Starting phenix.real_space_refine on Wed Mar 4 09:51:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e0f_47354/03_2026/9e0f_47354.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e0f_47354/03_2026/9e0f_47354.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9e0f_47354/03_2026/9e0f_47354.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e0f_47354/03_2026/9e0f_47354.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9e0f_47354/03_2026/9e0f_47354.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e0f_47354/03_2026/9e0f_47354.map" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 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 Zn 9 6.06 5 S 111 5.16 5 C 7760 2.51 5 N 2148 2.21 5 O 2159 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12187 Number of models: 1 Model: "" Number of chains: 7 Chain: "V" Number of atoms: 2793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2793 Classifications: {'peptide': 349} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 331} Chain breaks: 3 Chain: "Z" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1478 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 11, 'TRANS': 170} Chain breaks: 4 Chain: "U" Number of atoms: 3404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3404 Classifications: {'peptide': 424} Link IDs: {'PTRANS': 22, 'TRANS': 401} Chain breaks: 1 Chain: "Y" Number of atoms: 4451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 555, 4451 Classifications: {'peptide': 555} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 523} Chain breaks: 3 Chain: "V" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "U" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' ZN': 3} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Chain: "Y" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' ZN': 3} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 163 SG CYS V 415 78.720 33.663 113.393 1.00143.23 S ATOM 183 SG CYS V 418 77.095 34.986 110.101 1.00149.23 S ATOM 313 SG CYS V 435 77.286 37.510 112.664 1.00157.83 S ATOM 335 SG CYS V 438 74.906 34.945 113.039 1.00154.66 S ATOM 517 SG CYS V 458 68.906 26.267 119.261 1.00153.82 S ATOM 537 SG CYS V 461 70.462 26.942 115.367 1.00147.29 S ATOM 679 SG CYS V 480 68.800 23.985 116.131 1.00145.05 S ATOM 701 SG CYS V 483 72.124 24.624 117.075 1.00134.91 S ATOM 606 SG CYS V 470 64.589 21.779 130.803 1.00138.20 S ATOM 639 SG CYS V 475 66.015 25.839 131.035 1.00155.33 S ATOM 854 SG CYS V 504 68.060 23.280 129.950 1.00143.28 S ATOM 880 SG CYS V 507 67.480 23.392 133.293 1.00135.31 S ATOM 4438 SG CYS U 494 25.910 54.689 107.330 1.00310.54 S ATOM 4458 SG CYS U 497 27.324 50.893 108.301 1.00312.31 S ATOM 4580 SG CYS U 514 28.604 53.993 110.256 1.00306.09 S ATOM 4603 SG CYS U 517 29.545 53.313 107.427 1.00287.06 S ATOM 4771 SG CYS U 537 30.330 52.452 96.056 1.00291.25 S ATOM 4792 SG CYS U 540 29.910 50.572 99.755 1.00285.85 S ATOM 4929 SG CYS U 559 28.773 49.204 96.333 1.00300.80 S ATOM 4951 SG CYS U 562 26.821 51.030 98.048 1.00315.77 S ATOM 4855 SG CYS U 549 31.387 58.752 85.241 1.00307.19 S ATOM 4889 SG CYS U 554 33.003 61.110 87.473 1.00276.55 S ATOM 5102 SG CYS U 583 29.538 59.721 88.225 1.00311.80 S ATOM 5128 SG CYS U 586 30.190 62.771 86.397 1.00318.83 S ATOM 8889 SG CYS Y 494 111.245 56.611 57.340 1.00245.73 S ATOM 8909 SG CYS Y 497 110.122 52.479 56.612 1.00262.42 S ATOM 9031 SG CYS Y 514 108.728 55.385 54.687 1.00239.12 S ATOM 9054 SG CYS Y 517 107.728 54.326 57.542 1.00230.19 S ATOM 9222 SG CYS Y 537 107.483 54.924 68.797 1.00271.23 S ATOM 9243 SG CYS Y 540 107.788 52.317 65.782 1.00287.65 S ATOM 9380 SG CYS Y 559 109.064 51.494 69.243 1.00264.63 S ATOM 9402 SG CYS Y 562 110.906 53.518 66.911 1.00267.64 S ATOM 9306 SG CYS Y 549 105.157 61.979 79.301 1.00274.80 S ATOM 9340 SG CYS Y 554 103.056 63.822 77.162 1.00252.13 S ATOM 9553 SG CYS Y 583 107.128 63.611 76.686 1.00264.71 S ATOM 9579 SG CYS Y 586 106.071 66.189 78.484 1.00273.35 S Time building chain proxies: 2.77, per 1000 atoms: 0.23 Number of scatterers: 12187 At special positions: 0 Unit cell: (138.276, 107.64, 166.428, 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) Zn 9 29.99 S 111 16.00 O 2159 8.00 N 2148 7.00 C 7760 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 536.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN U1001 " pdb="ZN ZN U1001 " - pdb=" SG CYS U 517 " pdb="ZN ZN U1001 " - pdb=" SG CYS U 494 " pdb="ZN ZN U1001 " - pdb=" SG CYS U 497 " pdb="ZN ZN U1001 " - pdb=" SG CYS U 514 " pdb=" ZN U1002 " pdb="ZN ZN U1002 " - pdb=" SG CYS U 559 " pdb="ZN ZN U1002 " - pdb=" SG CYS U 540 " pdb="ZN ZN U1002 " - pdb=" SG CYS U 537 " pdb="ZN ZN U1002 " - pdb=" SG CYS U 562 " pdb=" ZN U1003 " pdb="ZN ZN U1003 " - pdb=" SG CYS U 583 " pdb="ZN ZN U1003 " - pdb=" SG CYS U 554 " pdb="ZN ZN U1003 " - pdb=" SG CYS U 586 " pdb="ZN ZN U1003 " - pdb=" SG CYS U 549 " pdb=" ZN V1001 " pdb="ZN ZN V1001 " - pdb=" SG CYS V 418 " pdb="ZN ZN V1001 " - pdb=" SG CYS V 435 " pdb="ZN ZN V1001 " - pdb=" SG CYS V 415 " pdb="ZN ZN V1001 " - pdb=" SG CYS V 438 " pdb=" ZN V1002 " pdb="ZN ZN V1002 " - pdb=" SG CYS V 480 " pdb="ZN ZN V1002 " - pdb=" SG CYS V 458 " pdb="ZN ZN V1002 " - pdb=" SG CYS V 461 " pdb="ZN ZN V1002 " - pdb=" SG CYS V 483 " pdb=" ZN V1003 " pdb="ZN ZN V1003 " - pdb=" SG CYS V 504 " pdb="ZN ZN V1003 " - pdb=" SG CYS V 507 " pdb="ZN ZN V1003 " - pdb=" SG CYS V 470 " pdb="ZN ZN V1003 " - pdb=" SG CYS V 475 " pdb=" ZN Y1001 " pdb="ZN ZN Y1001 " - pdb=" SG CYS Y 497 " pdb="ZN ZN Y1001 " - pdb=" SG CYS Y 514 " pdb="ZN ZN Y1001 " - pdb=" SG CYS Y 517 " pdb="ZN ZN Y1001 " - pdb=" SG CYS Y 494 " pdb=" ZN Y1002 " pdb="ZN ZN Y1002 " - pdb=" SG CYS Y 537 " pdb="ZN ZN Y1002 " - pdb=" SG CYS Y 562 " pdb="ZN ZN Y1002 " - pdb=" SG CYS Y 540 " pdb="ZN ZN Y1002 " - pdb=" SG CYS Y 559 " pdb=" ZN Y1003 " pdb="ZN ZN Y1003 " - pdb=" SG CYS Y 583 " pdb="ZN ZN Y1003 " - pdb=" SG CYS Y 549 " pdb="ZN ZN Y1003 " - pdb=" SG CYS Y 554 " pdb="ZN ZN Y1003 " - pdb=" SG CYS Y 586 " Number of angles added : 54 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2784 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 15 sheets defined 38.1% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'V' and resid 396 through 407 removed outlier: 3.841A pdb=" N ALA V 405 " --> pdb=" O ALA V 401 " (cutoff:3.500A) Processing helix chain 'V' and resid 435 through 445 Processing helix chain 'V' and resid 481 through 487 Processing helix chain 'V' and resid 491 through 499 removed outlier: 4.005A pdb=" N LEU V 498 " --> pdb=" O ALA V 494 " (cutoff:3.500A) Processing helix chain 'V' and resid 521 through 532 removed outlier: 3.518A pdb=" N SER V 532 " --> pdb=" O ALA V 528 " (cutoff:3.500A) Processing helix chain 'V' and resid 565 through 575 Processing helix chain 'V' and resid 589 through 598 removed outlier: 3.799A pdb=" N VAL V 593 " --> pdb=" O GLU V 589 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL V 596 " --> pdb=" O ALA V 592 " (cutoff:3.500A) Processing helix chain 'V' and resid 613 through 620 removed outlier: 3.773A pdb=" N GLU V 617 " --> pdb=" O LYS V 613 " (cutoff:3.500A) Processing helix chain 'V' and resid 650 through 663 removed outlier: 3.502A pdb=" N GLU V 654 " --> pdb=" O ARG V 650 " (cutoff:3.500A) Processing helix chain 'V' and resid 683 through 695 Processing helix chain 'V' and resid 751 through 760 removed outlier: 4.420A pdb=" N VAL V 755 " --> pdb=" O TRP V 751 " (cutoff:3.500A) Processing helix chain 'V' and resid 760 through 766 removed outlier: 3.790A pdb=" N LYS V 764 " --> pdb=" O PHE V 760 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP V 765 " --> pdb=" O ALA V 761 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR V 766 " --> pdb=" O PRO V 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 760 through 766' Processing helix chain 'Z' and resid 565 through 574 Processing helix chain 'Z' and resid 587 through 598 removed outlier: 3.667A pdb=" N ILE Z 591 " --> pdb=" O CYS Z 587 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N HIS Z 598 " --> pdb=" O GLY Z 594 " (cutoff:3.500A) Processing helix chain 'Z' and resid 612 through 620 Processing helix chain 'Z' and resid 645 through 663 Processing helix chain 'Z' and resid 683 through 695 Processing helix chain 'Z' and resid 753 through 760 Processing helix chain 'Z' and resid 760 through 767 Processing helix chain 'U' and resid 477 through 485 Processing helix chain 'U' and resid 489 through 493 removed outlier: 3.519A pdb=" N ILE U 493 " --> pdb=" O ILE U 490 " (cutoff:3.500A) Processing helix chain 'U' and resid 514 through 525 Processing helix chain 'U' and resid 560 through 567 Processing helix chain 'U' and resid 570 through 578 Processing helix chain 'U' and resid 600 through 611 removed outlier: 3.553A pdb=" N PHE U 609 " --> pdb=" O LEU U 605 " (cutoff:3.500A) Processing helix chain 'U' and resid 627 through 631 removed outlier: 3.565A pdb=" N ARG U 631 " --> pdb=" O ALA U 628 " (cutoff:3.500A) Processing helix chain 'U' and resid 644 through 654 Processing helix chain 'U' and resid 666 through 677 Processing helix chain 'U' and resid 691 through 698 Processing helix chain 'U' and resid 725 through 728 Processing helix chain 'U' and resid 729 through 742 Processing helix chain 'U' and resid 762 through 774 Processing helix chain 'U' and resid 814 through 819 removed outlier: 3.656A pdb=" N CYS U 818 " --> pdb=" O GLU U 814 " (cutoff:3.500A) Processing helix chain 'U' and resid 860 through 868 Processing helix chain 'U' and resid 881 through 892 Processing helix chain 'U' and resid 894 through 903 Processing helix chain 'U' and resid 904 through 908 Processing helix chain 'Y' and resid 82 through 88 Processing helix chain 'Y' and resid 88 through 107 removed outlier: 3.725A pdb=" N ARG Y 92 " --> pdb=" O GLN Y 88 " (cutoff:3.500A) Processing helix chain 'Y' and resid 125 through 138 Proline residue: Y 131 - end of helix removed outlier: 3.511A pdb=" N GLY Y 138 " --> pdb=" O GLU Y 134 " (cutoff:3.500A) Processing helix chain 'Y' and resid 144 through 149 Processing helix chain 'Y' and resid 477 through 484 Processing helix chain 'Y' and resid 489 through 493 removed outlier: 3.649A pdb=" N ILE Y 493 " --> pdb=" O ILE Y 490 " (cutoff:3.500A) Processing helix chain 'Y' and resid 514 through 525 Processing helix chain 'Y' and resid 560 through 566 Processing helix chain 'Y' and resid 571 through 578 Processing helix chain 'Y' and resid 600 through 611 removed outlier: 3.730A pdb=" N GLN Y 606 " --> pdb=" O PRO Y 602 " (cutoff:3.500A) Processing helix chain 'Y' and resid 644 through 654 removed outlier: 3.664A pdb=" N LEU Y 648 " --> pdb=" O ALA Y 644 " (cutoff:3.500A) Processing helix chain 'Y' and resid 666 through 677 Processing helix chain 'Y' and resid 686 through 690 Processing helix chain 'Y' and resid 691 through 698 Processing helix chain 'Y' and resid 725 through 728 removed outlier: 3.690A pdb=" N GLY Y 728 " --> pdb=" O GLU Y 725 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 725 through 728' Processing helix chain 'Y' and resid 729 through 742 removed outlier: 3.838A pdb=" N GLU Y 733 " --> pdb=" O ARG Y 729 " (cutoff:3.500A) Processing helix chain 'Y' and resid 762 through 774 Processing helix chain 'Y' and resid 814 through 819 removed outlier: 3.744A pdb=" N CYS Y 818 " --> pdb=" O GLU Y 814 " (cutoff:3.500A) Processing helix chain 'Y' and resid 860 through 869 Processing helix chain 'Y' and resid 881 through 892 Processing helix chain 'Y' and resid 894 through 903 Processing helix chain 'Y' and resid 904 through 908 removed outlier: 3.757A pdb=" N GLU Y 907 " --> pdb=" O PRO Y 904 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'V' and resid 467 through 469 removed outlier: 3.754A pdb=" N PHE V 479 " --> pdb=" O LEU V 468 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'V' and resid 512 through 513 Processing sheet with id=AA3, first strand: chain 'V' and resid 578 through 584 removed outlier: 5.585A pdb=" N ILE V 555 " --> pdb=" O VAL V 578 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS V 580 " --> pdb=" O ILE V 555 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER V 584 " --> pdb=" O SER V 559 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N VAL V 625 " --> pdb=" O MET V 675 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N GLU V 677 " --> pdb=" O VAL V 625 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N GLY V 627 " --> pdb=" O GLU V 677 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N VAL V 679 " --> pdb=" O GLY V 627 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG V 713 " --> pdb=" O ILE V 701 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE V 701 " --> pdb=" O ARG V 713 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'Z' and resid 603 through 605 removed outlier: 8.938A pdb=" N LYS Z 603 " --> pdb=" O GLY Z 579 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N TYR Z 581 " --> pdb=" O LYS Z 603 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N VAL Z 605 " --> pdb=" O TYR Z 581 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ALA Z 583 " --> pdb=" O VAL Z 605 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ILE Z 555 " --> pdb=" O GLY Z 579 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N TYR Z 581 " --> pdb=" O ILE Z 555 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N VAL Z 557 " --> pdb=" O TYR Z 581 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ALA Z 583 " --> pdb=" O VAL Z 557 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N SER Z 559 " --> pdb=" O ALA Z 583 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL Z 625 " --> pdb=" O MET Z 675 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N GLU Z 677 " --> pdb=" O VAL Z 625 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N GLY Z 627 " --> pdb=" O GLU Z 677 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'U' and resid 504 through 505 Processing sheet with id=AA6, first strand: chain 'U' and resid 546 through 548 Processing sheet with id=AA7, first strand: chain 'U' and resid 591 through 592 Processing sheet with id=AA8, first strand: chain 'U' and resid 682 through 684 removed outlier: 8.943A pdb=" N MET U 682 " --> pdb=" O ASP U 658 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N TYR U 660 " --> pdb=" O MET U 682 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N VAL U 684 " --> pdb=" O TYR U 660 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ALA U 662 " --> pdb=" O VAL U 684 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ILE U 634 " --> pdb=" O ASP U 658 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N TYR U 660 " --> pdb=" O ILE U 634 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL U 636 " --> pdb=" O TYR U 660 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ALA U 662 " --> pdb=" O VAL U 636 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N SER U 638 " --> pdb=" O ALA U 662 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLY U 707 " --> pdb=" O LEU U 639 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL U 704 " --> pdb=" O LEU U 754 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N GLU U 756 " --> pdb=" O VAL U 704 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N GLY U 706 " --> pdb=" O GLU U 756 " (cutoff:3.500A) removed outlier: 9.775A pdb=" N VAL U 758 " --> pdb=" O GLY U 706 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'U' and resid 823 through 825 removed outlier: 4.298A pdb=" N VAL U 850 " --> pdb=" O ASP U 857 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Y' and resid 62 through 66 removed outlier: 5.204A pdb=" N SER Y 30 " --> pdb=" O LEU Y 26 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LEU Y 26 " --> pdb=" O SER Y 30 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'Y' and resid 504 through 505 Processing sheet with id=AB3, first strand: chain 'Y' and resid 546 through 548 Processing sheet with id=AB4, first strand: chain 'Y' and resid 591 through 592 Processing sheet with id=AB5, first strand: chain 'Y' and resid 681 through 684 removed outlier: 7.687A pdb=" N ILE Y 634 " --> pdb=" O ASP Y 658 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N TYR Y 660 " --> pdb=" O ILE Y 634 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N VAL Y 636 " --> pdb=" O TYR Y 660 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ALA Y 662 " --> pdb=" O VAL Y 636 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N SER Y 638 " --> pdb=" O ALA Y 662 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL Y 704 " --> pdb=" O LEU Y 754 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N GLU Y 756 " --> pdb=" O VAL Y 704 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'Y' and resid 824 through 825 removed outlier: 3.917A pdb=" N VAL Y 850 " --> pdb=" O ASP Y 857 " (cutoff:3.500A) 401 hydrogen bonds defined for protein. 1125 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: 1.80 Time building geometry restraints manager: 1.15 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: 3693 1.34 - 1.46: 1872 1.46 - 1.58: 6771 1.58 - 1.70: 0 1.70 - 1.82: 152 Bond restraints: 12488 Sorted by residual: bond pdb=" C LYS U 829 " pdb=" N VAL U 830 " ideal model delta sigma weight residual 1.329 1.260 0.069 1.32e-02 5.74e+03 2.75e+01 bond pdb=" N VAL U 665 " pdb=" CA VAL U 665 " ideal model delta sigma weight residual 1.456 1.493 -0.036 9.50e-03 1.11e+04 1.45e+01 bond pdb=" N VAL U 716 " pdb=" CA VAL U 716 " ideal model delta sigma weight residual 1.462 1.496 -0.034 1.06e-02 8.90e+03 1.04e+01 bond pdb=" N ILE V 602 " pdb=" CA ILE V 602 " ideal model delta sigma weight residual 1.455 1.493 -0.037 1.18e-02 7.18e+03 1.01e+01 bond pdb=" N VAL U 690 " pdb=" CA VAL U 690 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.19e-02 7.06e+03 9.90e+00 ... (remaining 12483 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 11601 1.40 - 2.80: 4483 2.80 - 4.20: 738 4.20 - 5.59: 41 5.59 - 6.99: 5 Bond angle restraints: 16868 Sorted by residual: angle pdb=" C SER V 752 " pdb=" N VAL V 753 " pdb=" CA VAL V 753 " ideal model delta sigma weight residual 120.33 125.49 -5.16 8.00e-01 1.56e+00 4.15e+01 angle pdb=" C PHE Y 16 " pdb=" N GLY Y 17 " pdb=" CA GLY Y 17 " ideal model delta sigma weight residual 119.92 123.78 -3.86 9.60e-01 1.09e+00 1.61e+01 angle pdb=" CA GLY V 535 " pdb=" C GLY V 535 " pdb=" O GLY V 535 " ideal model delta sigma weight residual 121.64 118.19 3.45 9.20e-01 1.18e+00 1.40e+01 angle pdb=" C VAL V 481 " pdb=" N GLU V 482 " pdb=" CA GLU V 482 " ideal model delta sigma weight residual 120.28 125.26 -4.98 1.34e+00 5.57e-01 1.38e+01 angle pdb=" N VAL U 665 " pdb=" CA VAL U 665 " pdb=" C VAL U 665 " ideal model delta sigma weight residual 113.53 109.91 3.62 9.80e-01 1.04e+00 1.36e+01 ... (remaining 16863 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.94: 7106 14.94 - 29.89: 262 29.89 - 44.83: 39 44.83 - 59.77: 2 59.77 - 74.72: 3 Dihedral angle restraints: 7412 sinusoidal: 3076 harmonic: 4336 Sorted by residual: dihedral pdb=" CA GLU U 523 " pdb=" C GLU U 523 " pdb=" N CYS U 524 " pdb=" CA CYS U 524 " ideal model delta harmonic sigma weight residual -180.00 -157.43 -22.57 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA ASN V 422 " pdb=" C ASN V 422 " pdb=" N PRO V 423 " pdb=" CA PRO V 423 " ideal model delta harmonic sigma weight residual 180.00 158.00 22.00 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA GLU V 500 " pdb=" C GLU V 500 " pdb=" N PRO V 501 " pdb=" CA PRO V 501 " ideal model delta harmonic sigma weight residual 0.00 -21.71 21.71 0 5.00e+00 4.00e-02 1.89e+01 ... (remaining 7409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 668 0.039 - 0.079: 552 0.079 - 0.118: 348 0.118 - 0.157: 157 0.157 - 0.196: 31 Chirality restraints: 1756 Sorted by residual: chirality pdb=" CA LEU Y 639 " pdb=" N LEU Y 639 " pdb=" C LEU Y 639 " pdb=" CB LEU Y 639 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.63e-01 chirality pdb=" CA ILE U 858 " pdb=" N ILE U 858 " pdb=" C ILE U 858 " pdb=" CB ILE U 858 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.21e-01 chirality pdb=" CA ILE Z 547 " pdb=" N ILE Z 547 " pdb=" C ILE Z 547 " pdb=" CB ILE Z 547 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.87e-01 ... (remaining 1753 not shown) Planarity restraints: 2189 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU Y 99 " -0.009 2.00e-02 2.50e+03 1.89e-02 3.58e+00 pdb=" C LEU Y 99 " 0.033 2.00e-02 2.50e+03 pdb=" O LEU Y 99 " -0.012 2.00e-02 2.50e+03 pdb=" N GLN Y 100 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS U 829 " -0.007 2.00e-02 2.50e+03 1.55e-02 2.40e+00 pdb=" C LYS U 829 " 0.027 2.00e-02 2.50e+03 pdb=" O LYS U 829 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL U 830 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY Y 17 " 0.008 2.00e-02 2.50e+03 1.54e-02 2.38e+00 pdb=" C GLY Y 17 " -0.027 2.00e-02 2.50e+03 pdb=" O GLY Y 17 " 0.010 2.00e-02 2.50e+03 pdb=" N ILE Y 18 " 0.009 2.00e-02 2.50e+03 ... (remaining 2186 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 311 2.70 - 3.25: 10816 3.25 - 3.80: 17481 3.80 - 4.35: 23547 4.35 - 4.90: 37784 Nonbonded interactions: 89939 Sorted by model distance: nonbonded pdb=" OG SER U 663 " pdb=" O GLY U 685 " model vdw 2.154 3.040 nonbonded pdb=" CB VAL U 759 " pdb=" O ALA U 791 " model vdw 2.282 3.470 nonbonded pdb=" O PHE U 640 " pdb=" N SAH U1004 " model vdw 2.283 3.120 nonbonded pdb=" O PHE Y 640 " pdb=" OXT SAH Y1004 " model vdw 2.306 3.040 nonbonded pdb=" OD1 ASP Y 641 " pdb=" N ALA Y 644 " model vdw 2.331 3.120 ... (remaining 89934 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic 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: 10.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.770 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5126 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 : 0.013 0.777 12525 Z= 1.095 Angle : 1.605 29.670 16922 Z= 1.039 Chirality : 0.073 0.196 1756 Planarity : 0.003 0.038 2189 Dihedral : 8.352 74.718 4628 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.90 (0.17), residues: 1480 helix: -2.21 (0.17), residues: 501 sheet: -1.14 (0.37), residues: 161 loop : -1.89 (0.17), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Y 891 TYR 0.022 0.002 TYR U 683 PHE 0.024 0.002 PHE Y 57 TRP 0.024 0.002 TRP Y 32 HIS 0.007 0.002 HIS Z 657 Details of bonding type rmsd covalent geometry : bond 0.01124 (12488) covalent geometry : angle 1.37948 (16868) hydrogen bonds : bond 0.19389 ( 401) hydrogen bonds : angle 8.11962 ( 1125) metal coordination : bond 0.02784 ( 36) metal coordination : angle 14.57527 ( 54) Misc. bond : bond 0.77680 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 327 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 624 LEU cc_start: 0.6659 (tp) cc_final: 0.6426 (tp) REVERT: V 686 ASP cc_start: 0.8066 (m-30) cc_final: 0.7719 (m-30) REVERT: V 690 ILE cc_start: 0.8375 (mt) cc_final: 0.8151 (mt) REVERT: V 691 SER cc_start: 0.8815 (m) cc_final: 0.8267 (p) REVERT: V 722 MET cc_start: 0.5745 (mtp) cc_final: 0.5544 (mtp) REVERT: Z 659 LEU cc_start: 0.8114 (tp) cc_final: 0.7855 (tp) REVERT: Z 673 PHE cc_start: 0.6166 (m-80) cc_final: 0.5947 (m-80) REVERT: Z 675 MET cc_start: 0.4959 (tmm) cc_final: 0.4731 (tmm) REVERT: Z 687 LYS cc_start: 0.8335 (ttpt) cc_final: 0.7774 (ttpt) REVERT: Z 757 ARG cc_start: 0.7751 (ptt90) cc_final: 0.7372 (ptt90) REVERT: U 548 MET cc_start: 0.7437 (mtm) cc_final: 0.6927 (mtm) REVERT: U 623 TYR cc_start: 0.6066 (m-80) cc_final: 0.5721 (m-80) REVERT: U 692 GLN cc_start: 0.6934 (tt0) cc_final: 0.6603 (tt0) REVERT: U 694 HIS cc_start: 0.7898 (m170) cc_final: 0.7551 (m90) REVERT: U 695 ILE cc_start: 0.8244 (mm) cc_final: 0.7940 (tt) REVERT: U 724 TYR cc_start: 0.7216 (m-80) cc_final: 0.6909 (m-80) REVERT: U 733 GLU cc_start: 0.7164 (mm-30) cc_final: 0.6634 (mm-30) REVERT: U 756 GLU cc_start: 0.5784 (tm-30) cc_final: 0.5403 (tm-30) REVERT: U 779 MET cc_start: 0.6321 (tmm) cc_final: 0.6097 (tmm) REVERT: U 816 GLN cc_start: 0.7725 (tp40) cc_final: 0.7410 (tp40) REVERT: U 876 ASP cc_start: 0.7036 (t0) cc_final: 0.6664 (t0) REVERT: U 883 LEU cc_start: 0.7593 (mt) cc_final: 0.7327 (mt) REVERT: U 898 ILE cc_start: 0.8451 (mm) cc_final: 0.8227 (mm) REVERT: Y 585 MET cc_start: 0.7930 (mmm) cc_final: 0.7581 (mmm) REVERT: Y 607 MET cc_start: 0.6842 (mtm) cc_final: 0.6122 (mtm) REVERT: Y 636 VAL cc_start: 0.8334 (t) cc_final: 0.8112 (m) REVERT: Y 687 VAL cc_start: 0.8284 (t) cc_final: 0.8062 (p) REVERT: Y 694 HIS cc_start: 0.7880 (m170) cc_final: 0.7463 (m90) REVERT: Y 701 PHE cc_start: 0.7030 (m-80) cc_final: 0.6776 (m-80) REVERT: Y 754 LEU cc_start: 0.8461 (tt) cc_final: 0.8218 (tp) REVERT: Y 773 LEU cc_start: 0.8150 (mt) cc_final: 0.7926 (mt) REVERT: Y 798 LEU cc_start: 0.7611 (mp) cc_final: 0.6392 (mt) REVERT: Y 852 MET cc_start: 0.5093 (ttt) cc_final: 0.4827 (ttt) REVERT: Y 865 GLU cc_start: 0.7312 (mt-10) cc_final: 0.6919 (mt-10) REVERT: Y 887 ARG cc_start: 0.7618 (ptt180) cc_final: 0.7289 (ttp-110) REVERT: Y 888 LEU cc_start: 0.8855 (mt) cc_final: 0.8629 (mt) REVERT: Y 907 GLU cc_start: 0.7319 (mm-30) cc_final: 0.6880 (mm-30) outliers start: 0 outliers final: 0 residues processed: 327 average time/residue: 0.1418 time to fit residues: 62.9413 Evaluate side-chains 286 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 98 optimal weight: 40.0000 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 0.0970 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 20.0000 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.2980 chunk 55 optimal weight: 9.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 613 HIS U 847 HIS ** Y 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 696 GLN ** Y 900 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4997 r_free = 0.4997 target = 0.266618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.228552 restraints weight = 26526.090| |-----------------------------------------------------------------------------| r_work (start): 0.4581 rms_B_bonded: 4.37 r_work (final): 0.4581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5469 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12525 Z= 0.155 Angle : 0.645 11.704 16922 Z= 0.303 Chirality : 0.040 0.137 1756 Planarity : 0.005 0.086 2189 Dihedral : 4.284 25.660 1672 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.07 % Allowed : 7.10 % Favored : 91.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.20), residues: 1480 helix: -0.03 (0.22), residues: 505 sheet: -0.55 (0.38), residues: 158 loop : -1.21 (0.19), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.036 0.001 ARG Y 891 TYR 0.018 0.001 TYR Z 714 PHE 0.029 0.002 PHE U 731 TRP 0.013 0.001 TRP Y 795 HIS 0.006 0.001 HIS Y 677 Details of bonding type rmsd covalent geometry : bond 0.00316 (12488) covalent geometry : angle 0.58863 (16868) hydrogen bonds : bond 0.04025 ( 401) hydrogen bonds : angle 5.29833 ( 1125) metal coordination : bond 0.00511 ( 36) metal coordination : angle 4.71850 ( 54) Misc. bond : bond 0.00064 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 306 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 654 GLU cc_start: 0.6150 (mt-10) cc_final: 0.5826 (mt-10) REVERT: V 688 ARG cc_start: 0.7315 (mtt180) cc_final: 0.6830 (mtt180) REVERT: V 691 SER cc_start: 0.8860 (m) cc_final: 0.8304 (p) REVERT: V 722 MET cc_start: 0.6548 (mtp) cc_final: 0.6260 (mtp) REVERT: U 548 MET cc_start: 0.6508 (mtm) cc_final: 0.6204 (mtm) REVERT: U 663 SER cc_start: 0.8264 (p) cc_final: 0.7869 (p) REVERT: U 686 ASP cc_start: 0.6685 (t0) cc_final: 0.5868 (t70) REVERT: U 691 THR cc_start: 0.6903 (p) cc_final: 0.6294 (p) REVERT: U 692 GLN cc_start: 0.7056 (tt0) cc_final: 0.6769 (tt0) REVERT: U 694 HIS cc_start: 0.8143 (m170) cc_final: 0.7937 (m90) REVERT: U 724 TYR cc_start: 0.7754 (m-80) cc_final: 0.7434 (m-80) REVERT: U 733 GLU cc_start: 0.7098 (mm-30) cc_final: 0.6852 (mm-30) REVERT: U 735 TYR cc_start: 0.5406 (t80) cc_final: 0.5132 (t80) REVERT: U 756 GLU cc_start: 0.6035 (tm-30) cc_final: 0.5801 (tm-30) REVERT: U 771 ARG cc_start: 0.6936 (ttp-170) cc_final: 0.6626 (ttp-170) REVERT: U 779 MET cc_start: 0.6496 (tmm) cc_final: 0.6084 (tmm) REVERT: U 789 HIS cc_start: 0.5589 (t-170) cc_final: 0.5105 (t-170) REVERT: U 816 GLN cc_start: 0.7935 (tp40) cc_final: 0.7558 (tp40) REVERT: U 876 ASP cc_start: 0.7077 (t0) cc_final: 0.6678 (t0) REVERT: U 898 ILE cc_start: 0.8557 (mm) cc_final: 0.8279 (mm) REVERT: Y 585 MET cc_start: 0.8009 (mmm) cc_final: 0.7717 (mmm) REVERT: Y 607 MET cc_start: 0.6685 (mtm) cc_final: 0.6016 (mtm) REVERT: Y 661 ILE cc_start: 0.7907 (mp) cc_final: 0.7629 (mp) REVERT: Y 667 GLU cc_start: 0.6393 (mm-30) cc_final: 0.6090 (mm-30) REVERT: Y 739 HIS cc_start: 0.6666 (t70) cc_final: 0.6446 (t70) REVERT: Y 749 ARG cc_start: 0.7294 (ttp-170) cc_final: 0.6944 (tmm-80) REVERT: Y 773 LEU cc_start: 0.8257 (mt) cc_final: 0.8023 (mt) REVERT: Y 816 GLN cc_start: 0.7244 (tp40) cc_final: 0.7009 (tp40) REVERT: Y 885 ARG cc_start: 0.8098 (mtp180) cc_final: 0.7691 (mtp85) REVERT: Y 887 ARG cc_start: 0.7584 (ptt180) cc_final: 0.7344 (ttp80) REVERT: Y 907 GLU cc_start: 0.7110 (mm-30) cc_final: 0.6837 (mm-30) outliers start: 14 outliers final: 4 residues processed: 310 average time/residue: 0.1412 time to fit residues: 59.2486 Evaluate side-chains 289 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 285 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 763 LEU Chi-restraints excluded: chain U residue 634 ILE Chi-restraints excluded: chain U residue 875 THR Chi-restraints excluded: chain Y residue 671 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 94 optimal weight: 20.0000 chunk 119 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 98 optimal weight: 40.0000 chunk 20 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 406 ASN Z 660 ASN U 515 GLN U 612 ASN U 656 GLN ** U 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 129 ASN Y 613 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4912 r_free = 0.4912 target = 0.257950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.215338 restraints weight = 24601.895| |-----------------------------------------------------------------------------| r_work (start): 0.4439 rms_B_bonded: 4.32 r_work (final): 0.4439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5813 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 12525 Z= 0.287 Angle : 0.814 14.416 16922 Z= 0.395 Chirality : 0.047 0.226 1756 Planarity : 0.007 0.149 2189 Dihedral : 5.089 50.828 1672 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.90 % Allowed : 8.63 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.20), residues: 1480 helix: -0.03 (0.22), residues: 514 sheet: -0.17 (0.39), residues: 159 loop : -1.18 (0.19), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.043 0.001 ARG U 484 TYR 0.027 0.002 TYR U 660 PHE 0.024 0.002 PHE V 715 TRP 0.029 0.002 TRP Y 753 HIS 0.010 0.002 HIS Y 677 Details of bonding type rmsd covalent geometry : bond 0.00591 (12488) covalent geometry : angle 0.78455 (16868) hydrogen bonds : bond 0.05212 ( 401) hydrogen bonds : angle 5.58921 ( 1125) metal coordination : bond 0.00492 ( 36) metal coordination : angle 3.89410 ( 54) Misc. bond : bond 0.01205 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 297 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 400 MET cc_start: 0.5822 (ttt) cc_final: 0.5617 (ttp) REVERT: V 722 MET cc_start: 0.6847 (mtp) cc_final: 0.6563 (mtp) REVERT: Z 656 TYR cc_start: 0.7865 (t80) cc_final: 0.7525 (t80) REVERT: U 638 SER cc_start: 0.8072 (t) cc_final: 0.7771 (t) REVERT: U 643 ILE cc_start: 0.8974 (OUTLIER) cc_final: 0.8699 (mt) REVERT: U 663 SER cc_start: 0.8118 (p) cc_final: 0.7910 (p) REVERT: U 675 VAL cc_start: 0.8446 (t) cc_final: 0.8109 (m) REVERT: U 688 ARG cc_start: 0.7315 (mtm-85) cc_final: 0.6671 (ttm110) REVERT: U 695 ILE cc_start: 0.8769 (tt) cc_final: 0.8556 (tt) REVERT: U 733 GLU cc_start: 0.7385 (mm-30) cc_final: 0.6929 (mm-30) REVERT: U 756 GLU cc_start: 0.6906 (tm-30) cc_final: 0.6643 (tm-30) REVERT: U 758 VAL cc_start: 0.8564 (p) cc_final: 0.8275 (m) REVERT: U 761 MET cc_start: 0.6515 (tmm) cc_final: 0.6251 (tmm) REVERT: U 771 ARG cc_start: 0.7048 (ttp-170) cc_final: 0.6759 (ttp-170) REVERT: U 779 MET cc_start: 0.7234 (tmm) cc_final: 0.6753 (tmm) REVERT: U 789 HIS cc_start: 0.6361 (t-170) cc_final: 0.4700 (t-90) REVERT: U 865 GLU cc_start: 0.7167 (mt-10) cc_final: 0.6749 (mt-10) REVERT: U 876 ASP cc_start: 0.7111 (t0) cc_final: 0.6781 (t0) REVERT: U 887 ARG cc_start: 0.7224 (ptt180) cc_final: 0.6909 (tmm-80) REVERT: U 898 ILE cc_start: 0.8357 (mm) cc_final: 0.8128 (mm) REVERT: U 907 GLU cc_start: 0.6307 (mm-30) cc_final: 0.6071 (mm-30) REVERT: Y 585 MET cc_start: 0.8083 (mmm) cc_final: 0.7839 (mmm) REVERT: Y 607 MET cc_start: 0.6564 (mtm) cc_final: 0.5924 (mtm) REVERT: Y 667 GLU cc_start: 0.6618 (mm-30) cc_final: 0.6284 (mm-30) REVERT: Y 708 SER cc_start: 0.7563 (m) cc_final: 0.7318 (m) REVERT: Y 732 PHE cc_start: 0.7913 (m-80) cc_final: 0.7633 (m-80) REVERT: Y 755 PHE cc_start: 0.7853 (t80) cc_final: 0.7439 (t80) REVERT: Y 773 LEU cc_start: 0.8423 (mt) cc_final: 0.8061 (mt) REVERT: Y 865 GLU cc_start: 0.7415 (mt-10) cc_final: 0.6872 (mt-10) REVERT: Y 885 ARG cc_start: 0.8343 (mtp180) cc_final: 0.8062 (mtp180) REVERT: Y 887 ARG cc_start: 0.7655 (ptt180) cc_final: 0.7426 (ttp80) REVERT: Y 889 LEU cc_start: 0.8752 (mt) cc_final: 0.8517 (mm) outliers start: 38 outliers final: 14 residues processed: 309 average time/residue: 0.1487 time to fit residues: 61.1731 Evaluate side-chains 299 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 284 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 755 VAL Chi-restraints excluded: chain Z residue 608 VAL Chi-restraints excluded: chain U residue 618 ASP Chi-restraints excluded: chain U residue 634 ILE Chi-restraints excluded: chain U residue 643 ILE Chi-restraints excluded: chain U residue 661 ILE Chi-restraints excluded: chain U residue 669 SER Chi-restraints excluded: chain U residue 689 SER Chi-restraints excluded: chain U residue 738 LEU Chi-restraints excluded: chain Y residue 71 MET Chi-restraints excluded: chain Y residue 655 ILE Chi-restraints excluded: chain Y residue 671 THR Chi-restraints excluded: chain Y residue 691 THR Chi-restraints excluded: chain Y residue 737 LEU Chi-restraints excluded: chain Y residue 813 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 95 optimal weight: 50.0000 chunk 28 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 65 optimal weight: 50.0000 chunk 26 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 612 ASN U 678 GLN ** U 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 678 GLN Y 789 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4908 r_free = 0.4908 target = 0.257575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.215232 restraints weight = 24387.100| |-----------------------------------------------------------------------------| r_work (start): 0.4427 rms_B_bonded: 4.30 r_work (final): 0.4427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5854 moved from start: 0.4374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12525 Z= 0.209 Angle : 0.670 15.321 16922 Z= 0.320 Chirality : 0.043 0.294 1756 Planarity : 0.005 0.100 2189 Dihedral : 4.800 50.183 1672 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.37 % Allowed : 11.00 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.20), residues: 1480 helix: 0.32 (0.22), residues: 514 sheet: 0.12 (0.40), residues: 161 loop : -0.98 (0.20), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG U 484 TYR 0.024 0.002 TYR Z 714 PHE 0.020 0.002 PHE Y 732 TRP 0.015 0.001 TRP Y 795 HIS 0.015 0.001 HIS Z 657 Details of bonding type rmsd covalent geometry : bond 0.00438 (12488) covalent geometry : angle 0.64006 (16868) hydrogen bonds : bond 0.04152 ( 401) hydrogen bonds : angle 5.19173 ( 1125) metal coordination : bond 0.00422 ( 36) metal coordination : angle 3.55153 ( 54) Misc. bond : bond 0.00256 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 289 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 656 TYR cc_start: 0.7725 (t80) cc_final: 0.7306 (t80) REVERT: Z 676 PHE cc_start: 0.6130 (t80) cc_final: 0.5878 (t80) REVERT: U 638 SER cc_start: 0.8112 (t) cc_final: 0.7838 (t) REVERT: U 652 ASP cc_start: 0.7578 (t0) cc_final: 0.7304 (t0) REVERT: U 658 ASP cc_start: 0.7208 (t0) cc_final: 0.6958 (t0) REVERT: U 663 SER cc_start: 0.8269 (p) cc_final: 0.8031 (p) REVERT: U 688 ARG cc_start: 0.7218 (mtm-85) cc_final: 0.6686 (ttm110) REVERT: U 695 ILE cc_start: 0.8667 (tt) cc_final: 0.8415 (tt) REVERT: U 733 GLU cc_start: 0.7314 (mm-30) cc_final: 0.6840 (mm-30) REVERT: U 756 GLU cc_start: 0.7069 (tm-30) cc_final: 0.6754 (tm-30) REVERT: U 758 VAL cc_start: 0.8611 (p) cc_final: 0.8308 (m) REVERT: U 771 ARG cc_start: 0.6864 (ttp-170) cc_final: 0.6570 (ttp-170) REVERT: U 779 MET cc_start: 0.7197 (tmm) cc_final: 0.6843 (tmm) REVERT: U 818 CYS cc_start: 0.7450 (m) cc_final: 0.7218 (m) REVERT: U 865 GLU cc_start: 0.7132 (mt-10) cc_final: 0.6872 (mt-10) REVERT: U 876 ASP cc_start: 0.7169 (t0) cc_final: 0.6721 (t0) REVERT: U 887 ARG cc_start: 0.7371 (ptt180) cc_final: 0.6993 (tmm-80) REVERT: U 898 ILE cc_start: 0.8322 (mm) cc_final: 0.8049 (mm) REVERT: U 907 GLU cc_start: 0.6314 (mm-30) cc_final: 0.6103 (mm-30) REVERT: Y 585 MET cc_start: 0.8072 (mmm) cc_final: 0.7852 (mmm) REVERT: Y 607 MET cc_start: 0.6740 (mtm) cc_final: 0.6141 (mtm) REVERT: Y 694 HIS cc_start: 0.7782 (m90) cc_final: 0.7562 (m90) REVERT: Y 698 TRP cc_start: 0.7749 (m-10) cc_final: 0.5473 (m-10) REVERT: Y 708 SER cc_start: 0.7674 (m) cc_final: 0.7424 (m) REVERT: Y 720 ARG cc_start: 0.7445 (ptm-80) cc_final: 0.7218 (ptm-80) REVERT: Y 755 PHE cc_start: 0.7754 (t80) cc_final: 0.7379 (t80) REVERT: Y 773 LEU cc_start: 0.8367 (mt) cc_final: 0.7993 (mt) REVERT: Y 865 GLU cc_start: 0.7161 (mt-10) cc_final: 0.6638 (mt-10) REVERT: Y 889 LEU cc_start: 0.8773 (mt) cc_final: 0.8562 (mm) outliers start: 31 outliers final: 20 residues processed: 300 average time/residue: 0.1429 time to fit residues: 57.1542 Evaluate side-chains 305 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 285 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 715 PHE Chi-restraints excluded: chain U residue 618 ASP Chi-restraints excluded: chain U residue 634 ILE Chi-restraints excluded: chain U residue 661 ILE Chi-restraints excluded: chain U residue 680 LYS Chi-restraints excluded: chain U residue 681 ILE Chi-restraints excluded: chain U residue 689 SER Chi-restraints excluded: chain U residue 738 LEU Chi-restraints excluded: chain U residue 875 THR Chi-restraints excluded: chain U residue 889 LEU Chi-restraints excluded: chain Y residue 71 MET Chi-restraints excluded: chain Y residue 548 MET Chi-restraints excluded: chain Y residue 655 ILE Chi-restraints excluded: chain Y residue 657 VAL Chi-restraints excluded: chain Y residue 663 SER Chi-restraints excluded: chain Y residue 671 THR Chi-restraints excluded: chain Y residue 678 GLN Chi-restraints excluded: chain Y residue 729 ARG Chi-restraints excluded: chain Y residue 737 LEU Chi-restraints excluded: chain Y residue 776 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 101 optimal weight: 9.9990 chunk 114 optimal weight: 0.0040 chunk 125 optimal weight: 0.8980 chunk 123 optimal weight: 0.7980 chunk 52 optimal weight: 0.0970 chunk 65 optimal weight: 40.0000 chunk 112 optimal weight: 0.8980 chunk 128 optimal weight: 0.0980 chunk 71 optimal weight: 0.4980 chunk 105 optimal weight: 40.0000 chunk 69 optimal weight: 0.5980 overall best weight: 0.2590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 406 ASN Z 657 HIS U 656 GLN ** U 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 789 HIS ** Y 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4928 r_free = 0.4928 target = 0.259373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.219244 restraints weight = 24486.744| |-----------------------------------------------------------------------------| r_work (start): 0.4489 rms_B_bonded: 4.24 r_work: 0.4271 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.4271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6087 moved from start: 0.4537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 12525 Z= 0.116 Angle : 0.599 12.597 16922 Z= 0.280 Chirality : 0.041 0.330 1756 Planarity : 0.004 0.067 2189 Dihedral : 4.433 50.325 1672 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.37 % Allowed : 11.84 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.21), residues: 1480 helix: 0.80 (0.23), residues: 513 sheet: 0.20 (0.40), residues: 162 loop : -0.76 (0.20), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG V 553 TYR 0.021 0.001 TYR Z 714 PHE 0.024 0.001 PHE V 672 TRP 0.030 0.001 TRP Z 674 HIS 0.010 0.001 HIS Z 657 Details of bonding type rmsd covalent geometry : bond 0.00255 (12488) covalent geometry : angle 0.56844 (16868) hydrogen bonds : bond 0.03495 ( 401) hydrogen bonds : angle 4.90258 ( 1125) metal coordination : bond 0.00369 ( 36) metal coordination : angle 3.38984 ( 54) Misc. bond : bond 0.00088 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 293 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 439 ARG cc_start: 0.7787 (ttp80) cc_final: 0.7335 (ttp80) REVERT: Z 674 TRP cc_start: 0.6252 (p90) cc_final: 0.5311 (p90) REVERT: Z 676 PHE cc_start: 0.6739 (t80) cc_final: 0.6437 (t80) REVERT: U 638 SER cc_start: 0.8423 (t) cc_final: 0.7505 (t) REVERT: U 641 ASP cc_start: 0.6905 (t70) cc_final: 0.6467 (t0) REVERT: U 652 ASP cc_start: 0.7820 (t0) cc_final: 0.7484 (t0) REVERT: U 658 ASP cc_start: 0.7570 (t0) cc_final: 0.7308 (t0) REVERT: U 688 ARG cc_start: 0.7634 (mtm-85) cc_final: 0.7005 (ttm110) REVERT: U 695 ILE cc_start: 0.8676 (tt) cc_final: 0.8422 (tt) REVERT: U 733 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7277 (mm-30) REVERT: U 756 GLU cc_start: 0.7555 (tm-30) cc_final: 0.7238 (tm-30) REVERT: U 758 VAL cc_start: 0.8668 (p) cc_final: 0.8376 (m) REVERT: U 761 MET cc_start: 0.6979 (tmm) cc_final: 0.6732 (tmm) REVERT: U 779 MET cc_start: 0.7711 (tmm) cc_final: 0.7211 (tmm) REVERT: U 789 HIS cc_start: 0.6638 (OUTLIER) cc_final: 0.5477 (t-90) REVERT: U 818 CYS cc_start: 0.7467 (m) cc_final: 0.7210 (m) REVERT: U 831 ARG cc_start: 0.7660 (mtp180) cc_final: 0.7353 (mtp180) REVERT: U 865 GLU cc_start: 0.7152 (mt-10) cc_final: 0.6861 (mt-10) REVERT: U 876 ASP cc_start: 0.7668 (t0) cc_final: 0.7149 (t0) REVERT: U 887 ARG cc_start: 0.7734 (ptt180) cc_final: 0.7398 (tmm-80) REVERT: U 898 ILE cc_start: 0.8424 (mm) cc_final: 0.8089 (mm) REVERT: U 907 GLU cc_start: 0.6829 (mm-30) cc_final: 0.6626 (mm-30) REVERT: Y 585 MET cc_start: 0.8050 (mmm) cc_final: 0.7832 (mmm) REVERT: Y 607 MET cc_start: 0.6901 (mtm) cc_final: 0.6272 (mtm) REVERT: Y 684 VAL cc_start: 0.8376 (OUTLIER) cc_final: 0.7469 (p) REVERT: Y 698 TRP cc_start: 0.7620 (m-10) cc_final: 0.5099 (m-10) REVERT: Y 742 ARG cc_start: 0.7700 (ttp-110) cc_final: 0.7421 (ttm-80) REVERT: Y 773 LEU cc_start: 0.8513 (mt) cc_final: 0.8132 (mt) REVERT: Y 865 GLU cc_start: 0.7120 (mt-10) cc_final: 0.6718 (mt-10) REVERT: Y 889 LEU cc_start: 0.8787 (mt) cc_final: 0.8565 (mm) outliers start: 31 outliers final: 22 residues processed: 304 average time/residue: 0.1399 time to fit residues: 56.6526 Evaluate side-chains 312 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 288 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 612 THR Chi-restraints excluded: chain V residue 654 GLU Chi-restraints excluded: chain V residue 715 PHE Chi-restraints excluded: chain Z residue 578 VAL Chi-restraints excluded: chain Z residue 700 MET Chi-restraints excluded: chain U residue 618 ASP Chi-restraints excluded: chain U residue 634 ILE Chi-restraints excluded: chain U residue 661 ILE Chi-restraints excluded: chain U residue 680 LYS Chi-restraints excluded: chain U residue 689 SER Chi-restraints excluded: chain U residue 738 LEU Chi-restraints excluded: chain U residue 749 ARG Chi-restraints excluded: chain U residue 789 HIS Chi-restraints excluded: chain U residue 875 THR Chi-restraints excluded: chain U residue 883 LEU Chi-restraints excluded: chain U residue 889 LEU Chi-restraints excluded: chain Y residue 71 MET Chi-restraints excluded: chain Y residue 548 MET Chi-restraints excluded: chain Y residue 655 ILE Chi-restraints excluded: chain Y residue 684 VAL Chi-restraints excluded: chain Y residue 729 ARG Chi-restraints excluded: chain Y residue 737 LEU Chi-restraints excluded: chain Y residue 776 ASN Chi-restraints excluded: chain Y residue 900 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 121 optimal weight: 5.9990 chunk 37 optimal weight: 8.9990 chunk 117 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 134 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 112 optimal weight: 0.1980 chunk 110 optimal weight: 50.0000 chunk 127 optimal weight: 1.9990 chunk 77 optimal weight: 0.2980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 406 ASN ** Z 657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 612 ASN U 656 GLN ** U 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4888 r_free = 0.4888 target = 0.256789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.211806 restraints weight = 24411.419| |-----------------------------------------------------------------------------| r_work (start): 0.4368 rms_B_bonded: 4.42 r_work (final): 0.4368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5995 moved from start: 0.5122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 12525 Z= 0.279 Angle : 0.706 12.306 16922 Z= 0.349 Chirality : 0.045 0.307 1756 Planarity : 0.005 0.108 2189 Dihedral : 4.978 55.001 1672 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.06 % Allowed : 12.22 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.21), residues: 1480 helix: 0.46 (0.23), residues: 513 sheet: 0.13 (0.39), residues: 161 loop : -0.92 (0.20), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG U 882 TYR 0.023 0.002 TYR V 766 PHE 0.019 0.002 PHE U 732 TRP 0.020 0.002 TRP Z 674 HIS 0.034 0.002 HIS U 789 Details of bonding type rmsd covalent geometry : bond 0.00578 (12488) covalent geometry : angle 0.68269 (16868) hydrogen bonds : bond 0.04656 ( 401) hydrogen bonds : angle 5.43429 ( 1125) metal coordination : bond 0.00402 ( 36) metal coordination : angle 3.26799 ( 54) Misc. bond : bond 0.00015 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 286 time to evaluate : 0.426 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: Z 674 TRP cc_start: 0.6365 (p90) cc_final: 0.5740 (p90) REVERT: Z 676 PHE cc_start: 0.6271 (t80) cc_final: 0.5978 (t80) REVERT: Z 682 MET cc_start: 0.3892 (mmm) cc_final: 0.3679 (mmm) REVERT: U 618 ASP cc_start: 0.7004 (OUTLIER) cc_final: 0.5266 (m-30) REVERT: U 638 SER cc_start: 0.8198 (t) cc_final: 0.7898 (t) REVERT: U 643 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8683 (mt) REVERT: U 652 ASP cc_start: 0.7718 (t0) cc_final: 0.7473 (t0) REVERT: U 658 ASP cc_start: 0.7230 (t0) cc_final: 0.6985 (t0) REVERT: U 672 VAL cc_start: 0.8365 (t) cc_final: 0.7779 (m) REVERT: U 688 ARG cc_start: 0.7171 (mtm-85) cc_final: 0.6816 (ttm110) REVERT: U 695 ILE cc_start: 0.8757 (tt) cc_final: 0.8461 (tt) REVERT: U 756 GLU cc_start: 0.7163 (tm-30) cc_final: 0.6840 (tm-30) REVERT: U 758 VAL cc_start: 0.8658 (p) cc_final: 0.8369 (t) REVERT: U 761 MET cc_start: 0.6534 (tmm) cc_final: 0.6301 (tmm) REVERT: U 779 MET cc_start: 0.7185 (tmm) cc_final: 0.6880 (tmm) REVERT: U 789 HIS cc_start: 0.6567 (t-170) cc_final: 0.4704 (t-90) REVERT: U 865 GLU cc_start: 0.7067 (mt-10) cc_final: 0.6853 (mt-10) REVERT: U 876 ASP cc_start: 0.7132 (t0) cc_final: 0.6552 (t0) REVERT: U 887 ARG cc_start: 0.7327 (ptt180) cc_final: 0.6965 (tmm-80) REVERT: U 898 ILE cc_start: 0.8372 (mm) cc_final: 0.8130 (mm) REVERT: Y 684 VAL cc_start: 0.8706 (OUTLIER) cc_final: 0.7890 (p) REVERT: Y 773 LEU cc_start: 0.8356 (mt) cc_final: 0.7945 (mt) REVERT: Y 801 MET cc_start: 0.6792 (mtp) cc_final: 0.6427 (mtm) REVERT: Y 865 GLU cc_start: 0.7323 (mt-10) cc_final: 0.6848 (mt-10) REVERT: Y 889 LEU cc_start: 0.8832 (mt) cc_final: 0.8603 (mm) outliers start: 40 outliers final: 30 residues processed: 296 average time/residue: 0.1537 time to fit residues: 60.3754 Evaluate side-chains 312 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 279 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 560 LEU Chi-restraints excluded: chain V residue 612 THR Chi-restraints excluded: chain V residue 654 GLU Chi-restraints excluded: chain V residue 696 CYS Chi-restraints excluded: chain V residue 715 PHE Chi-restraints excluded: chain Z residue 578 VAL Chi-restraints excluded: chain Z residue 608 VAL Chi-restraints excluded: chain Z residue 675 MET Chi-restraints excluded: chain Z residue 679 VAL Chi-restraints excluded: chain U residue 560 VAL Chi-restraints excluded: chain U residue 618 ASP Chi-restraints excluded: chain U residue 632 LYS Chi-restraints excluded: chain U residue 634 ILE Chi-restraints excluded: chain U residue 643 ILE Chi-restraints excluded: chain U residue 661 ILE Chi-restraints excluded: chain U residue 678 GLN Chi-restraints excluded: chain U residue 680 LYS Chi-restraints excluded: chain U residue 689 SER Chi-restraints excluded: chain U residue 749 ARG Chi-restraints excluded: chain U residue 863 GLU Chi-restraints excluded: chain U residue 875 THR Chi-restraints excluded: chain U residue 883 LEU Chi-restraints excluded: chain U residue 889 LEU Chi-restraints excluded: chain Y residue 71 MET Chi-restraints excluded: chain Y residue 548 MET Chi-restraints excluded: chain Y residue 655 ILE Chi-restraints excluded: chain Y residue 663 SER Chi-restraints excluded: chain Y residue 671 THR Chi-restraints excluded: chain Y residue 684 VAL Chi-restraints excluded: chain Y residue 729 ARG Chi-restraints excluded: chain Y residue 737 LEU Chi-restraints excluded: chain Y residue 776 ASN Chi-restraints excluded: chain Y residue 813 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 94 optimal weight: 20.0000 chunk 77 optimal weight: 0.1980 chunk 69 optimal weight: 0.5980 chunk 52 optimal weight: 0.0970 chunk 86 optimal weight: 0.5980 chunk 118 optimal weight: 40.0000 chunk 125 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 72 optimal weight: 0.0770 chunk 30 optimal weight: 3.9990 overall best weight: 0.3136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 406 ASN ** Z 657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 656 GLN Y 821 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4915 r_free = 0.4915 target = 0.258408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.215557 restraints weight = 24358.498| |-----------------------------------------------------------------------------| r_work (start): 0.4435 rms_B_bonded: 4.33 r_work (final): 0.4435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5840 moved from start: 0.5178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12525 Z= 0.122 Angle : 0.610 12.972 16922 Z= 0.288 Chirality : 0.041 0.342 1756 Planarity : 0.004 0.057 2189 Dihedral : 4.496 54.006 1672 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.22 % Allowed : 14.59 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.21), residues: 1480 helix: 0.88 (0.23), residues: 512 sheet: 0.20 (0.39), residues: 161 loop : -0.74 (0.21), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG U 882 TYR 0.024 0.001 TYR Z 661 PHE 0.013 0.001 PHE Y 755 TRP 0.018 0.001 TRP U 860 HIS 0.014 0.001 HIS Z 657 Details of bonding type rmsd covalent geometry : bond 0.00264 (12488) covalent geometry : angle 0.58544 (16868) hydrogen bonds : bond 0.03452 ( 401) hydrogen bonds : angle 4.96922 ( 1125) metal coordination : bond 0.00348 ( 36) metal coordination : angle 3.10030 ( 54) Misc. bond : bond 0.00008 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 287 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 439 ARG cc_start: 0.7737 (ttp80) cc_final: 0.7146 (ttp80) REVERT: V 506 MET cc_start: 0.6987 (mmm) cc_final: 0.6526 (mmm) REVERT: V 663 ARG cc_start: 0.6780 (ttm-80) cc_final: 0.6523 (ttm170) REVERT: Z 674 TRP cc_start: 0.5968 (p90) cc_final: 0.5428 (p90) REVERT: Z 676 PHE cc_start: 0.6152 (t80) cc_final: 0.5915 (t80) REVERT: U 618 ASP cc_start: 0.7147 (OUTLIER) cc_final: 0.5476 (m-30) REVERT: U 638 SER cc_start: 0.8082 (t) cc_final: 0.6950 (t) REVERT: U 641 ASP cc_start: 0.6685 (t70) cc_final: 0.6247 (t0) REVERT: U 652 ASP cc_start: 0.7472 (t0) cc_final: 0.7208 (t0) REVERT: U 658 ASP cc_start: 0.7130 (t0) cc_final: 0.6924 (t0) REVERT: U 688 ARG cc_start: 0.7125 (mtm-85) cc_final: 0.6792 (ttm110) REVERT: U 695 ILE cc_start: 0.8651 (tt) cc_final: 0.8368 (tt) REVERT: U 756 GLU cc_start: 0.7178 (tm-30) cc_final: 0.6886 (tm-30) REVERT: U 761 MET cc_start: 0.6465 (tmm) cc_final: 0.6083 (tmm) REVERT: U 779 MET cc_start: 0.7197 (tmm) cc_final: 0.6819 (tmm) REVERT: U 865 GLU cc_start: 0.6978 (mt-10) cc_final: 0.6729 (mt-10) REVERT: U 866 ARG cc_start: 0.7542 (ttm110) cc_final: 0.7315 (tpp80) REVERT: U 887 ARG cc_start: 0.7153 (ptt180) cc_final: 0.6776 (tmm-80) REVERT: U 898 ILE cc_start: 0.8273 (mm) cc_final: 0.7913 (mm) REVERT: Y 684 VAL cc_start: 0.8467 (OUTLIER) cc_final: 0.7651 (p) REVERT: Y 773 LEU cc_start: 0.8268 (mt) cc_final: 0.7840 (mt) REVERT: Y 801 MET cc_start: 0.6650 (mtp) cc_final: 0.6246 (mtp) REVERT: Y 865 GLU cc_start: 0.7109 (mt-10) cc_final: 0.6622 (mt-10) REVERT: Y 889 LEU cc_start: 0.8758 (mt) cc_final: 0.8538 (mm) outliers start: 29 outliers final: 25 residues processed: 296 average time/residue: 0.1561 time to fit residues: 61.1441 Evaluate side-chains 308 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 281 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 500 GLU Chi-restraints excluded: chain V residue 560 LEU Chi-restraints excluded: chain V residue 578 VAL Chi-restraints excluded: chain V residue 612 THR Chi-restraints excluded: chain V residue 654 GLU Chi-restraints excluded: chain V residue 696 CYS Chi-restraints excluded: chain V residue 715 PHE Chi-restraints excluded: chain Z residue 578 VAL Chi-restraints excluded: chain U residue 560 VAL Chi-restraints excluded: chain U residue 607 MET Chi-restraints excluded: chain U residue 618 ASP Chi-restraints excluded: chain U residue 634 ILE Chi-restraints excluded: chain U residue 653 LEU Chi-restraints excluded: chain U residue 661 ILE Chi-restraints excluded: chain U residue 680 LYS Chi-restraints excluded: chain U residue 693 LYS Chi-restraints excluded: chain U residue 749 ARG Chi-restraints excluded: chain U residue 875 THR Chi-restraints excluded: chain U residue 883 LEU Chi-restraints excluded: chain Y residue 71 MET Chi-restraints excluded: chain Y residue 548 MET Chi-restraints excluded: chain Y residue 618 ASP Chi-restraints excluded: chain Y residue 655 ILE Chi-restraints excluded: chain Y residue 684 VAL Chi-restraints excluded: chain Y residue 729 ARG Chi-restraints excluded: chain Y residue 737 LEU Chi-restraints excluded: chain Y residue 900 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 121 optimal weight: 10.0000 chunk 22 optimal weight: 0.0980 chunk 127 optimal weight: 0.0870 chunk 134 optimal weight: 0.0010 chunk 117 optimal weight: 6.9990 chunk 94 optimal weight: 40.0000 chunk 43 optimal weight: 2.9990 chunk 2 optimal weight: 0.0010 chunk 97 optimal weight: 50.0000 chunk 45 optimal weight: 0.0570 chunk 47 optimal weight: 0.6980 overall best weight: 0.0488 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 657 HIS U 789 HIS U 821 HIS Y 656 GLN Y 821 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4927 r_free = 0.4927 target = 0.259597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.217900 restraints weight = 24613.061| |-----------------------------------------------------------------------------| r_work (start): 0.4470 rms_B_bonded: 4.30 r_work (final): 0.4470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5719 moved from start: 0.5194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12525 Z= 0.098 Angle : 0.593 12.048 16922 Z= 0.278 Chirality : 0.040 0.292 1756 Planarity : 0.004 0.056 2189 Dihedral : 4.162 51.340 1672 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.14 % Allowed : 15.20 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.21), residues: 1480 helix: 1.18 (0.24), residues: 509 sheet: 0.29 (0.39), residues: 162 loop : -0.59 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Y 882 TYR 0.013 0.001 TYR Z 714 PHE 0.029 0.001 PHE U 732 TRP 0.012 0.001 TRP U 860 HIS 0.011 0.001 HIS Z 657 Details of bonding type rmsd covalent geometry : bond 0.00214 (12488) covalent geometry : angle 0.57048 (16868) hydrogen bonds : bond 0.02922 ( 401) hydrogen bonds : angle 4.64082 ( 1125) metal coordination : bond 0.00324 ( 36) metal coordination : angle 2.93713 ( 54) Misc. bond : bond 0.00002 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 287 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 439 ARG cc_start: 0.7745 (ttp80) cc_final: 0.7138 (ttp80) REVERT: V 506 MET cc_start: 0.6902 (mmm) cc_final: 0.6452 (mmm) REVERT: Z 610 ASN cc_start: 0.6854 (t0) cc_final: 0.6626 (t0) REVERT: Z 674 TRP cc_start: 0.5881 (p90) cc_final: 0.5310 (p90) REVERT: Z 676 PHE cc_start: 0.6181 (t80) cc_final: 0.5914 (t80) REVERT: U 638 SER cc_start: 0.8025 (t) cc_final: 0.6928 (t) REVERT: U 641 ASP cc_start: 0.6672 (t70) cc_final: 0.6264 (t0) REVERT: U 649 VAL cc_start: 0.8431 (t) cc_final: 0.8094 (m) REVERT: U 652 ASP cc_start: 0.7409 (t0) cc_final: 0.7119 (t0) REVERT: U 688 ARG cc_start: 0.7032 (mtm-85) cc_final: 0.6674 (ttm110) REVERT: U 695 ILE cc_start: 0.8621 (tt) cc_final: 0.8329 (tt) REVERT: U 756 GLU cc_start: 0.7128 (tm-30) cc_final: 0.6839 (tm-30) REVERT: U 758 VAL cc_start: 0.8482 (p) cc_final: 0.8155 (m) REVERT: U 773 LEU cc_start: 0.8107 (mt) cc_final: 0.7726 (mt) REVERT: U 779 MET cc_start: 0.7078 (tmm) cc_final: 0.6746 (tmm) REVERT: U 818 CYS cc_start: 0.7459 (m) cc_final: 0.6991 (m) REVERT: U 865 GLU cc_start: 0.6927 (mt-10) cc_final: 0.6567 (mt-10) REVERT: U 876 ASP cc_start: 0.6722 (t0) cc_final: 0.6474 (t0) REVERT: U 885 ARG cc_start: 0.7859 (ttt180) cc_final: 0.7618 (ttt180) REVERT: U 887 ARG cc_start: 0.7120 (ptt180) cc_final: 0.6818 (tmm-80) REVERT: U 898 ILE cc_start: 0.8221 (mm) cc_final: 0.7860 (mm) REVERT: Y 684 VAL cc_start: 0.8150 (OUTLIER) cc_final: 0.7285 (p) REVERT: Y 761 MET cc_start: 0.5710 (tpp) cc_final: 0.5325 (tpp) REVERT: Y 773 LEU cc_start: 0.8216 (mt) cc_final: 0.7831 (mt) REVERT: Y 823 ARG cc_start: 0.7423 (mmm-85) cc_final: 0.7045 (mtt90) REVERT: Y 865 GLU cc_start: 0.7042 (mt-10) cc_final: 0.6581 (mt-10) outliers start: 28 outliers final: 23 residues processed: 295 average time/residue: 0.1617 time to fit residues: 62.7397 Evaluate side-chains 306 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 282 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 560 LEU Chi-restraints excluded: chain V residue 578 VAL Chi-restraints excluded: chain V residue 654 GLU Chi-restraints excluded: chain V residue 715 PHE Chi-restraints excluded: chain V residue 722 MET Chi-restraints excluded: chain Z residue 578 VAL Chi-restraints excluded: chain U residue 560 VAL Chi-restraints excluded: chain U residue 607 MET Chi-restraints excluded: chain U residue 634 ILE Chi-restraints excluded: chain U residue 661 ILE Chi-restraints excluded: chain U residue 680 LYS Chi-restraints excluded: chain U residue 749 ARG Chi-restraints excluded: chain U residue 789 HIS Chi-restraints excluded: chain U residue 875 THR Chi-restraints excluded: chain U residue 883 LEU Chi-restraints excluded: chain U residue 889 LEU Chi-restraints excluded: chain Y residue 71 MET Chi-restraints excluded: chain Y residue 548 MET Chi-restraints excluded: chain Y residue 618 ASP Chi-restraints excluded: chain Y residue 661 ILE Chi-restraints excluded: chain Y residue 684 VAL Chi-restraints excluded: chain Y residue 729 ARG Chi-restraints excluded: chain Y residue 737 LEU Chi-restraints excluded: chain Y residue 900 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 98 optimal weight: 50.0000 chunk 58 optimal weight: 40.0000 chunk 68 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 33 optimal weight: 0.0270 chunk 122 optimal weight: 0.0870 chunk 39 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 65 optimal weight: 50.0000 chunk 79 optimal weight: 0.2980 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 656 GLN U 789 HIS U 821 HIS Y 656 GLN Y 821 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4910 r_free = 0.4910 target = 0.258001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.215064 restraints weight = 24341.528| |-----------------------------------------------------------------------------| r_work (start): 0.4435 rms_B_bonded: 4.40 r_work (final): 0.4435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5836 moved from start: 0.5363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 12525 Z= 0.133 Angle : 0.620 11.225 16922 Z= 0.294 Chirality : 0.041 0.281 1756 Planarity : 0.004 0.061 2189 Dihedral : 4.210 51.716 1672 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.37 % Allowed : 15.74 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.22), residues: 1480 helix: 1.24 (0.24), residues: 509 sheet: 0.35 (0.39), residues: 162 loop : -0.55 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG V 713 TYR 0.030 0.001 TYR Z 661 PHE 0.030 0.001 PHE U 732 TRP 0.012 0.001 TRP Z 674 HIS 0.017 0.001 HIS Z 657 Details of bonding type rmsd covalent geometry : bond 0.00292 (12488) covalent geometry : angle 0.59970 (16868) hydrogen bonds : bond 0.03181 ( 401) hydrogen bonds : angle 4.65623 ( 1125) metal coordination : bond 0.00320 ( 36) metal coordination : angle 2.86048 ( 54) Misc. bond : bond 0.00010 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 284 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 506 MET cc_start: 0.7024 (mmm) cc_final: 0.6555 (mmm) REVERT: V 551 ARG cc_start: 0.6420 (mtp-110) cc_final: 0.6209 (mtp85) REVERT: Z 674 TRP cc_start: 0.5994 (p90) cc_final: 0.5335 (p90) REVERT: Z 676 PHE cc_start: 0.6196 (t80) cc_final: 0.5955 (t80) REVERT: U 638 SER cc_start: 0.8063 (t) cc_final: 0.7067 (t) REVERT: U 641 ASP cc_start: 0.6717 (t70) cc_final: 0.6325 (t0) REVERT: U 643 ILE cc_start: 0.8846 (pt) cc_final: 0.8512 (mt) REVERT: U 649 VAL cc_start: 0.8477 (t) cc_final: 0.8084 (p) REVERT: U 652 ASP cc_start: 0.7464 (t0) cc_final: 0.7171 (t0) REVERT: U 688 ARG cc_start: 0.7056 (mtm-85) cc_final: 0.6735 (ttm110) REVERT: U 695 ILE cc_start: 0.8631 (tt) cc_final: 0.8361 (tt) REVERT: U 756 GLU cc_start: 0.7177 (tm-30) cc_final: 0.6866 (tm-30) REVERT: U 758 VAL cc_start: 0.8510 (p) cc_final: 0.8165 (m) REVERT: U 773 LEU cc_start: 0.8157 (mt) cc_final: 0.7870 (mt) REVERT: U 779 MET cc_start: 0.6995 (tmm) cc_final: 0.6706 (tmm) REVERT: U 818 CYS cc_start: 0.7271 (m) cc_final: 0.6893 (m) REVERT: U 865 GLU cc_start: 0.7053 (mt-10) cc_final: 0.6653 (mt-10) REVERT: U 876 ASP cc_start: 0.6846 (t0) cc_final: 0.6488 (t0) REVERT: U 885 ARG cc_start: 0.7871 (ttt180) cc_final: 0.7613 (ttt180) REVERT: U 887 ARG cc_start: 0.7202 (ptt180) cc_final: 0.6897 (tmm-80) REVERT: U 898 ILE cc_start: 0.8301 (mm) cc_final: 0.7876 (mm) REVERT: Y 684 VAL cc_start: 0.8305 (OUTLIER) cc_final: 0.7509 (p) REVERT: Y 720 ARG cc_start: 0.7686 (ptm-80) cc_final: 0.7336 (ptm-80) REVERT: Y 761 MET cc_start: 0.5862 (tpp) cc_final: 0.5561 (tpp) REVERT: Y 773 LEU cc_start: 0.8233 (mt) cc_final: 0.7859 (mt) REVERT: Y 865 GLU cc_start: 0.7118 (mt-10) cc_final: 0.6650 (mt-10) REVERT: Y 889 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8409 (mm) outliers start: 31 outliers final: 22 residues processed: 294 average time/residue: 0.1489 time to fit residues: 57.9867 Evaluate side-chains 304 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 280 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 560 LEU Chi-restraints excluded: chain V residue 578 VAL Chi-restraints excluded: chain V residue 715 PHE Chi-restraints excluded: chain V residue 722 MET Chi-restraints excluded: chain Z residue 578 VAL Chi-restraints excluded: chain U residue 560 VAL Chi-restraints excluded: chain U residue 607 MET Chi-restraints excluded: chain U residue 634 ILE Chi-restraints excluded: chain U residue 653 LEU Chi-restraints excluded: chain U residue 661 ILE Chi-restraints excluded: chain U residue 680 LYS Chi-restraints excluded: chain U residue 749 ARG Chi-restraints excluded: chain U residue 789 HIS Chi-restraints excluded: chain U residue 875 THR Chi-restraints excluded: chain U residue 883 LEU Chi-restraints excluded: chain U residue 889 LEU Chi-restraints excluded: chain Y residue 71 MET Chi-restraints excluded: chain Y residue 548 MET Chi-restraints excluded: chain Y residue 618 ASP Chi-restraints excluded: chain Y residue 655 ILE Chi-restraints excluded: chain Y residue 684 VAL Chi-restraints excluded: chain Y residue 729 ARG Chi-restraints excluded: chain Y residue 737 LEU Chi-restraints excluded: chain Y residue 889 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 41 optimal weight: 0.9990 chunk 112 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 78 optimal weight: 0.4980 chunk 102 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 72 optimal weight: 0.4980 chunk 123 optimal weight: 0.7980 chunk 120 optimal weight: 30.0000 chunk 18 optimal weight: 0.0770 chunk 116 optimal weight: 0.0870 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 656 GLN U 789 HIS Y 656 GLN Y 776 ASN Y 821 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4908 r_free = 0.4908 target = 0.258022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.215002 restraints weight = 24427.244| |-----------------------------------------------------------------------------| r_work (start): 0.4433 rms_B_bonded: 4.41 r_work (final): 0.4433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5830 moved from start: 0.5460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12525 Z= 0.127 Angle : 0.617 11.830 16922 Z= 0.292 Chirality : 0.041 0.201 1756 Planarity : 0.004 0.058 2189 Dihedral : 4.204 52.140 1672 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.99 % Allowed : 15.89 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.22), residues: 1480 helix: 1.28 (0.24), residues: 507 sheet: 0.40 (0.38), residues: 161 loop : -0.54 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG U 790 TYR 0.035 0.001 TYR Z 661 PHE 0.034 0.001 PHE U 732 TRP 0.016 0.001 TRP Y 860 HIS 0.011 0.001 HIS U 789 Details of bonding type rmsd covalent geometry : bond 0.00281 (12488) covalent geometry : angle 0.59712 (16868) hydrogen bonds : bond 0.03169 ( 401) hydrogen bonds : angle 4.60477 ( 1125) metal coordination : bond 0.00325 ( 36) metal coordination : angle 2.81531 ( 54) Misc. bond : bond 0.00014 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 281 time to evaluate : 0.459 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: V 506 MET cc_start: 0.6998 (mmm) cc_final: 0.6562 (mmm) REVERT: V 551 ARG cc_start: 0.6278 (mtp-110) cc_final: 0.6063 (mtp85) REVERT: V 692 ARG cc_start: 0.6920 (mmt-90) cc_final: 0.6711 (mmt-90) REVERT: Z 674 TRP cc_start: 0.6000 (p90) cc_final: 0.5479 (p90) REVERT: Z 676 PHE cc_start: 0.6207 (t80) cc_final: 0.5959 (t80) REVERT: Z 692 ARG cc_start: 0.7613 (ttp-110) cc_final: 0.7290 (ttp-110) REVERT: U 638 SER cc_start: 0.8073 (t) cc_final: 0.7054 (t) REVERT: U 641 ASP cc_start: 0.6736 (t70) cc_final: 0.6328 (t0) REVERT: U 643 ILE cc_start: 0.8839 (pt) cc_final: 0.8513 (mt) REVERT: U 647 LEU cc_start: 0.8468 (tp) cc_final: 0.8173 (tt) REVERT: U 649 VAL cc_start: 0.8405 (t) cc_final: 0.8002 (p) REVERT: U 652 ASP cc_start: 0.7474 (t0) cc_final: 0.7180 (t0) REVERT: U 688 ARG cc_start: 0.7123 (mtm-85) cc_final: 0.6865 (ttm110) REVERT: U 695 ILE cc_start: 0.8642 (tt) cc_final: 0.8369 (tt) REVERT: U 733 GLU cc_start: 0.7389 (mm-30) cc_final: 0.6889 (mm-30) REVERT: U 756 GLU cc_start: 0.7189 (tm-30) cc_final: 0.6894 (tm-30) REVERT: U 758 VAL cc_start: 0.8490 (p) cc_final: 0.8177 (t) REVERT: U 773 LEU cc_start: 0.8184 (mt) cc_final: 0.7926 (mt) REVERT: U 779 MET cc_start: 0.6944 (tmm) cc_final: 0.6641 (tmm) REVERT: U 818 CYS cc_start: 0.7371 (m) cc_final: 0.7052 (m) REVERT: U 865 GLU cc_start: 0.7061 (mt-10) cc_final: 0.6699 (mt-10) REVERT: U 876 ASP cc_start: 0.6850 (t0) cc_final: 0.6487 (t0) REVERT: U 885 ARG cc_start: 0.7881 (ttt180) cc_final: 0.7634 (ttt180) REVERT: U 887 ARG cc_start: 0.7264 (ptt180) cc_final: 0.6925 (tmm-80) REVERT: U 898 ILE cc_start: 0.8303 (mm) cc_final: 0.7857 (mm) REVERT: Y 657 VAL cc_start: 0.8335 (OUTLIER) cc_final: 0.7947 (m) REVERT: Y 659 ARG cc_start: 0.7768 (ptp90) cc_final: 0.7561 (ptt-90) REVERT: Y 684 VAL cc_start: 0.8327 (OUTLIER) cc_final: 0.7525 (p) REVERT: Y 720 ARG cc_start: 0.7697 (ptm-80) cc_final: 0.7333 (ptm-80) REVERT: Y 742 ARG cc_start: 0.7516 (ttm110) cc_final: 0.7198 (ttp-110) REVERT: Y 773 LEU cc_start: 0.8207 (mt) cc_final: 0.7869 (mt) REVERT: Y 865 GLU cc_start: 0.7167 (mt-10) cc_final: 0.6685 (mt-10) REVERT: Y 889 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8413 (mm) outliers start: 26 outliers final: 21 residues processed: 288 average time/residue: 0.1471 time to fit residues: 56.5755 Evaluate side-chains 303 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 279 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 560 LEU Chi-restraints excluded: chain V residue 578 VAL Chi-restraints excluded: chain V residue 715 PHE Chi-restraints excluded: chain V residue 722 MET Chi-restraints excluded: chain Z residue 578 VAL Chi-restraints excluded: chain U residue 560 VAL Chi-restraints excluded: chain U residue 607 MET Chi-restraints excluded: chain U residue 634 ILE Chi-restraints excluded: chain U residue 653 LEU Chi-restraints excluded: chain U residue 680 LYS Chi-restraints excluded: chain U residue 749 ARG Chi-restraints excluded: chain U residue 789 HIS Chi-restraints excluded: chain U residue 875 THR Chi-restraints excluded: chain U residue 883 LEU Chi-restraints excluded: chain Y residue 71 MET Chi-restraints excluded: chain Y residue 548 MET Chi-restraints excluded: chain Y residue 618 ASP Chi-restraints excluded: chain Y residue 655 ILE Chi-restraints excluded: chain Y residue 657 VAL Chi-restraints excluded: chain Y residue 684 VAL Chi-restraints excluded: chain Y residue 729 ARG Chi-restraints excluded: chain Y residue 737 LEU Chi-restraints excluded: chain Y residue 776 ASN Chi-restraints excluded: chain Y residue 889 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 36 optimal weight: 0.8980 chunk 125 optimal weight: 0.0370 chunk 3 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 83 optimal weight: 0.2980 chunk 69 optimal weight: 0.5980 chunk 148 optimal weight: 0.9990 chunk 87 optimal weight: 0.0570 chunk 37 optimal weight: 0.9980 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 515 GLN U 789 HIS U 821 HIS Y 656 GLN ** Y 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 776 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4909 r_free = 0.4909 target = 0.258145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.215838 restraints weight = 24326.777| |-----------------------------------------------------------------------------| r_work (start): 0.4444 rms_B_bonded: 4.28 r_work (final): 0.4444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5786 moved from start: 0.5525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12525 Z= 0.123 Angle : 0.612 11.861 16922 Z= 0.288 Chirality : 0.040 0.205 1756 Planarity : 0.004 0.059 2189 Dihedral : 4.178 52.220 1672 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.14 % Allowed : 15.89 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.22), residues: 1480 helix: 1.30 (0.24), residues: 507 sheet: 0.51 (0.38), residues: 158 loop : -0.52 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Z 692 TYR 0.031 0.001 TYR Z 661 PHE 0.034 0.001 PHE U 732 TRP 0.014 0.001 TRP Y 860 HIS 0.021 0.001 HIS U 789 Details of bonding type rmsd covalent geometry : bond 0.00272 (12488) covalent geometry : angle 0.59266 (16868) hydrogen bonds : bond 0.03137 ( 401) hydrogen bonds : angle 4.57158 ( 1125) metal coordination : bond 0.00318 ( 36) metal coordination : angle 2.77374 ( 54) Misc. bond : bond 0.00010 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3297.60 seconds wall clock time: 57 minutes 5.77 seconds (3425.77 seconds total)