Starting phenix.real_space_refine on Sun Jun 22 01:03:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8juw_36665/06_2025/8juw_36665_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8juw_36665/06_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_36665/06_2025/8juw_36665.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8juw_36665/06_2025/8juw_36665.map" model { file = "/net/cci-nas-00/data/ceres_data/8juw_36665/06_2025/8juw_36665_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8juw_36665/06_2025/8juw_36665_neut.cif" } resolution = 3.79 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 17 5.49 5 S 110 5.16 5 C 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 16.98, per 1000 atoms: 0.67 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: 6.94 Conformation dependent library (CDL) restraints added in 3.5 seconds 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: 2.86 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: 9.45 Time building geometry restraints manager: 8.18 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: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.060 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 61.370 Find NCS groups from input model: 2.200 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.060 ------------------------------------------------------------------------------- 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 : 9.39 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (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 TRP 0.026 0.002 TRP A 505 HIS 0.008 0.001 HIS E 726 PHE 0.027 0.002 PHE B 831 TYR 0.019 0.002 TYR F 823 ARG 0.010 0.001 ARG B 794 Details of bonding type rmsd hydrogen bonds : bond 0.21389 ( 983) hydrogen bonds : angle 7.00296 ( 2844) covalent geometry : bond 0.00619 (25837) covalent geometry : angle 0.80121 (35025) 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 : 3.107 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: 0.4412 time to fit residues: 268.5359 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 : 3.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 5.9990 chunk 236 optimal weight: 7.9990 chunk 131 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 159 optimal weight: 2.9990 chunk 126 optimal weight: 0.6980 chunk 244 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 chunk 148 optimal weight: 3.9990 chunk 182 optimal weight: 1.9990 chunk 283 optimal weight: 6.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.107567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.073509 restraints weight = 86962.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.075327 restraints weight = 47598.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.076445 restraints weight = 32899.350| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 25845 Z= 0.161 Angle : 0.691 10.857 35025 Z= 0.348 Chirality : 0.045 0.172 3949 Planarity : 0.005 0.057 4490 Dihedral : 9.459 175.626 3582 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.37 % Favored : 93.54 % Rotamer: Outliers : 1.19 % Allowed : 8.89 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.15), residues: 3110 helix: 0.32 (0.14), residues: 1415 sheet: 0.20 (0.28), residues: 373 loop : -1.56 (0.17), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 865 HIS 0.008 0.001 HIS B 611 PHE 0.016 0.001 PHE F 465 TYR 0.018 0.002 TYR A 448 ARG 0.010 0.001 ARG A 496 Details of bonding type rmsd hydrogen bonds : bond 0.05554 ( 983) hydrogen bonds : angle 5.15485 ( 2844) covalent geometry : bond 0.00365 (25837) covalent geometry : angle 0.69084 (35025) Misc. bond : bond 0.00392 ( 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 251 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 218 time to evaluate : 3.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 560 ASP cc_start: 0.7537 (t0) cc_final: 0.7316 (t70) REVERT: A 605 LYS cc_start: 0.9015 (tttt) cc_final: 0.8793 (mtpt) REVERT: A 615 TRP cc_start: 0.4689 (m-10) cc_final: 0.3608 (m100) REVERT: A 686 MET cc_start: 0.5257 (pmm) cc_final: 0.4582 (pmm) REVERT: A 848 GLU cc_start: 0.7667 (tp30) cc_final: 0.7380 (tp30) REVERT: E 523 MET cc_start: 0.7482 (tpt) cc_final: 0.7231 (tpp) REVERT: E 559 MET cc_start: 0.8723 (mmm) cc_final: 0.8462 (mmp) REVERT: F 441 MET cc_start: 0.5303 (ptm) cc_final: 0.4966 (ptt) REVERT: F 457 ILE cc_start: 0.6047 (mm) cc_final: 0.5639 (pt) REVERT: F 686 MET cc_start: 0.3646 (pmm) cc_final: 0.3301 (ptm) outliers start: 33 outliers final: 18 residues processed: 234 average time/residue: 0.3804 time to fit residues: 142.5001 Evaluate side-chains 199 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 181 time to evaluate : 4.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 LEU 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 476 VAL 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 199 optimal weight: 0.9980 chunk 48 optimal weight: 8.9990 chunk 137 optimal weight: 0.5980 chunk 117 optimal weight: 2.9990 chunk 297 optimal weight: 0.5980 chunk 161 optimal weight: 3.9990 chunk 196 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 304 optimal weight: 20.0000 chunk 252 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1381 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.108267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.074553 restraints weight = 86220.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.076367 restraints weight = 47243.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.077534 restraints weight = 32675.153| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25845 Z= 0.118 Angle : 0.607 10.113 35025 Z= 0.303 Chirality : 0.042 0.169 3949 Planarity : 0.004 0.051 4490 Dihedral : 8.921 172.306 3582 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.69 % Favored : 93.25 % Rotamer: Outliers : 1.66 % Allowed : 10.72 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.16), residues: 3110 helix: 0.61 (0.14), residues: 1417 sheet: 0.42 (0.28), residues: 372 loop : -1.41 (0.17), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 865 HIS 0.005 0.000 HIS A 815 PHE 0.028 0.001 PHE F 452 TYR 0.032 0.001 TYR F 448 ARG 0.021 0.000 ARG C1367 Details of bonding type rmsd hydrogen bonds : bond 0.03980 ( 983) hydrogen bonds : angle 4.55176 ( 2844) covalent geometry : bond 0.00263 (25837) covalent geometry : angle 0.60655 (35025) Misc. bond : bond 0.00288 ( 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 261 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 215 time to evaluate : 3.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 615 TRP cc_start: 0.4719 (m-10) cc_final: 0.3662 (m100) REVERT: A 699 GLN cc_start: 0.7519 (tm-30) cc_final: 0.7234 (tm-30) REVERT: A 826 ASP cc_start: 0.8433 (t70) cc_final: 0.8077 (m-30) REVERT: A 848 GLU cc_start: 0.7564 (tp30) cc_final: 0.7194 (tp30) REVERT: A 1375 LEU cc_start: 0.5785 (OUTLIER) cc_final: 0.5571 (pp) REVERT: B 651 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.7675 (mm) REVERT: B 1379 MET cc_start: 0.8125 (mmt) cc_final: 0.7652 (mmt) REVERT: C 495 MET cc_start: 0.8185 (tmm) cc_final: 0.7974 (tmm) REVERT: E 530 PHE cc_start: 0.7400 (m-80) cc_final: 0.6752 (m-10) REVERT: E 558 LEU cc_start: 0.5829 (OUTLIER) cc_final: 0.5558 (pt) REVERT: E 938 LEU cc_start: 0.7285 (OUTLIER) cc_final: 0.6991 (pp) REVERT: F 441 MET cc_start: 0.5105 (ptm) cc_final: 0.4813 (ptp) REVERT: F 457 ILE cc_start: 0.6149 (mm) cc_final: 0.5732 (pt) REVERT: F 686 MET cc_start: 0.3577 (pmm) cc_final: 0.3188 (ptm) REVERT: F 1365 ARG cc_start: 0.7607 (mmp80) cc_final: 0.7174 (mmp80) outliers start: 46 outliers final: 19 residues processed: 246 average time/residue: 0.5129 time to fit residues: 204.8484 Evaluate side-chains 211 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 188 time to evaluate : 3.327 ------------------------------------------------------------------------------- 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 638 ASP Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 1375 LEU Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 651 LEU 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 880 LEU Chi-restraints excluded: chain D residue 630 ASN Chi-restraints excluded: chain D residue 694 VAL Chi-restraints excluded: chain D residue 1373 THR Chi-restraints excluded: chain E residue 558 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 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 641 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 70 optimal weight: 2.9990 chunk 149 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 195 optimal weight: 4.9990 chunk 113 optimal weight: 0.8980 chunk 259 optimal weight: 9.9990 chunk 136 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 81 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 289 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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** B 684 GLN B1330 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.106502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.074751 restraints weight = 86436.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.075902 restraints weight = 51379.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.076272 restraints weight = 38560.653| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 25845 Z= 0.145 Angle : 0.612 10.015 35025 Z= 0.303 Chirality : 0.042 0.236 3949 Planarity : 0.005 0.076 4490 Dihedral : 8.606 173.144 3582 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.40 % Favored : 93.54 % Rotamer: Outliers : 1.73 % Allowed : 12.49 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.16), residues: 3110 helix: 0.78 (0.14), residues: 1421 sheet: 0.38 (0.28), residues: 381 loop : -1.35 (0.18), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 865 HIS 0.003 0.001 HIS D 434 PHE 0.019 0.001 PHE F 596 TYR 0.024 0.001 TYR A 858 ARG 0.007 0.000 ARG A 576 Details of bonding type rmsd hydrogen bonds : bond 0.03936 ( 983) hydrogen bonds : angle 4.43098 ( 2844) covalent geometry : bond 0.00340 (25837) covalent geometry : angle 0.61198 (35025) Misc. bond : bond 0.00322 ( 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 241 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 193 time to evaluate : 4.163 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: 0.8653 (OUTLIER) cc_final: 0.8357 (pp) REVERT: A 615 TRP cc_start: 0.5255 (m-10) cc_final: 0.4040 (m100) REVERT: A 686 MET cc_start: 0.4997 (pmm) cc_final: 0.4592 (pmm) REVERT: A 699 GLN cc_start: 0.7554 (tm-30) cc_final: 0.7247 (tm-30) REVERT: A 826 ASP cc_start: 0.8583 (t70) cc_final: 0.8269 (m-30) REVERT: A 848 GLU cc_start: 0.7628 (tp30) cc_final: 0.7286 (tp30) REVERT: A 1375 LEU cc_start: 0.5497 (OUTLIER) cc_final: 0.4637 (pp) REVERT: A 1379 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7416 (mtm) REVERT: B 686 MET cc_start: 0.7880 (tmm) cc_final: 0.7672 (tmm) REVERT: B 1379 MET cc_start: 0.8173 (mmt) cc_final: 0.7723 (mmt) REVERT: C 873 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8928 (tt) REVERT: D 717 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.8964 (mm) REVERT: E 686 MET cc_start: 0.8205 (tpp) cc_final: 0.7922 (tpp) REVERT: E 938 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.7097 (pp) REVERT: F 441 MET cc_start: 0.4962 (ptm) cc_final: 0.4484 (ptt) REVERT: F 457 ILE cc_start: 0.6644 (mm) cc_final: 0.6212 (pt) REVERT: F 659 TYR cc_start: 0.6268 (t80) cc_final: 0.5323 (m-80) REVERT: F 686 MET cc_start: 0.2489 (pmm) cc_final: 0.1028 (ptm) REVERT: F 893 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7437 (mt) REVERT: F 1365 ARG cc_start: 0.7611 (mmp80) cc_final: 0.7250 (mmp80) outliers start: 48 outliers final: 25 residues processed: 228 average time/residue: 0.6079 time to fit residues: 230.6975 Evaluate side-chains 200 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 168 time to evaluate : 7.040 ------------------------------------------------------------------------------- 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 825 LEU Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 1375 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 C residue 648 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 D residue 471 THR 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 880 LEU Chi-restraints excluded: chain E residue 428 VAL Chi-restraints excluded: chain E residue 558 LEU 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 938 LEU Chi-restraints excluded: chain E residue 1382 GLU Chi-restraints excluded: chain F residue 476 VAL Chi-restraints excluded: chain F residue 641 SER Chi-restraints excluded: chain F residue 833 VAL 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 15 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 271 optimal weight: 3.9990 chunk 269 optimal weight: 0.0470 chunk 80 optimal weight: 0.1980 chunk 210 optimal weight: 2.9990 chunk 244 optimal weight: 9.9990 chunk 175 optimal weight: 0.0270 chunk 72 optimal weight: 0.9990 chunk 28 optimal weight: 0.2980 overall best weight: 0.3138 ------------------------------------------------------------------------------- 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** B1330 HIS E1385 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.108139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.076757 restraints weight = 87041.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.077969 restraints weight = 52305.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.078497 restraints weight = 35865.280| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 25845 Z= 0.104 Angle : 0.574 10.085 35025 Z= 0.281 Chirality : 0.041 0.162 3949 Planarity : 0.004 0.071 4490 Dihedral : 8.219 174.154 3582 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.05 % Favored : 93.89 % Rotamer: Outliers : 1.80 % Allowed : 13.21 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.16), residues: 3110 helix: 0.92 (0.15), residues: 1419 sheet: 0.64 (0.29), residues: 366 loop : -1.29 (0.18), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 505 HIS 0.004 0.000 HIS A 815 PHE 0.021 0.001 PHE F 452 TYR 0.026 0.001 TYR A 858 ARG 0.006 0.000 ARG A 576 Details of bonding type rmsd hydrogen bonds : bond 0.03172 ( 983) hydrogen bonds : angle 4.12280 ( 2844) covalent geometry : bond 0.00231 (25837) covalent geometry : angle 0.57440 (35025) Misc. bond : bond 0.00238 ( 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 257 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 207 time to evaluate : 3.375 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: 0.8477 (OUTLIER) cc_final: 0.8106 (pp) REVERT: A 615 TRP cc_start: 0.5282 (m-10) cc_final: 0.4049 (m100) REVERT: A 686 MET cc_start: 0.5035 (pmm) cc_final: 0.4701 (pmm) REVERT: A 699 GLN cc_start: 0.7557 (tm-30) cc_final: 0.7194 (tm-30) REVERT: A 826 ASP cc_start: 0.8590 (t0) cc_final: 0.8312 (m-30) REVERT: A 848 GLU cc_start: 0.7716 (tp30) cc_final: 0.7311 (tp30) REVERT: A 1375 LEU cc_start: 0.5565 (OUTLIER) cc_final: 0.5343 (pp) REVERT: B 545 ASP cc_start: 0.7787 (t0) cc_final: 0.7314 (m-30) REVERT: C 873 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8898 (tt) REVERT: D 705 VAL cc_start: 0.8822 (OUTLIER) cc_final: 0.8607 (t) REVERT: D 717 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.8949 (mm) REVERT: E 423 VAL cc_start: 0.8156 (OUTLIER) cc_final: 0.7825 (t) REVERT: E 530 PHE cc_start: 0.7315 (m-80) cc_final: 0.6613 (m-10) REVERT: E 686 MET cc_start: 0.8250 (tpp) cc_final: 0.7980 (tpp) REVERT: E 938 LEU cc_start: 0.7547 (OUTLIER) cc_final: 0.7295 (pp) REVERT: F 441 MET cc_start: 0.5068 (ptm) cc_final: 0.4608 (ptp) REVERT: F 457 ILE cc_start: 0.6529 (mm) cc_final: 0.6082 (pt) REVERT: F 686 MET cc_start: 0.2558 (pmm) cc_final: 0.0860 (ptm) REVERT: F 893 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7374 (mt) REVERT: F 1365 ARG cc_start: 0.7780 (mmp80) cc_final: 0.7514 (mmp80) outliers start: 50 outliers final: 21 residues processed: 244 average time/residue: 0.3989 time to fit residues: 160.5002 Evaluate side-chains 212 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 183 time to evaluate : 4.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 825 LEU Chi-restraints excluded: chain A residue 1375 LEU Chi-restraints excluded: chain B residue 475 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 717 LEU Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain E residue 428 VAL 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 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 641 SER Chi-restraints excluded: chain F residue 681 VAL Chi-restraints excluded: chain F residue 833 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 192 optimal weight: 1.9990 chunk 28 optimal weight: 0.2980 chunk 209 optimal weight: 9.9990 chunk 74 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 66 optimal weight: 0.0170 chunk 45 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 228 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 chunk 225 optimal weight: 20.0000 overall best weight: 0.5818 ------------------------------------------------------------------------------- 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 = 0.3865 r_free = 0.3865 target = 0.107721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.075755 restraints weight = 86905.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.077351 restraints weight = 49928.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.077828 restraints weight = 33369.646| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 25845 Z= 0.102 Angle : 0.582 14.609 35025 Z= 0.281 Chirality : 0.041 0.168 3949 Planarity : 0.004 0.068 4490 Dihedral : 7.983 176.738 3582 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.79 % Favored : 94.15 % Rotamer: Outliers : 1.48 % Allowed : 14.14 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.16), residues: 3110 helix: 1.04 (0.15), residues: 1419 sheet: 0.70 (0.29), residues: 369 loop : -1.20 (0.18), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 615 HIS 0.004 0.000 HIS A 815 PHE 0.016 0.001 PHE F 452 TYR 0.018 0.001 TYR F 659 ARG 0.010 0.000 ARG A 576 Details of bonding type rmsd hydrogen bonds : bond 0.03052 ( 983) hydrogen bonds : angle 4.03151 ( 2844) covalent geometry : bond 0.00232 (25837) covalent geometry : angle 0.58207 (35025) Misc. bond : bond 0.00235 ( 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 239 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 198 time to evaluate : 3.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 556 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8061 (pp) REVERT: A 576 ARG cc_start: 0.8099 (ttp-110) cc_final: 0.7399 (mtm110) REVERT: A 615 TRP cc_start: 0.5301 (m-10) cc_final: 0.4084 (m100) REVERT: A 686 MET cc_start: 0.5069 (pmm) cc_final: 0.4709 (pmm) REVERT: A 699 GLN cc_start: 0.7659 (tm-30) cc_final: 0.7261 (tm-30) REVERT: A 848 GLU cc_start: 0.7813 (tp30) cc_final: 0.7350 (tp30) REVERT: A 1375 LEU cc_start: 0.5552 (OUTLIER) cc_final: 0.4855 (pp) REVERT: A 1379 MET cc_start: 0.7939 (OUTLIER) cc_final: 0.7387 (mtm) REVERT: B 545 ASP cc_start: 0.7911 (t0) cc_final: 0.7370 (m-30) REVERT: D 705 VAL cc_start: 0.8873 (OUTLIER) cc_final: 0.8650 (t) REVERT: D 717 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.8923 (mm) REVERT: E 423 VAL cc_start: 0.8176 (OUTLIER) cc_final: 0.7860 (t) REVERT: E 530 PHE cc_start: 0.7285 (m-80) cc_final: 0.6581 (m-10) REVERT: E 686 MET cc_start: 0.8187 (tpp) cc_final: 0.7945 (tpp) REVERT: E 938 LEU cc_start: 0.7471 (OUTLIER) cc_final: 0.7217 (pp) REVERT: F 441 MET cc_start: 0.5135 (ptm) cc_final: 0.4716 (ptp) REVERT: F 457 ILE cc_start: 0.6484 (mm) cc_final: 0.6036 (pt) REVERT: F 659 TYR cc_start: 0.6488 (t80) cc_final: 0.5530 (m-80) REVERT: F 686 MET cc_start: 0.2912 (pmm) cc_final: 0.1390 (ptm) REVERT: F 893 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7343 (mt) REVERT: F 1365 ARG cc_start: 0.7835 (mmp80) cc_final: 0.7565 (mmp80) outliers start: 41 outliers final: 22 residues processed: 226 average time/residue: 0.3770 time to fit residues: 143.5390 Evaluate side-chains 212 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 182 time to evaluate : 3.151 ------------------------------------------------------------------------------- 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 825 LEU Chi-restraints excluded: chain A residue 1375 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 C residue 648 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 717 LEU 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 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 938 LEU Chi-restraints excluded: chain E residue 1382 GLU Chi-restraints excluded: chain F residue 444 PHE 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 182 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 289 optimal weight: 5.9990 chunk 35 optimal weight: 0.2980 chunk 207 optimal weight: 0.0370 chunk 44 optimal weight: 8.9990 chunk 135 optimal weight: 2.9990 chunk 291 optimal weight: 0.6980 chunk 185 optimal weight: 0.6980 chunk 192 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.108131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.077248 restraints weight = 87372.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.077062 restraints weight = 57266.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.078342 restraints weight = 46492.447| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 25845 Z= 0.100 Angle : 0.579 13.852 35025 Z= 0.277 Chirality : 0.041 0.171 3949 Planarity : 0.004 0.063 4490 Dihedral : 7.769 177.187 3582 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.85 % Favored : 94.08 % Rotamer: Outliers : 1.58 % Allowed : 14.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.16), residues: 3110 helix: 1.09 (0.15), residues: 1425 sheet: 0.76 (0.28), residues: 371 loop : -1.12 (0.18), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 615 HIS 0.003 0.000 HIS A 815 PHE 0.014 0.001 PHE F 452 TYR 0.016 0.001 TYR A 915 ARG 0.007 0.000 ARG B 543 Details of bonding type rmsd hydrogen bonds : bond 0.02872 ( 983) hydrogen bonds : angle 3.93826 ( 2844) covalent geometry : bond 0.00228 (25837) covalent geometry : angle 0.57877 (35025) Misc. bond : bond 0.00219 ( 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 248 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 204 time to evaluate : 2.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 686 MET cc_start: 0.4941 (pmm) cc_final: 0.4620 (pmm) REVERT: A 699 GLN cc_start: 0.7702 (tm-30) cc_final: 0.7331 (tm-30) REVERT: A 848 GLU cc_start: 0.7791 (tp30) cc_final: 0.7332 (tp30) REVERT: A 1375 LEU cc_start: 0.5709 (OUTLIER) cc_final: 0.4998 (pp) REVERT: A 1379 MET cc_start: 0.7893 (OUTLIER) cc_final: 0.7325 (mtm) REVERT: B 510 GLU cc_start: 0.8028 (mp0) cc_final: 0.7750 (mp0) REVERT: B 545 ASP cc_start: 0.7861 (t0) cc_final: 0.7324 (m-30) REVERT: B 840 GLU cc_start: 0.7086 (tm-30) cc_final: 0.6746 (tm-30) REVERT: B 1379 MET cc_start: 0.8280 (mmt) cc_final: 0.7850 (mmt) REVERT: C 591 ASP cc_start: 0.7948 (m-30) cc_final: 0.7740 (m-30) REVERT: D 705 VAL cc_start: 0.8881 (OUTLIER) cc_final: 0.8664 (t) REVERT: D 717 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8966 (mm) REVERT: E 530 PHE cc_start: 0.7286 (m-80) cc_final: 0.6583 (m-10) REVERT: E 686 MET cc_start: 0.8166 (tpp) cc_final: 0.7924 (tpp) REVERT: E 720 LEU cc_start: 0.7204 (OUTLIER) cc_final: 0.6928 (pp) REVERT: E 938 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7368 (pp) REVERT: F 441 MET cc_start: 0.5166 (ptm) cc_final: 0.4728 (ptp) REVERT: F 457 ILE cc_start: 0.6525 (mm) cc_final: 0.6050 (pt) REVERT: F 893 LEU cc_start: 0.7606 (OUTLIER) cc_final: 0.7322 (mt) REVERT: F 1365 ARG cc_start: 0.7829 (mmp80) cc_final: 0.7579 (mmp80) outliers start: 44 outliers final: 25 residues processed: 232 average time/residue: 0.3392 time to fit residues: 129.8474 Evaluate side-chains 215 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 183 time to evaluate : 4.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 PHE Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 1375 LEU Chi-restraints excluded: chain A residue 1379 MET Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 651 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 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 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 D residue 1381 GLN 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 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 938 LEU Chi-restraints excluded: chain E residue 1382 GLU Chi-restraints excluded: chain F residue 444 PHE Chi-restraints excluded: chain F residue 681 VAL 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 277 optimal weight: 7.9990 chunk 222 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 256 optimal weight: 6.9990 chunk 224 optimal weight: 10.0000 chunk 162 optimal weight: 8.9990 chunk 47 optimal weight: 0.5980 chunk 137 optimal weight: 0.5980 chunk 278 optimal weight: 9.9990 chunk 273 optimal weight: 5.9990 chunk 266 optimal weight: 8.9990 overall best weight: 3.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 GLN B1330 HIS ** D 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.102862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.072385 restraints weight = 87927.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.072227 restraints weight = 57286.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.073241 restraints weight = 40194.238| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 25845 Z= 0.261 Angle : 0.761 15.557 35025 Z= 0.375 Chirality : 0.046 0.185 3949 Planarity : 0.005 0.077 4490 Dihedral : 8.527 178.985 3582 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.30 % Favored : 92.60 % Rotamer: Outliers : 1.87 % Allowed : 15.26 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.16), residues: 3110 helix: 0.77 (0.14), residues: 1417 sheet: 0.36 (0.28), residues: 377 loop : -1.37 (0.18), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 866 HIS 0.004 0.001 HIS B1366 PHE 0.027 0.002 PHE D 517 TYR 0.017 0.002 TYR C1364 ARG 0.009 0.001 ARG B 543 Details of bonding type rmsd hydrogen bonds : bond 0.05075 ( 983) hydrogen bonds : angle 4.63113 ( 2844) covalent geometry : bond 0.00616 (25837) covalent geometry : angle 0.76097 (35025) Misc. bond : bond 0.00475 ( 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 221 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 169 time to evaluate : 2.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 686 MET cc_start: 0.5057 (pmm) cc_final: 0.4320 (pmm) REVERT: A 699 GLN cc_start: 0.7942 (tm-30) cc_final: 0.7537 (tm-30) REVERT: A 848 GLU cc_start: 0.8006 (tp30) cc_final: 0.7617 (tp30) REVERT: A 1375 LEU cc_start: 0.5625 (OUTLIER) cc_final: 0.4852 (pp) REVERT: A 1379 MET cc_start: 0.7971 (OUTLIER) cc_final: 0.7401 (mtm) REVERT: B 545 ASP cc_start: 0.8435 (t0) cc_final: 0.8023 (m-30) REVERT: B 1379 MET cc_start: 0.8310 (mmt) cc_final: 0.7969 (mmt) REVERT: C 873 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9025 (tt) REVERT: D 556 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9070 (tt) REVERT: D 665 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7812 (mt) REVERT: D 717 LEU cc_start: 0.9447 (OUTLIER) cc_final: 0.8973 (mm) REVERT: E 686 MET cc_start: 0.8311 (tpp) cc_final: 0.7956 (tpp) REVERT: E 720 LEU cc_start: 0.7287 (OUTLIER) cc_final: 0.6988 (pp) REVERT: F 441 MET cc_start: 0.4756 (ptm) cc_final: 0.4333 (ptp) REVERT: F 457 ILE cc_start: 0.6894 (mm) cc_final: 0.6501 (pt) REVERT: F 567 GLU cc_start: 0.6854 (mp0) cc_final: 0.5973 (tt0) REVERT: F 686 MET cc_start: 0.1619 (pmm) cc_final: 0.0450 (ptm) REVERT: F 893 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7324 (mt) outliers start: 52 outliers final: 33 residues processed: 209 average time/residue: 0.3478 time to fit residues: 117.7466 Evaluate side-chains 194 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 153 time to evaluate : 2.855 ------------------------------------------------------------------------------- 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 558 LEU Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 1375 LEU Chi-restraints excluded: chain A residue 1379 MET Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 716 ILE Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 687 ILE 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 D residue 471 THR Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 630 ASN Chi-restraints excluded: chain D residue 665 LEU Chi-restraints excluded: chain D residue 694 VAL Chi-restraints excluded: chain D residue 709 LEU 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 484 CYS 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 1382 GLU Chi-restraints excluded: chain F residue 444 PHE Chi-restraints excluded: chain F residue 495 MET Chi-restraints excluded: chain F residue 681 VAL 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 49 optimal weight: 8.9990 chunk 140 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 123 optimal weight: 0.8980 chunk 148 optimal weight: 0.9980 chunk 280 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 278 optimal weight: 0.0670 chunk 42 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 145 optimal weight: 0.9990 overall best weight: 0.7922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1330 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.105740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.073988 restraints weight = 87201.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.075184 restraints weight = 50271.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.074873 restraints weight = 38926.699| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25845 Z= 0.114 Angle : 0.630 15.623 35025 Z= 0.303 Chirality : 0.042 0.150 3949 Planarity : 0.004 0.064 4490 Dihedral : 8.114 173.155 3582 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.88 % Favored : 94.05 % Rotamer: Outliers : 1.26 % Allowed : 16.08 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.16), residues: 3110 helix: 1.03 (0.14), residues: 1434 sheet: 0.63 (0.28), residues: 368 loop : -1.22 (0.18), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 615 HIS 0.003 0.000 HIS B 548 PHE 0.013 0.001 PHE D 517 TYR 0.022 0.001 TYR F 659 ARG 0.010 0.000 ARG A 576 Details of bonding type rmsd hydrogen bonds : bond 0.03338 ( 983) hydrogen bonds : angle 4.08635 ( 2844) covalent geometry : bond 0.00263 (25837) covalent geometry : angle 0.62974 (35025) Misc. bond : bond 0.00280 ( 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 220 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 185 time to evaluate : 2.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 576 ARG cc_start: 0.8046 (ttp-110) cc_final: 0.7441 (mtm110) REVERT: A 686 MET cc_start: 0.5274 (pmm) cc_final: 0.4845 (pmm) REVERT: A 699 GLN cc_start: 0.7907 (tm-30) cc_final: 0.7504 (tm-30) REVERT: A 826 ASP cc_start: 0.8429 (t70) cc_final: 0.8219 (m-30) REVERT: A 848 GLU cc_start: 0.7859 (tp30) cc_final: 0.7502 (tp30) REVERT: A 1375 LEU cc_start: 0.5724 (OUTLIER) cc_final: 0.4926 (pp) REVERT: A 1379 MET cc_start: 0.7900 (OUTLIER) cc_final: 0.7328 (mtm) REVERT: B 545 ASP cc_start: 0.8232 (t0) cc_final: 0.7979 (m-30) REVERT: B 840 GLU cc_start: 0.7306 (tm-30) cc_final: 0.7029 (tm-30) REVERT: C 591 ASP cc_start: 0.7815 (m-30) cc_final: 0.7603 (m-30) REVERT: D 717 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9000 (mm) REVERT: E 686 MET cc_start: 0.8217 (tpp) cc_final: 0.7862 (tpp) REVERT: E 720 LEU cc_start: 0.7254 (OUTLIER) cc_final: 0.6905 (pp) REVERT: F 441 MET cc_start: 0.4456 (ptm) cc_final: 0.4082 (ptm) REVERT: F 457 ILE cc_start: 0.6653 (mm) cc_final: 0.6300 (pt) REVERT: F 567 GLU cc_start: 0.6631 (mp0) cc_final: 0.5813 (tt0) REVERT: F 686 MET cc_start: 0.2299 (pmm) cc_final: 0.1221 (ptm) REVERT: F 718 GLU cc_start: 0.9149 (tm-30) cc_final: 0.8900 (tm-30) REVERT: F 893 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.7302 (mt) outliers start: 35 outliers final: 23 residues processed: 209 average time/residue: 0.3417 time to fit residues: 117.1801 Evaluate side-chains 204 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 176 time to evaluate : 2.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 PHE Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 1375 LEU Chi-restraints excluded: chain A residue 1379 MET Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain C residue 648 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 717 LEU Chi-restraints excluded: chain D residue 798 VAL 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 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 681 VAL 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 291 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 203 optimal weight: 2.9990 chunk 251 optimal weight: 9.9990 chunk 23 optimal weight: 20.0000 chunk 55 optimal weight: 0.1980 chunk 236 optimal weight: 5.9990 chunk 202 optimal weight: 4.9990 chunk 310 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 186 optimal weight: 0.0980 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 434 HIS B1330 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.104161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.073190 restraints weight = 87423.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.073278 restraints weight = 62253.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.074236 restraints weight = 39820.197| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 25845 Z= 0.172 Angle : 0.669 14.594 35025 Z= 0.323 Chirality : 0.043 0.282 3949 Planarity : 0.005 0.068 4490 Dihedral : 8.149 171.942 3582 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.01 % Favored : 92.89 % Rotamer: Outliers : 1.30 % Allowed : 16.01 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.16), residues: 3110 helix: 1.04 (0.14), residues: 1430 sheet: 0.48 (0.28), residues: 371 loop : -1.25 (0.18), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 865 HIS 0.003 0.001 HIS D 434 PHE 0.017 0.001 PHE D 517 TYR 0.013 0.001 TYR A 448 ARG 0.014 0.000 ARG B 543 Details of bonding type rmsd hydrogen bonds : bond 0.03856 ( 983) hydrogen bonds : angle 4.25836 ( 2844) covalent geometry : bond 0.00408 (25837) covalent geometry : angle 0.66908 (35025) Misc. bond : bond 0.00423 ( 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 207 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 171 time to evaluate : 2.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 576 ARG cc_start: 0.8107 (ttp-110) cc_final: 0.7497 (mtm110) REVERT: A 686 MET cc_start: 0.4970 (pmm) cc_final: 0.4568 (pmm) REVERT: A 699 GLN cc_start: 0.8020 (tm-30) cc_final: 0.7605 (tm-30) REVERT: A 826 ASP cc_start: 0.8562 (t70) cc_final: 0.8130 (t0) REVERT: A 848 GLU cc_start: 0.7851 (tp30) cc_final: 0.7450 (tp30) REVERT: A 1375 LEU cc_start: 0.5721 (OUTLIER) cc_final: 0.4934 (pp) REVERT: A 1379 MET cc_start: 0.7851 (OUTLIER) cc_final: 0.7321 (mtm) REVERT: B 510 GLU cc_start: 0.8138 (mp0) cc_final: 0.7866 (mp0) REVERT: B 545 ASP cc_start: 0.8379 (t0) cc_final: 0.8124 (m-30) REVERT: B 840 GLU cc_start: 0.7462 (tm-30) cc_final: 0.7182 (tm-30) REVERT: C 591 ASP cc_start: 0.7940 (m-30) cc_final: 0.7698 (m-30) REVERT: D 717 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.8958 (mm) REVERT: E 686 MET cc_start: 0.8253 (tpp) cc_final: 0.7865 (tpp) REVERT: E 720 LEU cc_start: 0.7343 (OUTLIER) cc_final: 0.7014 (pp) REVERT: F 441 MET cc_start: 0.4567 (ptm) cc_final: 0.4152 (ptp) REVERT: F 457 ILE cc_start: 0.6897 (mm) cc_final: 0.6522 (pt) REVERT: F 567 GLU cc_start: 0.6846 (mp0) cc_final: 0.6022 (tt0) REVERT: F 686 MET cc_start: 0.1951 (pmm) cc_final: 0.0793 (ptm) REVERT: F 718 GLU cc_start: 0.9149 (tm-30) cc_final: 0.8835 (mt-10) REVERT: F 893 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.7324 (mt) outliers start: 36 outliers final: 28 residues processed: 195 average time/residue: 0.3511 time to fit residues: 110.1910 Evaluate side-chains 197 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 164 time to evaluate : 2.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 PHE Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 1375 LEU Chi-restraints excluded: chain A residue 1379 MET Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain C residue 648 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 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 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 E residue 1382 GLU Chi-restraints excluded: chain F residue 444 PHE 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 301 optimal weight: 0.0980 chunk 222 optimal weight: 0.0020 chunk 71 optimal weight: 3.9990 chunk 203 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 278 optimal weight: 2.9990 chunk 289 optimal weight: 6.9990 chunk 122 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 154 optimal weight: 0.9980 chunk 237 optimal weight: 2.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1330 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.105942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.074301 restraints weight = 86302.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.075925 restraints weight = 48853.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.076282 restraints weight = 32855.203| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25845 Z= 0.110 Angle : 0.618 14.415 35025 Z= 0.296 Chirality : 0.041 0.145 3949 Planarity : 0.004 0.067 4490 Dihedral : 7.872 165.026 3582 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.11 % Favored : 93.83 % Rotamer: Outliers : 1.40 % Allowed : 16.08 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.16), residues: 3110 helix: 1.16 (0.14), residues: 1434 sheet: 0.69 (0.28), residues: 373 loop : -1.20 (0.18), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 615 HIS 0.004 0.000 HIS A 815 PHE 0.011 0.001 PHE D 517 TYR 0.033 0.001 TYR F 659 ARG 0.009 0.000 ARG A 576 Details of bonding type rmsd hydrogen bonds : bond 0.03051 ( 983) hydrogen bonds : angle 3.97974 ( 2844) covalent geometry : bond 0.00253 (25837) covalent geometry : angle 0.61773 (35025) Misc. bond : bond 0.00295 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8757.68 seconds wall clock time: 158 minutes 15.44 seconds (9495.44 seconds total)