E residue 649 CYS Chi-restraints excluded: chain E residue 712 THR Chi-restraints excluded: chain E residue 720 LEU Chi-restraints excluded: chain E residue 819 LYS Chi-restraints excluded: chain E residue 846 ILE Chi-restraints excluded: chain E residue 938 LEU Chi-restraints excluded: chain E residue 1382 GLU Chi-restraints excluded: chain F residue 441 MET Chi-restraints excluded: chain F residue 444 PHE Chi-restraints excluded: chain F residue 495 MET Chi-restraints excluded: chain F residue 598 LEU Chi-restraints excluded: chain F residue 681 VAL Chi-restraints excluded: chain F residue 789 MET Chi-restraints excluded: chain F residue 893 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 148 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 222 optimal weight: 0.0040 chunk 120 optimal weight: 0.0060 chunk 24 optimal weight: 0.0060 chunk 35 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 226 optimal weight: 10.0000 chunk 125 optimal weight: 3.9990 chunk 167 optimal weight: 0.9980 overall best weight: 0.3424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 546 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.106127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.075878 restraints weight = 87492.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.075601 restraints weight = 54803.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.076840 restraints weight = 45289.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.077193 restraints weight = 30128.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.077378 restraints weight = 27331.560| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.4301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.082 25845 Z= 0.106 Angle : 0.616 17.637 35025 Z= 0.294 Chirality : 0.042 0.241 3949 Planarity : 0.004 0.069 4490 Dihedral : 7.387 163.119 3582 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.88 % Favored : 94.05 % Rotamer: Outliers : 1.48 % Allowed : 17.13 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % 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: 0.24 (0.16), residues: 3110 helix: 1.21 (0.15), residues: 1421 sheet: 0.80 (0.28), residues: 376 loop : -1.22 (0.18), residues: 1313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B 543 TYR 0.033 0.001 TYR F 786 PHE 0.012 0.001 PHE C 911 TRP 0.012 0.001 TRP F 615 HIS 0.004 0.000 HIS F 863 Details of bonding type rmsd covalent geometry : bond 0.00241 (25837) covalent geometry : angle 0.61560 (35025) hydrogen bonds : bond 0.02862 ( 983) hydrogen bonds : angle 3.91091 ( 2844) Misc. bond : bond 0.00240 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6220 Ramachandran restraints generated. 3110 Oldfield, 0 Emsley, 3110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6220 Ramachandran restraints generated. 3110 Oldfield, 0 Emsley, 3110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 186 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 576 ARG cc_start: 0.8084 (ttp-110) cc_final: 0.7483 (mtm110) REVERT: A 683 MET cc_start: 0.7541 (mmm) cc_final: 0.6427 (tpt) REVERT: A 699 GLN cc_start: 0.7925 (tm-30) cc_final: 0.7590 (tm-30) REVERT: A 848 GLU cc_start: 0.7782 (tp30) cc_final: 0.7307 (tp30) REVERT: A 1375 LEU cc_start: 0.5376 (OUTLIER) cc_final: 0.4499 (pp) REVERT: A 1379 MET cc_start: 0.7802 (OUTLIER) cc_final: 0.7287 (mtm) REVERT: B 686 MET cc_start: 0.7751 (tmm) cc_final: 0.7467 (tmm) REVERT: B 1379 MET cc_start: 0.8351 (mmt) cc_final: 0.8004 (mmt) REVERT: C 591 ASP cc_start: 0.7981 (m-30) cc_final: 0.7775 (m-30) REVERT: D 559 MET cc_start: 0.8477 (tpt) cc_final: 0.8261 (tpt) REVERT: D 705 VAL cc_start: 0.8871 (OUTLIER) cc_final: 0.8654 (t) REVERT: D 848 GLU cc_start: 0.8777 (mm-30) cc_final: 0.8576 (mp0) REVERT: E 546 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7788 (tm-30) REVERT: E 559 MET cc_start: 0.8378 (mmp) cc_final: 0.7448 (ttt) REVERT: E 686 MET cc_start: 0.8198 (tpp) cc_final: 0.7833 (tpp) REVERT: E 720 LEU cc_start: 0.7298 (OUTLIER) cc_final: 0.7022 (pp) REVERT: F 441 MET cc_start: 0.4442 (OUTLIER) cc_final: 0.4026 (ptp) REVERT: F 457 ILE cc_start: 0.6720 (mm) cc_final: 0.6361 (pt) REVERT: F 686 MET cc_start: 0.2803 (pmm) cc_final: 0.1357 (ptm) REVERT: F 718 GLU cc_start: 0.9130 (tm-30) cc_final: 0.8828 (mt-10) REVERT: F 893 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7304 (mt) outliers start: 41 outliers final: 27 residues processed: 213 average time/residue: 0.1664 time to fit residues: 57.9264 Evaluate side-chains 206 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 172 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 PHE Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 1375 LEU Chi-restraints excluded: chain A residue 1379 MET Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain C residue 695 THR Chi-restraints excluded: chain C residue 786 TYR Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain D residue 471 THR Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 630 ASN Chi-restraints excluded: chain D residue 694 VAL Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain D residue 709 LEU Chi-restraints excluded: chain D residue 786 TYR Chi-restraints excluded: chain D residue 798 VAL Chi-restraints excluded: chain D residue 818 GLU Chi-restraints excluded: chain D residue 880 LEU Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 493 PHE Chi-restraints excluded: chain E residue 546 GLN Chi-restraints excluded: chain E residue 712 THR Chi-restraints excluded: chain E residue 720 LEU Chi-restraints excluded: chain E residue 846 ILE Chi-restraints excluded: chain E residue 1382 GLU Chi-restraints excluded: chain F residue 441 MET Chi-restraints excluded: chain F residue 444 PHE Chi-restraints excluded: chain F residue 495 MET Chi-restraints excluded: chain F residue 598 LEU Chi-restraints excluded: chain F residue 789 MET Chi-restraints excluded: chain F residue 893 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 192 optimal weight: 0.7980 chunk 225 optimal weight: 0.2980 chunk 74 optimal weight: 1.9990 chunk 237 optimal weight: 4.9990 chunk 245 optimal weight: 5.9990 chunk 220 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 285 optimal weight: 0.0470 chunk 198 optimal weight: 6.9990 chunk 180 optimal weight: 5.9990 chunk 196 optimal weight: 1.9990 overall best weight: 1.0282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 546 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.105502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.074462 restraints weight = 86723.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.075959 restraints weight = 56947.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.075827 restraints weight = 34687.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.076129 restraints weight = 33744.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.076196 restraints weight = 30596.378| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25845 Z= 0.113 Angle : 0.615 14.768 35025 Z= 0.295 Chirality : 0.042 0.239 3949 Planarity : 0.004 0.070 4490 Dihedral : 7.329 159.147 3582 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.14 % Favored : 93.79 % Rotamer: Outliers : 1.51 % Allowed : 17.60 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % 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: 0.29 (0.16), residues: 3110 helix: 1.26 (0.15), residues: 1427 sheet: 0.82 (0.28), residues: 370 loop : -1.20 (0.18), residues: 1313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 576 TYR 0.022 0.001 TYR F 659 PHE 0.010 0.001 PHE F 452 TRP 0.021 0.001 TRP F 615 HIS 0.004 0.000 HIS F 863 Details of bonding type rmsd covalent geometry : bond 0.00265 (25837) covalent geometry : angle 0.61526 (35025) hydrogen bonds : bond 0.03004 ( 983) hydrogen bonds : angle 3.91838 ( 2844) Misc. bond : bond 0.00259 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3845.50 seconds wall clock time: 67 minutes 21.97 seconds (4041.97 seconds total)