Starting phenix.real_space_refine on Sat Oct 31 07:24:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m0n_63559/10_2026/9m0n_63559.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m0n_63559/10_2026/9m0n_63559.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9m0n_63559/10_2026/9m0n_63559.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m0n_63559/10_2026/9m0n_63559.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9m0n_63559/10_2026/9m0n_63559.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m0n_63559/10_2026/9m0n_63559.map" } resolution = 2.74 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= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 138 5.16 5 C 25878 2.51 5 N 6894 2.21 5 O 7776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 156 residue(s): 0.22s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 40698 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 824, 6756 Classifications: {'peptide': 824} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 801} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 9.00, per 1000 atoms: 0.22 Number of scatterers: 40698 At special positions: 0 Unit cell: (164.8, 153.264, 299.112, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 138 16.00 P 12 15.00 O 7776 8.00 N 6894 7.00 C 25878 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=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.12 Conformation dependent library (CDL) restraints added in 1.7 seconds 9864 Ramachandran restraints generated. 4932 Oldfield, 0 Emsley, 4932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9624 Finding SS restraints... Secondary structure from input PDB file: 270 helices and 23 sheets defined 69.8% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 9 through 13 Processing helix chain 'A' and resid 16 through 25 Processing helix chain 'A' and resid 31 through 36 removed outlier: 3.898A pdb=" N PHE A 36 " --> pdb=" O ASP A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 53 Processing helix chain 'A' and resid 61 through 67 Processing helix chain 'A' and resid 67 through 83 Processing helix chain 'A' and resid 106 through 112 Processing helix chain 'A' and resid 120 through 140 Processing helix chain 'A' and resid 140 through 148 removed outlier: 3.643A pdb=" N GLU A 144 " --> pdb=" O HIS A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 166 Processing helix chain 'A' and resid 184 through 196 Processing helix chain 'A' and resid 215 through 225 Processing helix chain 'A' and resid 242 through 260 Processing helix chain 'A' and resid 280 through 290 Processing helix chain 'A' and resid 326 through 341 Processing helix chain 'A' and resid 347 through 356 Processing helix chain 'A' and resid 361 through 373 removed outlier: 3.637A pdb=" N VAL A 365 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG A 366 " --> pdb=" O PRO A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 399 removed outlier: 3.698A pdb=" N ASN A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 403 Processing helix chain 'A' and resid 405 through 418 removed outlier: 3.943A pdb=" N PHE A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 430 Processing helix chain 'A' and resid 431 through 445 Proline residue: A 437 - end of helix Processing helix chain 'A' and resid 461 through 471 Processing helix chain 'A' and resid 476 through 493 Processing helix chain 'A' and resid 502 through 514 Processing helix chain 'A' and resid 519 through 522 Processing helix chain 'A' and resid 523 through 538 removed outlier: 3.986A pdb=" N HIS A 527 " --> pdb=" O LEU A 523 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR A 528 " --> pdb=" O ILE A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 554 removed outlier: 3.716A pdb=" N VAL A 545 " --> pdb=" O SER A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 559 Processing helix chain 'A' and resid 560 through 579 Processing helix chain 'A' and resid 582 through 588 Processing helix chain 'A' and resid 592 through 607 removed outlier: 4.114A pdb=" N LYS A 596 " --> pdb=" O GLY A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 618 removed outlier: 4.131A pdb=" N ALA A 612 " --> pdb=" O ARG A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 640 Processing helix chain 'A' and resid 642 through 657 removed outlier: 3.755A pdb=" N ALA A 646 " --> pdb=" O GLU A 642 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N SER A 648 " --> pdb=" O ASP A 644 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N TYR A 649 " --> pdb=" O LYS A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 673 Processing helix chain 'A' and resid 679 through 696 removed outlier: 4.371A pdb=" N ILE A 683 " --> pdb=" O ASP A 679 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP A 696 " --> pdb=" O LEU A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 715 Processing helix chain 'A' and resid 718 through 733 Processing helix chain 'A' and resid 736 through 750 removed outlier: 4.501A pdb=" N LEU A 740 " --> pdb=" O SER A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 768 Processing helix chain 'A' and resid 774 through 789 Processing helix chain 'A' and resid 790 through 798 Processing helix chain 'A' and resid 798 through 805 Processing helix chain 'A' and resid 806 through 822 removed outlier: 3.694A pdb=" N GLY A 822 " --> pdb=" O LYS A 818 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 13 Processing helix chain 'B' and resid 16 through 25 Processing helix chain 'B' and resid 31 through 36 removed outlier: 3.897A pdb=" N PHE B 36 " --> pdb=" O ASP B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 53 Processing helix chain 'B' and resid 61 through 67 Processing helix chain 'B' and resid 67 through 83 Processing helix chain 'B' and resid 106 through 112 Processing helix chain 'B' and resid 120 through 140 Processing helix chain 'B' and resid 140 through 148 removed outlier: 3.643A pdb=" N GLU B 144 " --> pdb=" O HIS B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 166 Processing helix chain 'B' and resid 184 through 196 Processing helix chain 'B' and resid 215 through 225 Processing helix chain 'B' and resid 242 through 260 Processing helix chain 'B' and resid 280 through 290 Processing helix chain 'B' and resid 326 through 341 Processing helix chain 'B' and resid 347 through 356 Processing helix chain 'B' and resid 361 through 373 removed outlier: 3.636A pdb=" N VAL B 365 " --> pdb=" O LEU B 361 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG B 366 " --> pdb=" O PRO B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 399 removed outlier: 3.698A pdb=" N ASN B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 403 Processing helix chain 'B' and resid 405 through 418 removed outlier: 3.943A pdb=" N PHE B 418 " --> pdb=" O LEU B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 430 Processing helix chain 'B' and resid 431 through 445 Proline residue: B 437 - end of helix Processing helix chain 'B' and resid 461 through 471 Processing helix chain 'B' and resid 476 through 493 Processing helix chain 'B' and resid 502 through 514 Processing helix chain 'B' and resid 519 through 522 Processing helix chain 'B' and resid 523 through 538 removed outlier: 3.986A pdb=" N HIS B 527 " --> pdb=" O LEU B 523 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR B 528 " --> pdb=" O ILE B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 554 removed outlier: 3.717A pdb=" N VAL B 545 " --> pdb=" O SER B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 559 Processing helix chain 'B' and resid 560 through 579 Processing helix chain 'B' and resid 582 through 588 Processing helix chain 'B' and resid 592 through 607 removed outlier: 4.113A pdb=" N LYS B 596 " --> pdb=" O GLY B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 618 removed outlier: 4.130A pdb=" N ALA B 612 " --> pdb=" O ARG B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 640 Processing helix chain 'B' and resid 642 through 657 removed outlier: 3.755A pdb=" N ALA B 646 " --> pdb=" O GLU B 642 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N SER B 648 " --> pdb=" O ASP B 644 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N TYR B 649 " --> pdb=" O LYS B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 673 Processing helix chain 'B' and resid 679 through 696 removed outlier: 4.371A pdb=" N ILE B 683 " --> pdb=" O ASP B 679 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASP B 696 " --> pdb=" O LEU B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 697 through 715 Processing helix chain 'B' and resid 718 through 733 Processing helix chain 'B' and resid 736 through 750 removed outlier: 4.502A pdb=" N LEU B 740 " --> pdb=" O SER B 736 " (cutoff:3.500A) Processing helix chain 'B' and resid 753 through 768 Processing helix chain 'B' and resid 774 through 789 Processing helix chain 'B' and resid 790 through 798 Processing helix chain 'B' and resid 798 through 805 Processing helix chain 'B' and resid 806 through 822 removed outlier: 3.695A pdb=" N GLY B 822 " --> pdb=" O LYS B 818 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 13 Processing helix chain 'C' and resid 16 through 25 Processing helix chain 'C' and resid 31 through 36 removed outlier: 3.898A pdb=" N PHE C 36 " --> pdb=" O ASP C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 53 Processing helix chain 'C' and resid 61 through 67 Processing helix chain 'C' and resid 67 through 83 Processing helix chain 'C' and resid 106 through 112 Processing helix chain 'C' and resid 120 through 140 Processing helix chain 'C' and resid 140 through 148 removed outlier: 3.642A pdb=" N GLU C 144 " --> pdb=" O HIS C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 166 Processing helix chain 'C' and resid 184 through 196 Processing helix chain 'C' and resid 215 through 225 Processing helix chain 'C' and resid 242 through 260 Processing helix chain 'C' and resid 280 through 290 Processing helix chain 'C' and resid 326 through 341 Processing helix chain 'C' and resid 347 through 356 Processing helix chain 'C' and resid 361 through 373 removed outlier: 3.637A pdb=" N VAL C 365 " --> pdb=" O LEU C 361 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG C 366 " --> pdb=" O PRO C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 399 removed outlier: 3.698A pdb=" N ASN C 391 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 403 Processing helix chain 'C' and resid 405 through 418 removed outlier: 3.943A pdb=" N PHE C 418 " --> pdb=" O LEU C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 430 Processing helix chain 'C' and resid 431 through 445 Proline residue: C 437 - end of helix Processing helix chain 'C' and resid 461 through 471 Processing helix chain 'C' and resid 476 through 493 Processing helix chain 'C' and resid 502 through 514 Processing helix chain 'C' and resid 519 through 522 Processing helix chain 'C' and resid 523 through 538 removed outlier: 3.986A pdb=" N HIS C 527 " --> pdb=" O LEU C 523 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR C 528 " --> pdb=" O ILE C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 554 removed outlier: 3.717A pdb=" N VAL C 545 " --> pdb=" O SER C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 559 Processing helix chain 'C' and resid 560 through 579 Processing helix chain 'C' and resid 582 through 588 Processing helix chain 'C' and resid 592 through 607 removed outlier: 4.114A pdb=" N LYS C 596 " --> pdb=" O GLY C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 618 removed outlier: 4.131A pdb=" N ALA C 612 " --> pdb=" O ARG C 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 640 Processing helix chain 'C' and resid 642 through 657 removed outlier: 3.755A pdb=" N ALA C 646 " --> pdb=" O GLU C 642 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N SER C 648 " --> pdb=" O ASP C 644 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N TYR C 649 " --> pdb=" O LYS C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 660 through 673 Processing helix chain 'C' and resid 679 through 696 removed outlier: 4.372A pdb=" N ILE C 683 " --> pdb=" O ASP C 679 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP C 696 " --> pdb=" O LEU C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 697 through 715 Processing helix chain 'C' and resid 718 through 733 Processing helix chain 'C' and resid 736 through 750 removed outlier: 4.502A pdb=" N LEU C 740 " --> pdb=" O SER C 736 " (cutoff:3.500A) Processing helix chain 'C' and resid 753 through 768 Processing helix chain 'C' and resid 774 through 789 Processing helix chain 'C' and resid 790 through 798 Processing helix chain 'C' and resid 798 through 805 Processing helix chain 'C' and resid 806 through 822 removed outlier: 3.695A pdb=" N GLY C 822 " --> pdb=" O LYS C 818 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 13 Processing helix chain 'D' and resid 16 through 25 Processing helix chain 'D' and resid 31 through 36 removed outlier: 3.898A pdb=" N PHE D 36 " --> pdb=" O ASP D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 53 Processing helix chain 'D' and resid 61 through 67 Processing helix chain 'D' and resid 67 through 83 Processing helix chain 'D' and resid 106 through 112 Processing helix chain 'D' and resid 120 through 140 Processing helix chain 'D' and resid 140 through 148 removed outlier: 3.642A pdb=" N GLU D 144 " --> pdb=" O HIS D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 166 Processing helix chain 'D' and resid 184 through 196 Processing helix chain 'D' and resid 215 through 225 Processing helix chain 'D' and resid 242 through 260 Processing helix chain 'D' and resid 280 through 290 Processing helix chain 'D' and resid 326 through 341 Processing helix chain 'D' and resid 347 through 356 Processing helix chain 'D' and resid 361 through 373 removed outlier: 3.637A pdb=" N VAL D 365 " --> pdb=" O LEU D 361 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG D 366 " --> pdb=" O PRO D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 399 removed outlier: 3.698A pdb=" N ASN D 391 " --> pdb=" O LEU D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 403 Processing helix chain 'D' and resid 405 through 418 removed outlier: 3.943A pdb=" N PHE D 418 " --> pdb=" O LEU D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 430 Processing helix chain 'D' and resid 431 through 445 Proline residue: D 437 - end of helix Processing helix chain 'D' and resid 461 through 471 Processing helix chain 'D' and resid 476 through 493 Processing helix chain 'D' and resid 502 through 514 Processing helix chain 'D' and resid 519 through 522 Processing helix chain 'D' and resid 523 through 538 removed outlier: 3.986A pdb=" N HIS D 527 " --> pdb=" O LEU D 523 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR D 528 " --> pdb=" O ILE D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 554 removed outlier: 3.716A pdb=" N VAL D 545 " --> pdb=" O SER D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 559 Processing helix chain 'D' and resid 560 through 579 Processing helix chain 'D' and resid 582 through 588 Processing helix chain 'D' and resid 592 through 607 removed outlier: 4.113A pdb=" N LYS D 596 " --> pdb=" O GLY D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 608 through 618 removed outlier: 4.132A pdb=" N ALA D 612 " --> pdb=" O ARG D 608 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 640 Processing helix chain 'D' and resid 642 through 657 removed outlier: 3.754A pdb=" N ALA D 646 " --> pdb=" O GLU D 642 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N SER D 648 " --> pdb=" O ASP D 644 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N TYR D 649 " --> pdb=" O LYS D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 660 through 673 Processing helix chain 'D' and resid 679 through 696 removed outlier: 4.371A pdb=" N ILE D 683 " --> pdb=" O ASP D 679 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP D 696 " --> pdb=" O LEU D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 697 through 715 Processing helix chain 'D' and resid 718 through 733 Processing helix chain 'D' and resid 736 through 750 removed outlier: 4.501A pdb=" N LEU D 740 " --> pdb=" O SER D 736 " (cutoff:3.500A) Processing helix chain 'D' and resid 753 through 768 Processing helix chain 'D' and resid 774 through 789 Processing helix chain 'D' and resid 790 through 798 Processing helix chain 'D' and resid 798 through 805 Processing helix chain 'D' and resid 806 through 822 removed outlier: 3.695A pdb=" N GLY D 822 " --> pdb=" O LYS D 818 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 13 Processing helix chain 'E' and resid 16 through 25 Processing helix chain 'E' and resid 31 through 36 removed outlier: 3.898A pdb=" N PHE E 36 " --> pdb=" O ASP E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 53 Processing helix chain 'E' and resid 61 through 67 Processing helix chain 'E' and resid 67 through 83 Processing helix chain 'E' and resid 106 through 112 Processing helix chain 'E' and resid 120 through 140 Processing helix chain 'E' and resid 140 through 148 removed outlier: 3.643A pdb=" N GLU E 144 " --> pdb=" O HIS E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 166 Processing helix chain 'E' and resid 184 through 196 Processing helix chain 'E' and resid 215 through 225 Processing helix chain 'E' and resid 242 through 260 Processing helix chain 'E' and resid 280 through 290 Processing helix chain 'E' and resid 326 through 341 Processing helix chain 'E' and resid 347 through 356 Processing helix chain 'E' and resid 361 through 373 removed outlier: 3.637A pdb=" N VAL E 365 " --> pdb=" O LEU E 361 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG E 366 " --> pdb=" O PRO E 362 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 399 removed outlier: 3.698A pdb=" N ASN E 391 " --> pdb=" O LEU E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 400 through 403 Processing helix chain 'E' and resid 405 through 418 removed outlier: 3.942A pdb=" N PHE E 418 " --> pdb=" O LEU E 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 422 through 430 Processing helix chain 'E' and resid 431 through 445 Proline residue: E 437 - end of helix Processing helix chain 'E' and resid 461 through 471 Processing helix chain 'E' and resid 476 through 493 Processing helix chain 'E' and resid 502 through 514 Processing helix chain 'E' and resid 519 through 522 Processing helix chain 'E' and resid 523 through 538 removed outlier: 3.985A pdb=" N HIS E 527 " --> pdb=" O LEU E 523 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR E 528 " --> pdb=" O ILE E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 541 through 554 removed outlier: 3.716A pdb=" N VAL E 545 " --> pdb=" O SER E 541 " (cutoff:3.500A) Processing helix chain 'E' and resid 555 through 559 Processing helix chain 'E' and resid 560 through 579 Processing helix chain 'E' and resid 582 through 588 Processing helix chain 'E' and resid 592 through 607 removed outlier: 4.113A pdb=" N LYS E 596 " --> pdb=" O GLY E 592 " (cutoff:3.500A) Processing helix chain 'E' and resid 608 through 618 removed outlier: 4.130A pdb=" N ALA E 612 " --> pdb=" O ARG E 608 " (cutoff:3.500A) Processing helix chain 'E' and resid 625 through 640 Processing helix chain 'E' and resid 642 through 657 removed outlier: 3.755A pdb=" N ALA E 646 " --> pdb=" O GLU E 642 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N SER E 648 " --> pdb=" O ASP E 644 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N TYR E 649 " --> pdb=" O LYS E 645 " (cutoff:3.500A) Processing helix chain 'E' and resid 660 through 673 Processing helix chain 'E' and resid 679 through 696 removed outlier: 4.371A pdb=" N ILE E 683 " --> pdb=" O ASP E 679 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASP E 696 " --> pdb=" O LEU E 692 " (cutoff:3.500A) Processing helix chain 'E' and resid 697 through 715 Processing helix chain 'E' and resid 718 through 733 Processing helix chain 'E' and resid 736 through 750 removed outlier: 4.501A pdb=" N LEU E 740 " --> pdb=" O SER E 736 " (cutoff:3.500A) Processing helix chain 'E' and resid 753 through 768 Processing helix chain 'E' and resid 774 through 789 Processing helix chain 'E' and resid 790 through 798 Processing helix chain 'E' and resid 798 through 805 Processing helix chain 'E' and resid 806 through 822 removed outlier: 3.695A pdb=" N GLY E 822 " --> pdb=" O LYS E 818 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 13 Processing helix chain 'F' and resid 16 through 25 Processing helix chain 'F' and resid 31 through 36 removed outlier: 3.898A pdb=" N PHE F 36 " --> pdb=" O ASP F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 53 Processing helix chain 'F' and resid 61 through 67 Processing helix chain 'F' and resid 67 through 83 Processing helix chain 'F' and resid 106 through 113 Processing helix chain 'F' and resid 120 through 140 Processing helix chain 'F' and resid 140 through 148 removed outlier: 3.643A pdb=" N GLU F 144 " --> pdb=" O HIS F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 166 Processing helix chain 'F' and resid 184 through 196 Processing helix chain 'F' and resid 215 through 225 Processing helix chain 'F' and resid 242 through 260 Processing helix chain 'F' and resid 280 through 290 Processing helix chain 'F' and resid 326 through 341 Processing helix chain 'F' and resid 347 through 356 Processing helix chain 'F' and resid 361 through 373 removed outlier: 3.637A pdb=" N VAL F 365 " --> pdb=" O LEU F 361 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG F 366 " --> pdb=" O PRO F 362 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 399 removed outlier: 3.698A pdb=" N ASN F 391 " --> pdb=" O LEU F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 403 Processing helix chain 'F' and resid 405 through 418 removed outlier: 3.943A pdb=" N PHE F 418 " --> pdb=" O LEU F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 422 through 430 Processing helix chain 'F' and resid 431 through 445 Proline residue: F 437 - end of helix Processing helix chain 'F' and resid 461 through 471 Processing helix chain 'F' and resid 476 through 493 Processing helix chain 'F' and resid 502 through 514 Processing helix chain 'F' and resid 519 through 522 Processing helix chain 'F' and resid 523 through 538 removed outlier: 3.986A pdb=" N HIS F 527 " --> pdb=" O LEU F 523 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR F 528 " --> pdb=" O ILE F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 541 through 554 removed outlier: 3.716A pdb=" N VAL F 545 " --> pdb=" O SER F 541 " (cutoff:3.500A) Processing helix chain 'F' and resid 555 through 559 Processing helix chain 'F' and resid 560 through 579 Processing helix chain 'F' and resid 582 through 588 Processing helix chain 'F' and resid 592 through 607 removed outlier: 4.114A pdb=" N LYS F 596 " --> pdb=" O GLY F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 608 through 618 removed outlier: 4.130A pdb=" N ALA F 612 " --> pdb=" O ARG F 608 " (cutoff:3.500A) Processing helix chain 'F' and resid 625 through 640 Processing helix chain 'F' and resid 642 through 657 removed outlier: 3.755A pdb=" N ALA F 646 " --> pdb=" O GLU F 642 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N SER F 648 " --> pdb=" O ASP F 644 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N TYR F 649 " --> pdb=" O LYS F 645 " (cutoff:3.500A) Processing helix chain 'F' and resid 660 through 673 Processing helix chain 'F' and resid 679 through 696 removed outlier: 4.372A pdb=" N ILE F 683 " --> pdb=" O ASP F 679 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP F 696 " --> pdb=" O LEU F 692 " (cutoff:3.500A) Processing helix chain 'F' and resid 697 through 715 Processing helix chain 'F' and resid 718 through 733 Processing helix chain 'F' and resid 736 through 750 removed outlier: 4.501A pdb=" N LEU F 740 " --> pdb=" O SER F 736 " (cutoff:3.500A) Processing helix chain 'F' and resid 753 through 768 Processing helix chain 'F' and resid 774 through 789 Processing helix chain 'F' and resid 790 through 798 Processing helix chain 'F' and resid 798 through 805 Processing helix chain 'F' and resid 806 through 822 removed outlier: 3.694A pdb=" N GLY F 822 " --> pdb=" O LYS F 818 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30 removed outlier: 6.791A pdb=" N ALA A 4 " --> pdb=" O ILE A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 41 removed outlier: 3.828A pdb=" N GLU A 40 " --> pdb=" O ASN B 114 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 113 through 115 removed outlier: 3.789A pdb=" N GLU C 40 " --> pdb=" O ASN A 114 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 207 through 210 removed outlier: 6.423A pdb=" N ILE A 208 " --> pdb=" O LEU A 267 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ILE A 264 " --> pdb=" O CYS A 299 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ALA A 301 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N PHE A 266 " --> pdb=" O ALA A 301 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE A 175 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N SER A 302 " --> pdb=" O ILE A 175 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ALA A 177 " --> pdb=" O SER A 302 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 420 through 421 Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 30 removed outlier: 6.791A pdb=" N ALA B 4 " --> pdb=" O ILE B 30 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 39 through 41 removed outlier: 3.837A pdb=" N GLU B 40 " --> pdb=" O ASN D 114 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 207 through 210 removed outlier: 6.423A pdb=" N ILE B 208 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ILE B 264 " --> pdb=" O CYS B 299 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ALA B 301 " --> pdb=" O ILE B 264 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N PHE B 266 " --> pdb=" O ALA B 301 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE B 175 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N SER B 302 " --> pdb=" O ILE B 175 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ALA B 177 " --> pdb=" O SER B 302 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 420 through 421 Processing sheet with id=AB1, first strand: chain 'C' and resid 29 through 30 removed outlier: 6.791A pdb=" N ALA C 4 " --> pdb=" O ILE C 30 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 113 through 115 removed outlier: 3.901A pdb=" N GLU F 40 " --> pdb=" O ASN C 114 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 207 through 210 removed outlier: 6.423A pdb=" N ILE C 208 " --> pdb=" O LEU C 267 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ILE C 264 " --> pdb=" O CYS C 299 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ALA C 301 " --> pdb=" O ILE C 264 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N PHE C 266 " --> pdb=" O ALA C 301 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE C 175 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N SER C 302 " --> pdb=" O ILE C 175 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ALA C 177 " --> pdb=" O SER C 302 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 420 through 421 Processing sheet with id=AB5, first strand: chain 'D' and resid 29 through 30 removed outlier: 6.791A pdb=" N ALA D 4 " --> pdb=" O ILE D 30 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 39 through 41 removed outlier: 3.830A pdb=" N GLU D 40 " --> pdb=" O ASN E 114 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 207 through 210 removed outlier: 6.423A pdb=" N ILE D 208 " --> pdb=" O LEU D 267 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ILE D 264 " --> pdb=" O CYS D 299 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ALA D 301 " --> pdb=" O ILE D 264 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N PHE D 266 " --> pdb=" O ALA D 301 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE D 175 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N SER D 302 " --> pdb=" O ILE D 175 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ALA D 177 " --> pdb=" O SER D 302 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 420 through 421 Processing sheet with id=AB9, first strand: chain 'E' and resid 29 through 30 removed outlier: 6.790A pdb=" N ALA E 4 " --> pdb=" O ILE E 30 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 207 through 210 removed outlier: 6.422A pdb=" N ILE E 208 " --> pdb=" O LEU E 267 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ILE E 264 " --> pdb=" O CYS E 299 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ALA E 301 " --> pdb=" O ILE E 264 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N PHE E 266 " --> pdb=" O ALA E 301 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE E 175 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N SER E 302 " --> pdb=" O ILE E 175 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ALA E 177 " --> pdb=" O SER E 302 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 420 through 421 Processing sheet with id=AC3, first strand: chain 'F' and resid 29 through 30 removed outlier: 6.790A pdb=" N ALA F 4 " --> pdb=" O ILE F 30 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 207 through 210 removed outlier: 6.423A pdb=" N ILE F 208 " --> pdb=" O LEU F 267 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ILE F 264 " --> pdb=" O CYS F 299 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ALA F 301 " --> pdb=" O ILE F 264 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N PHE F 266 " --> pdb=" O ALA F 301 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE F 175 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N SER F 302 " --> pdb=" O ILE F 175 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ALA F 177 " --> pdb=" O SER F 302 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 420 through 421 2377 hydrogen bonds defined for protein. 7005 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.39 Time building geometry restraints manager: 4.29 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: 13380 1.34 - 1.46: 8685 1.46 - 1.58: 19095 1.58 - 1.70: 18 1.70 - 1.82: 204 Bond restraints: 41382 Sorted by residual: bond pdb=" CB THR D 732 " pdb=" CG2 THR D 732 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.15e+00 bond pdb=" CB THR B 732 " pdb=" CG2 THR B 732 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.14e+00 bond pdb=" CB THR F 732 " pdb=" CG2 THR F 732 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.12e+00 bond pdb=" CB THR E 732 " pdb=" CG2 THR E 732 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.12e+00 bond pdb=" CB THR C 732 " pdb=" CG2 THR C 732 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.12e+00 ... (remaining 41377 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 55364 2.71 - 5.41: 330 5.41 - 8.12: 65 8.12 - 10.82: 29 10.82 - 13.53: 6 Bond angle restraints: 55794 Sorted by residual: angle pdb=" CG ARG C 186 " pdb=" CD ARG C 186 " pdb=" NE ARG C 186 " ideal model delta sigma weight residual 112.00 98.47 13.53 2.20e+00 2.07e-01 3.78e+01 angle pdb=" CG ARG E 186 " pdb=" CD ARG E 186 " pdb=" NE ARG E 186 " ideal model delta sigma weight residual 112.00 98.49 13.51 2.20e+00 2.07e-01 3.77e+01 angle pdb=" CG ARG A 186 " pdb=" CD ARG A 186 " pdb=" NE ARG A 186 " ideal model delta sigma weight residual 112.00 98.51 13.49 2.20e+00 2.07e-01 3.76e+01 angle pdb=" CG ARG B 186 " pdb=" CD ARG B 186 " pdb=" NE ARG B 186 " ideal model delta sigma weight residual 112.00 98.52 13.48 2.20e+00 2.07e-01 3.75e+01 angle pdb=" CG ARG F 186 " pdb=" CD ARG F 186 " pdb=" NE ARG F 186 " ideal model delta sigma weight residual 112.00 98.53 13.47 2.20e+00 2.07e-01 3.75e+01 ... (remaining 55789 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 21934 17.72 - 35.44: 2676 35.44 - 53.17: 785 53.17 - 70.89: 195 70.89 - 88.61: 72 Dihedral angle restraints: 25662 sinusoidal: 10884 harmonic: 14778 Sorted by residual: dihedral pdb=" CA TYR E 16 " pdb=" C TYR E 16 " pdb=" N VAL E 17 " pdb=" CA VAL E 17 " ideal model delta harmonic sigma weight residual -180.00 -159.22 -20.78 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA TYR A 16 " pdb=" C TYR A 16 " pdb=" N VAL A 17 " pdb=" CA VAL A 17 " ideal model delta harmonic sigma weight residual -180.00 -159.26 -20.74 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA TYR B 16 " pdb=" C TYR B 16 " pdb=" N VAL B 17 " pdb=" CA VAL B 17 " ideal model delta harmonic sigma weight residual -180.00 -159.26 -20.74 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 25659 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 4676 0.042 - 0.085: 1219 0.085 - 0.127: 336 0.127 - 0.170: 33 0.170 - 0.212: 6 Chirality restraints: 6270 Sorted by residual: chirality pdb=" CG LEU B 583 " pdb=" CB LEU B 583 " pdb=" CD1 LEU B 583 " pdb=" CD2 LEU B 583 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CG LEU E 583 " pdb=" CB LEU E 583 " pdb=" CD1 LEU E 583 " pdb=" CD2 LEU E 583 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CG LEU A 583 " pdb=" CB LEU A 583 " pdb=" CD1 LEU A 583 " pdb=" CD2 LEU A 583 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 6267 not shown) Planarity restraints: 7128 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 137 " 0.015 2.00e-02 2.50e+03 1.54e-02 5.92e+00 pdb=" CG TRP D 137 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP D 137 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP D 137 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 137 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP D 137 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 137 " 0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 137 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 137 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP D 137 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 137 " -0.015 2.00e-02 2.50e+03 1.54e-02 5.91e+00 pdb=" CG TRP C 137 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP C 137 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP C 137 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 137 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 137 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 137 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 137 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 137 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 137 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 137 " 0.015 2.00e-02 2.50e+03 1.53e-02 5.84e+00 pdb=" CG TRP B 137 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP B 137 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP B 137 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 137 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 137 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 137 " 0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 137 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 137 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 137 " -0.002 2.00e-02 2.50e+03 ... (remaining 7125 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 467 2.63 - 3.20: 37676 3.20 - 3.77: 63798 3.77 - 4.33: 90466 4.33 - 4.90: 147887 Nonbonded interactions: 340294 Sorted by model distance: nonbonded pdb=" NE ARG B 186 " pdb=" O1B ADP B 901 " model vdw 2.069 2.496 nonbonded pdb=" NE ARG D 186 " pdb=" O1B ADP D 901 " model vdw 2.069 2.496 nonbonded pdb=" NE ARG E 186 " pdb=" O1B ADP E 901 " model vdw 2.069 2.496 nonbonded pdb=" NE ARG F 186 " pdb=" O1B ADP F 901 " model vdw 2.069 2.496 nonbonded pdb=" NE ARG A 186 " pdb=" O1B ADP A 901 " model vdw 2.069 2.496 ... (remaining 340289 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: 0.14 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 11.960 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 0.860 Check model and map are aligned: 0.140 Set scattering table: 0.110 Process input model: 37.360 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.070 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:6.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 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 : 0.004 0.048 41394 Z= 0.166 Angle : 0.647 13.531 55794 Z= 0.331 Chirality : 0.042 0.212 6270 Planarity : 0.005 0.085 7128 Dihedral : 17.695 88.611 16038 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.66 % Favored : 97.22 % Rotamer: Outliers : 1.47 % Allowed : 18.03 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.30 (0.12), residues: 4932 helix: 1.39 (0.09), residues: 3282 sheet: 1.75 (0.39), residues: 144 loop : -0.29 (0.16), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 186 TYR 0.019 0.001 TYR A 654 PHE 0.017 0.002 PHE E 597 TRP 0.041 0.003 TRP D 137 HIS 0.004 0.001 HIS F 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (41382) covalent geometry : angle 0.64689 / 0.33 (55794) hydrogen bonds : bond 0.11923 / 7.85 ( 2377) hydrogen bonds : angle 4.71384 / 3.32 ( 7005) Misc. bond : bond 0.00562 / 0.36 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9864 Ramachandran restraints generated. 4932 Oldfield, 0 Emsley, 4932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9864 Ramachandran restraints generated. 4932 Oldfield, 0 Emsley, 4932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 4554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 604 time to evaluate : 1.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 328 LYS cc_start: 0.8776 (mttt) cc_final: 0.8362 (mmpt) REVERT: A 461 ASN cc_start: 0.8664 (OUTLIER) cc_final: 0.8230 (t0) REVERT: A 521 LYS cc_start: 0.8660 (pttm) cc_final: 0.8091 (ptpp) REVERT: A 555 LYS cc_start: 0.8075 (pptt) cc_final: 0.7758 (mmtt) REVERT: A 559 MET cc_start: 0.8175 (mtp) cc_final: 0.7885 (mtp) REVERT: A 561 ASN cc_start: 0.7094 (m-40) cc_final: 0.6823 (p0) REVERT: A 610 SER cc_start: 0.6801 (OUTLIER) cc_final: 0.6262 (t) REVERT: A 812 ARG cc_start: 0.6778 (ttp-110) cc_final: 0.6409 (ttp80) REVERT: B 211 ASP cc_start: 0.8253 (t70) cc_final: 0.7976 (t70) REVERT: B 261 LYS cc_start: 0.8607 (mtpt) cc_final: 0.8322 (mtmt) REVERT: B 262 GLU cc_start: 0.8364 (pt0) cc_final: 0.8068 (pt0) REVERT: B 285 MET cc_start: 0.7999 (OUTLIER) cc_final: 0.7563 (tpt) REVERT: B 477 ASP cc_start: 0.7872 (m-30) cc_final: 0.7284 (m-30) REVERT: B 490 ILE cc_start: 0.7888 (mm) cc_final: 0.7626 (mp) REVERT: B 507 THR cc_start: 0.8032 (m) cc_final: 0.7659 (t) REVERT: B 561 ASN cc_start: 0.7335 (m-40) cc_final: 0.7100 (p0) REVERT: B 631 ARG cc_start: 0.7417 (mtm180) cc_final: 0.7108 (mtm110) REVERT: B 642 GLU cc_start: 0.6902 (tp30) cc_final: 0.6189 (mm-30) REVERT: B 698 GLU cc_start: 0.7167 (mm-30) cc_final: 0.6869 (tp30) REVERT: C 18 ARG cc_start: 0.8574 (ttp-110) cc_final: 0.8291 (ttm-80) REVERT: C 27 GLU cc_start: 0.8424 (mp0) cc_final: 0.8055 (mm-30) REVERT: C 72 LYS cc_start: 0.8151 (ttmt) cc_final: 0.7917 (tmtt) REVERT: C 82 ASP cc_start: 0.7629 (m-30) cc_final: 0.7316 (m-30) REVERT: C 285 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.7856 (tpp) REVERT: C 457 MET cc_start: 0.8047 (ttp) cc_final: 0.7575 (ttp) REVERT: C 461 ASN cc_start: 0.8459 (OUTLIER) cc_final: 0.8164 (t0) REVERT: C 557 LYS cc_start: 0.8053 (mtpt) cc_final: 0.7747 (mppt) REVERT: C 559 MET cc_start: 0.8049 (mtp) cc_final: 0.7826 (mtp) REVERT: C 610 SER cc_start: 0.7313 (OUTLIER) cc_final: 0.6767 (t) REVERT: C 611 ASP cc_start: 0.7351 (OUTLIER) cc_final: 0.7092 (m-30) REVERT: C 641 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7409 (mp0) REVERT: C 705 LYS cc_start: 0.7799 (mttm) cc_final: 0.7208 (mmtm) REVERT: C 712 SER cc_start: 0.7653 (m) cc_final: 0.6768 (p) REVERT: D 261 LYS cc_start: 0.8603 (mtpt) cc_final: 0.8328 (mttt) REVERT: D 262 GLU cc_start: 0.8141 (pt0) cc_final: 0.7916 (pt0) REVERT: D 401 ARG cc_start: 0.8383 (ptp-170) cc_final: 0.8107 (ptm160) REVERT: D 477 ASP cc_start: 0.7209 (m-30) cc_final: 0.6964 (m-30) REVERT: D 488 LYS cc_start: 0.8091 (ttmt) cc_final: 0.7727 (tptt) REVERT: D 507 THR cc_start: 0.7815 (m) cc_final: 0.7514 (t) REVERT: D 537 ASN cc_start: 0.7583 (m110) cc_final: 0.6847 (p0) REVERT: D 631 ARG cc_start: 0.7371 (mtm180) cc_final: 0.6963 (mtm110) REVERT: D 690 THR cc_start: 0.8003 (m) cc_final: 0.7398 (t) REVERT: D 711 TYR cc_start: 0.6807 (t80) cc_final: 0.6365 (t80) REVERT: E 1 MET cc_start: 0.7553 (mmt) cc_final: 0.7336 (tpt) REVERT: E 488 LYS cc_start: 0.7482 (ttmt) cc_final: 0.7137 (mmmt) REVERT: E 537 ASN cc_start: 0.7489 (m110) cc_final: 0.6774 (p0) REVERT: E 596 LYS cc_start: 0.7345 (ptpp) cc_final: 0.7114 (pttm) REVERT: E 690 THR cc_start: 0.8036 (m) cc_final: 0.7591 (t) REVERT: E 765 LYS cc_start: 0.8653 (mtpt) cc_final: 0.8251 (tptp) REVERT: E 777 LEU cc_start: 0.7807 (mt) cc_final: 0.7474 (tp) REVERT: F 37 GLU cc_start: 0.7406 (mm-30) cc_final: 0.7037 (mt-10) REVERT: F 71 LYS cc_start: 0.8259 (mttt) cc_final: 0.7875 (mptt) REVERT: F 82 ASP cc_start: 0.7860 (m-30) cc_final: 0.7629 (m-30) REVERT: F 200 LYS cc_start: 0.6830 (OUTLIER) cc_final: 0.6373 (mmtp) REVERT: F 285 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7736 (mtm) REVERT: F 339 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7538 (mt-10) REVERT: F 609 LEU cc_start: 0.7963 (mt) cc_final: 0.7467 (tp) REVERT: F 656 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7440 (tm-30) REVERT: F 705 LYS cc_start: 0.8221 (mttm) cc_final: 0.7730 (mttp) REVERT: F 708 ASP cc_start: 0.7541 (m-30) cc_final: 0.7200 (m-30) REVERT: F 727 ASN cc_start: 0.7754 (m-40) cc_final: 0.7350 (m110) REVERT: F 785 MET cc_start: 0.6903 (tpt) cc_final: 0.6326 (tmt) outliers start: 67 outliers final: 20 residues processed: 651 average time/residue: 0.6986 time to fit residues: 557.7993 Evaluate side-chains 446 residues out of total 4554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 416 time to evaluate : 1.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 461 ASN Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 656 GLU Chi-restraints excluded: chain B residue 285 MET Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain B residue 656 GLU Chi-restraints excluded: chain C residue 285 MET Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 461 ASN Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain C residue 611 ASP Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 461 ASN Chi-restraints excluded: chain D residue 585 THR Chi-restraints excluded: chain D residue 610 SER Chi-restraints excluded: chain E residue 292 ASP Chi-restraints excluded: chain E residue 610 SER Chi-restraints excluded: chain E residue 611 ASP Chi-restraints excluded: chain F residue 200 LYS Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain F residue 610 SER Chi-restraints excluded: chain F residue 656 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: [432, 197, 388, 455, 215, 20, 132, 261, 248, 207, 470] chunk 432 optimal weight: 0.2980 chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 6.9990 chunk 455 optimal weight: 0.8980 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.0870 chunk 207 optimal weight: 0.7980 chunk 470 optimal weight: 4.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 527 HIS B 291 ASN B 461 ASN B 615 GLN C 252 ASN C 291 ASN C 527 HIS D 527 HIS ** E 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 527 HIS E 694 ASN F 99 ASN F 493 ASN F 527 HIS F 595 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.184800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.123563 restraints weight = 52354.188| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.87 r_work: 0.3333 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 41394 Z= 0.117 Angle : 0.540 10.743 55794 Z= 0.277 Chirality : 0.041 0.244 6270 Planarity : 0.004 0.039 7128 Dihedral : 5.775 58.929 5548 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.41 % Favored : 97.47 % Rotamer: Outliers : 1.69 % Allowed : 19.06 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.61 (0.12), residues: 4932 helix: 1.58 (0.09), residues: 3306 sheet: 1.30 (0.35), residues: 204 loop : -0.06 (0.17), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 812 TYR 0.012 0.001 TYR D 649 PHE 0.020 0.001 PHE E 597 TRP 0.021 0.002 TRP C 137 HIS 0.006 0.001 HIS F 595 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (41382) covalent geometry : angle 0.53978 / 0.28 (55794) hydrogen bonds : bond 0.03797 / 2.48 ( 2377) hydrogen bonds : angle 3.78292 / 2.71 ( 7005) Misc. bond : bond 0.00174 / 0.11 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9864 Ramachandran restraints generated. 4932 Oldfield, 0 Emsley, 4932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9864 Ramachandran restraints generated. 4932 Oldfield, 0 Emsley, 4932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 4554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 461 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 328 LYS cc_start: 0.8936 (mttt) cc_final: 0.8317 (mmpt) REVERT: A 401 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.8042 (ptp-170) REVERT: A 507 THR cc_start: 0.8097 (m) cc_final: 0.7882 (t) REVERT: A 521 LYS cc_start: 0.8571 (pttm) cc_final: 0.7979 (ptpp) REVERT: A 555 LYS cc_start: 0.7910 (pptt) cc_final: 0.7422 (mmtt) REVERT: A 559 MET cc_start: 0.7894 (mtp) cc_final: 0.7487 (mtp) REVERT: A 561 ASN cc_start: 0.7169 (m-40) cc_final: 0.6802 (m110) REVERT: A 642 GLU cc_start: 0.6562 (OUTLIER) cc_final: 0.5996 (mp0) REVERT: A 812 ARG cc_start: 0.6763 (ttp-110) cc_final: 0.6318 (ttp80) REVERT: B 27 GLU cc_start: 0.8454 (mp0) cc_final: 0.8099 (mm-30) REVERT: B 41 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.7468 (mtm-85) REVERT: B 211 ASP cc_start: 0.8258 (t70) cc_final: 0.7863 (t70) REVERT: B 248 LYS cc_start: 0.7738 (tmmt) cc_final: 0.7272 (tppt) REVERT: B 261 LYS cc_start: 0.8464 (mtpt) cc_final: 0.8135 (mtmt) REVERT: B 262 GLU cc_start: 0.8493 (pt0) cc_final: 0.8156 (pt0) REVERT: B 477 ASP cc_start: 0.7889 (m-30) cc_final: 0.7280 (m-30) REVERT: B 490 ILE cc_start: 0.7531 (mm) cc_final: 0.7282 (mp) REVERT: B 561 ASN cc_start: 0.7249 (m-40) cc_final: 0.6867 (p0) REVERT: B 631 ARG cc_start: 0.7094 (mtm180) cc_final: 0.6814 (mtm110) REVERT: B 642 GLU cc_start: 0.6680 (tp30) cc_final: 0.6408 (tp30) REVERT: C 27 GLU cc_start: 0.8377 (mp0) cc_final: 0.8039 (mm-30) REVERT: C 71 LYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7079 (mptt) REVERT: C 72 LYS cc_start: 0.7994 (ttmt) cc_final: 0.7626 (tmtt) REVERT: C 82 ASP cc_start: 0.7333 (m-30) cc_final: 0.6938 (m-30) REVERT: C 233 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.6885 (tt0) REVERT: C 457 MET cc_start: 0.7959 (ttp) cc_final: 0.7543 (ttp) REVERT: C 510 GLU cc_start: 0.7259 (mm-30) cc_final: 0.7026 (mp0) REVERT: C 557 LYS cc_start: 0.8383 (mtpt) cc_final: 0.7724 (mppt) REVERT: C 559 MET cc_start: 0.7552 (mtp) cc_final: 0.7220 (mtp) REVERT: C 582 ARG cc_start: 0.7932 (ttt180) cc_final: 0.7703 (ttt-90) REVERT: C 588 GLN cc_start: 0.7692 (mm-40) cc_final: 0.7477 (mm-40) REVERT: C 596 LYS cc_start: 0.7627 (OUTLIER) cc_final: 0.7238 (pttt) REVERT: C 610 SER cc_start: 0.7088 (p) cc_final: 0.6790 (t) REVERT: C 705 LYS cc_start: 0.7245 (mttm) cc_final: 0.6681 (mmtm) REVERT: D 261 LYS cc_start: 0.8465 (mtpt) cc_final: 0.8090 (mtmt) REVERT: D 262 GLU cc_start: 0.8292 (pt0) cc_final: 0.8022 (pt0) REVERT: D 401 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.8126 (ptm160) REVERT: D 477 ASP cc_start: 0.7368 (m-30) cc_final: 0.6938 (m-30) REVERT: D 488 LYS cc_start: 0.7829 (ttmt) cc_final: 0.7400 (tptt) REVERT: D 530 ARG cc_start: 0.7561 (tpm170) cc_final: 0.7348 (tpm170) REVERT: D 532 MET cc_start: 0.8250 (mtt) cc_final: 0.8006 (mtp) REVERT: D 537 ASN cc_start: 0.7659 (m110) cc_final: 0.6555 (p0) REVERT: D 596 LYS cc_start: 0.7396 (OUTLIER) cc_final: 0.6791 (pttt) REVERT: D 631 ARG cc_start: 0.6979 (mtm180) cc_final: 0.6589 (mtm110) REVERT: D 711 TYR cc_start: 0.6220 (t80) cc_final: 0.5768 (t80) REVERT: D 804 LYS cc_start: 0.6720 (mttm) cc_final: 0.6393 (ttmm) REVERT: E 1 MET cc_start: 0.7697 (mmt) cc_final: 0.7276 (tpt) REVERT: E 457 MET cc_start: 0.7969 (ttm) cc_final: 0.7708 (ttm) REVERT: E 488 LYS cc_start: 0.7069 (ttmt) cc_final: 0.6575 (mmmt) REVERT: E 537 ASN cc_start: 0.7435 (m110) cc_final: 0.6420 (p0) REVERT: E 596 LYS cc_start: 0.6808 (OUTLIER) cc_final: 0.6427 (pttm) REVERT: E 765 LYS cc_start: 0.8578 (mtpt) cc_final: 0.8172 (tptp) REVERT: F 37 GLU cc_start: 0.7210 (mm-30) cc_final: 0.6903 (mt-10) REVERT: F 82 ASP cc_start: 0.7494 (m-30) cc_final: 0.7227 (m-30) REVERT: F 101 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7439 (mt-10) REVERT: F 170 LYS cc_start: 0.7321 (OUTLIER) cc_final: 0.7099 (mmmt) REVERT: F 233 GLU cc_start: 0.7313 (tt0) cc_final: 0.7113 (tt0) REVERT: F 247 GLN cc_start: 0.7162 (OUTLIER) cc_final: 0.5828 (mp10) REVERT: F 285 MET cc_start: 0.7504 (ttp) cc_final: 0.7296 (mtm) REVERT: F 339 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7553 (mt-10) REVERT: F 401 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.8146 (ptm160) REVERT: F 557 LYS cc_start: 0.8064 (mtpt) cc_final: 0.7589 (mtmm) REVERT: F 705 LYS cc_start: 0.7502 (mttm) cc_final: 0.6957 (mttp) REVERT: F 727 ASN cc_start: 0.7322 (m-40) cc_final: 0.7064 (m-40) REVERT: F 785 MET cc_start: 0.6944 (tpt) cc_final: 0.6168 (tmm) outliers start: 77 outliers final: 18 residues processed: 513 average time/residue: 0.7007 time to fit residues: 438.5641 Evaluate side-chains 425 residues out of total 4554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 395 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 401 ARG Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain B residue 41 ARG Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 71 LYS Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 596 LYS Chi-restraints excluded: chain C residue 620 ILE Chi-restraints excluded: chain D residue 401 ARG Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 596 LYS Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain E residue 596 LYS Chi-restraints excluded: chain E residue 781 GLN Chi-restraints excluded: chain F residue 170 LYS Chi-restraints excluded: chain F residue 247 GLN Chi-restraints excluded: chain F residue 344 ASP Chi-restraints excluded: chain F residue 401 ARG Chi-restraints excluded: chain F residue 407 THR Chi-restraints excluded: chain F residue 584 LEU Chi-restraints excluded: chain F residue 585 THR Chi-restraints excluded: chain F residue 596 LYS Chi-restraints excluded: chain F residue 635 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: [57, 238, 405, 345, 421, 376, 106, 188, 356, 388, 246] chunk 57 optimal weight: 3.9990 chunk 238 optimal weight: 9.9990 chunk 405 optimal weight: 3.9990 chunk 345 optimal weight: 4.9990 chunk 421 optimal weight: 0.7980 chunk 376 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 chunk 356 optimal weight: 3.9990 chunk 388 optimal weight: 6.9990 chunk 246 optimal weight: 7.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 291 ASN C 291 ASN C 673 ASN D 493 ASN E 398 GLN E 588 GLN F 492 ASN F 493 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.179338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.124742 restraints weight = 51196.417| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.67 r_work: 0.3271 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 41394 Z= 0.232 Angle : 0.653 13.437 55794 Z= 0.328 Chirality : 0.045 0.279 6270 Planarity : 0.005 0.058 7128 Dihedral : 5.843 64.192 5496 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.00 % Favored : 96.86 % Rotamer: Outliers : 3.21 % Allowed : 18.77 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.30 (0.12), residues: 4932 helix: 1.36 (0.09), residues: 3318 sheet: 0.52 (0.34), residues: 210 loop : -0.12 (0.17), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 186 TYR 0.018 0.002 TYR D 649 PHE 0.017 0.002 PHE D 418 TRP 0.022 0.002 TRP A 137 HIS 0.006 0.002 HIS F 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00578 / 0.23 (41382) covalent geometry : angle 0.65288 / 0.33 (55794) hydrogen bonds : bond 0.04625 / 3.04 ( 2377) hydrogen bonds : angle 3.88562 / 2.79 ( 7005) Misc. bond : bond 0.00495 / 0.30 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9864 Ramachandran restraints generated. 4932 Oldfield, 0 Emsley, 4932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9864 Ramachandran restraints generated. 4932 Oldfield, 0 Emsley, 4932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 4554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 430 time to evaluate : 1.521 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.7895 (mptt) REVERT: A 27 GLU cc_start: 0.8585 (mp0) cc_final: 0.8233 (mm-30) REVERT: A 37 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7482 (mt-10) REVERT: A 41 ARG cc_start: 0.8105 (ptm-80) cc_final: 0.7868 (mtp180) REVERT: A 328 LYS cc_start: 0.8945 (mttt) cc_final: 0.8566 (mmpt) REVERT: A 401 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.7895 (ptp-170) REVERT: A 555 LYS cc_start: 0.8088 (pptt) cc_final: 0.7847 (mmtt) REVERT: A 559 MET cc_start: 0.7957 (mtp) cc_final: 0.7606 (mtp) REVERT: A 717 ASN cc_start: 0.6992 (OUTLIER) cc_final: 0.6602 (m-40) REVERT: B 27 GLU cc_start: 0.8446 (mp0) cc_final: 0.8190 (mm-30) REVERT: B 41 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7752 (mtm-85) REVERT: B 114 ASN cc_start: 0.8604 (t0) cc_final: 0.8298 (t0) REVERT: B 248 LYS cc_start: 0.7893 (tmmt) cc_final: 0.7532 (tppt) REVERT: B 261 LYS cc_start: 0.8571 (mtpt) cc_final: 0.8303 (mtmt) REVERT: B 262 GLU cc_start: 0.8517 (pt0) cc_final: 0.8219 (pt0) REVERT: B 401 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.8274 (ptm160) REVERT: B 477 ASP cc_start: 0.8000 (m-30) cc_final: 0.7553 (m-30) REVERT: B 490 ILE cc_start: 0.7890 (mm) cc_final: 0.7561 (mp) REVERT: B 537 ASN cc_start: 0.7793 (m110) cc_final: 0.7211 (p0) REVERT: B 561 ASN cc_start: 0.7512 (m-40) cc_final: 0.7155 (p0) REVERT: B 631 ARG cc_start: 0.7366 (mtm180) cc_final: 0.7013 (mtm110) REVERT: B 642 GLU cc_start: 0.6870 (tp30) cc_final: 0.6514 (mm-30) REVERT: B 785 MET cc_start: 0.7694 (OUTLIER) cc_final: 0.6879 (tpt) REVERT: C 14 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7621 (mp0) REVERT: C 71 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7535 (mptt) REVERT: C 72 LYS cc_start: 0.8197 (ttmt) cc_final: 0.7957 (tmtt) REVERT: C 82 ASP cc_start: 0.7983 (m-30) cc_final: 0.7491 (m-30) REVERT: C 233 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7188 (tt0) REVERT: C 457 MET cc_start: 0.8410 (ttp) cc_final: 0.8207 (ttp) REVERT: C 521 LYS cc_start: 0.8859 (pttm) cc_final: 0.8434 (pttm) REVERT: C 559 MET cc_start: 0.7875 (mtp) cc_final: 0.7574 (mtp) REVERT: C 596 LYS cc_start: 0.7901 (OUTLIER) cc_final: 0.7592 (pttt) REVERT: C 610 SER cc_start: 0.7361 (p) cc_final: 0.6868 (t) REVERT: C 705 LYS cc_start: 0.7661 (mttm) cc_final: 0.6972 (mttp) REVERT: C 785 MET cc_start: 0.7606 (mmp) cc_final: 0.7380 (mmm) REVERT: D 13 LYS cc_start: 0.7905 (OUTLIER) cc_final: 0.7656 (tppt) REVERT: D 27 GLU cc_start: 0.8505 (mp0) cc_final: 0.7913 (mm-30) REVERT: D 240 GLU cc_start: 0.6370 (OUTLIER) cc_final: 0.5862 (pp20) REVERT: D 261 LYS cc_start: 0.8632 (mtpt) cc_final: 0.8310 (mtmt) REVERT: D 401 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.8206 (ptm160) REVERT: D 477 ASP cc_start: 0.7452 (m-30) cc_final: 0.7158 (t70) REVERT: D 488 LYS cc_start: 0.8119 (ttmt) cc_final: 0.7721 (ttpp) REVERT: D 537 ASN cc_start: 0.7963 (m110) cc_final: 0.7017 (p0) REVERT: D 596 LYS cc_start: 0.7714 (OUTLIER) cc_final: 0.7051 (pttt) REVERT: D 631 ARG cc_start: 0.7159 (mtm180) cc_final: 0.6747 (mtm110) REVERT: D 711 TYR cc_start: 0.6747 (t80) cc_final: 0.6269 (t80) REVERT: D 726 ILE cc_start: 0.7514 (OUTLIER) cc_final: 0.7001 (tp) REVERT: D 804 LYS cc_start: 0.6942 (mttm) cc_final: 0.6567 (ttmm) REVERT: E 1 MET cc_start: 0.7841 (mmt) cc_final: 0.7404 (tpt) REVERT: E 40 GLU cc_start: 0.7011 (OUTLIER) cc_final: 0.6566 (mm-30) REVERT: E 339 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6916 (mt-10) REVERT: E 401 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7720 (ttm170) REVERT: E 431 ASP cc_start: 0.7142 (OUTLIER) cc_final: 0.6715 (t70) REVERT: E 440 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7301 (mt-10) REVERT: E 461 ASN cc_start: 0.8314 (OUTLIER) cc_final: 0.8093 (t0) REVERT: E 488 LYS cc_start: 0.7276 (ttmt) cc_final: 0.7061 (tttt) REVERT: E 537 ASN cc_start: 0.7418 (m110) cc_final: 0.6641 (p0) REVERT: E 596 LYS cc_start: 0.7057 (OUTLIER) cc_final: 0.6586 (pttm) REVERT: E 717 ASN cc_start: 0.5791 (OUTLIER) cc_final: 0.5308 (m-40) REVERT: E 765 LYS cc_start: 0.8639 (mtpt) cc_final: 0.8321 (tmmt) REVERT: E 766 MET cc_start: 0.7089 (OUTLIER) cc_final: 0.6462 (mtp) REVERT: E 777 LEU cc_start: 0.7792 (mt) cc_final: 0.7361 (tp) REVERT: E 781 GLN cc_start: 0.7770 (OUTLIER) cc_final: 0.7520 (pm20) REVERT: E 785 MET cc_start: 0.7161 (OUTLIER) cc_final: 0.6540 (tpt) REVERT: F 37 GLU cc_start: 0.7518 (mm-30) cc_final: 0.7058 (mm-30) REVERT: F 71 LYS cc_start: 0.8255 (mttt) cc_final: 0.7815 (mptt) REVERT: F 82 ASP cc_start: 0.7778 (m-30) cc_final: 0.7487 (m-30) REVERT: F 247 GLN cc_start: 0.7565 (OUTLIER) cc_final: 0.6000 (mp10) REVERT: F 248 LYS cc_start: 0.7755 (mmmt) cc_final: 0.6968 (tmmt) REVERT: F 401 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.8156 (ptm160) REVERT: F 557 LYS cc_start: 0.8057 (mtpt) cc_final: 0.7723 (mtmm) REVERT: F 588 GLN cc_start: 0.7613 (OUTLIER) cc_final: 0.7324 (mp10) REVERT: F 678 VAL cc_start: 0.4774 (OUTLIER) cc_final: 0.4377 (p) REVERT: F 705 LYS cc_start: 0.7823 (mttm) cc_final: 0.7177 (mttp) REVERT: F 708 ASP cc_start: 0.7135 (m-30) cc_final: 0.6935 (t0) REVERT: F 785 MET cc_start: 0.6809 (tpt) cc_final: 0.6261 (tmm) outliers start: 146 outliers final: 38 residues processed: 542 average time/residue: 0.7206 time to fit residues: 474.7926 Evaluate side-chains 451 residues out of total 4554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 384 time to evaluate : 1.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LYS Chi-restraints excluded: chain A residue 212 ARG Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 401 ARG Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain B residue 41 ARG Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 401 ARG Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 456 GLU Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 785 MET Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 71 LYS Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 596 LYS Chi-restraints excluded: chain C residue 620 ILE Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 240 GLU Chi-restraints excluded: chain D residue 401 ARG Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 589 LYS Chi-restraints excluded: chain D residue 596 LYS Chi-restraints excluded: chain D residue 685 LEU Chi-restraints excluded: chain D residue 719 VAL Chi-restraints excluded: chain D residue 726 ILE Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 339 GLU Chi-restraints excluded: chain E residue 401 ARG Chi-restraints excluded: chain E residue 407 THR Chi-restraints excluded: chain E residue 431 ASP Chi-restraints excluded: chain E residue 461 ASN Chi-restraints excluded: chain E residue 596 LYS Chi-restraints excluded: chain E residue 608 ARG Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain E residue 717 ASN Chi-restraints excluded: chain E residue 746 VAL Chi-restraints excluded: chain E residue 763 LEU Chi-restraints excluded: chain E residue 766 MET Chi-restraints excluded: chain E residue 767 LYS Chi-restraints excluded: chain E residue 781 GLN Chi-restraints excluded: chain E residue 785 MET Chi-restraints excluded: chain F residue 247 GLN Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain F residue 344 ASP Chi-restraints excluded: chain F residue 401 ARG Chi-restraints excluded: chain F residue 407 THR Chi-restraints excluded: chain F residue 584 LEU Chi-restraints excluded: chain F residue 588 GLN Chi-restraints excluded: chain F residue 589 LYS Chi-restraints excluded: chain F residue 596 LYS Chi-restraints excluded: chain F residue 625 VAL Chi-restraints excluded: chain F residue 678 VAL Chi-restraints excluded: chain F residue 719 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: [300, 112, 234, 63, 104, 251, 195, 422, 318, 126, 347] chunk 300 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 234 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 251 optimal weight: 4.9990 chunk 195 optimal weight: 3.9990 chunk 422 optimal weight: 0.9990 chunk 318 optimal weight: 0.9990 chunk 126 optimal weight: 0.5980 chunk 347 optimal weight: 0.8980 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 615 GLN C 291 ASN D 493 ASN F 493 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.182356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.123193 restraints weight = 51178.485| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.11 r_work: 0.3267 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 41394 Z= 0.121 Angle : 0.530 12.458 55794 Z= 0.270 Chirality : 0.041 0.363 6270 Planarity : 0.004 0.041 7128 Dihedral : 5.422 60.645 5496 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.49 % Favored : 97.36 % Rotamer: Outliers : 2.79 % Allowed : 19.50 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.56 (0.12), residues: 4932 helix: 1.59 (0.09), residues: 3312 sheet: 0.32 (0.35), residues: 216 loop : -0.06 (0.17), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 812 TYR 0.017 0.001 TYR E 711 PHE 0.018 0.001 PHE E 597 TRP 0.013 0.002 TRP C 282 HIS 0.005 0.001 HIS F 595 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (41382) covalent geometry : angle 0.53049 / 0.27 (55794) hydrogen bonds : bond 0.03596 / 2.35 ( 2377) hydrogen bonds : angle 3.66318 / 2.63 ( 7005) Misc. bond : bond 0.00186 / 0.11 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9864 Ramachandran restraints generated. 4932 Oldfield, 0 Emsley, 4932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9864 Ramachandran restraints generated. 4932 Oldfield, 0 Emsley, 4932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 4554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 424 time to evaluate : 1.623 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.7698 (mptt) REVERT: A 27 GLU cc_start: 0.8682 (mp0) cc_final: 0.8170 (mm-30) REVERT: A 41 ARG cc_start: 0.8016 (ptm-80) cc_final: 0.7630 (mtm-85) REVERT: A 68 GLU cc_start: 0.6536 (pm20) cc_final: 0.6296 (pp20) REVERT: A 328 LYS cc_start: 0.8990 (mttt) cc_final: 0.8493 (mmpt) REVERT: A 401 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.8073 (ptp-170) REVERT: A 507 THR cc_start: 0.8167 (m) cc_final: 0.7807 (t) REVERT: A 555 LYS cc_start: 0.8000 (pptt) cc_final: 0.7653 (mmtt) REVERT: A 559 MET cc_start: 0.7853 (mtp) cc_final: 0.7467 (mtp) REVERT: A 635 GLN cc_start: 0.7439 (OUTLIER) cc_final: 0.6780 (mp10) REVERT: A 717 ASN cc_start: 0.6755 (OUTLIER) cc_final: 0.6366 (m-40) REVERT: A 812 ARG cc_start: 0.6906 (ttp-110) cc_final: 0.6336 (ttp80) REVERT: B 18 ARG cc_start: 0.8669 (ttp-110) cc_final: 0.8439 (ttm-80) REVERT: B 27 GLU cc_start: 0.8426 (mp0) cc_final: 0.8081 (mm-30) REVERT: B 41 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7762 (mtm-85) REVERT: B 54 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8313 (mt-10) REVERT: B 114 ASN cc_start: 0.8549 (t0) cc_final: 0.8179 (t0) REVERT: B 244 GLU cc_start: 0.7552 (tt0) cc_final: 0.7141 (tm-30) REVERT: B 261 LYS cc_start: 0.8565 (mtpt) cc_final: 0.8248 (mtmt) REVERT: B 262 GLU cc_start: 0.8585 (pt0) cc_final: 0.8285 (pt0) REVERT: B 328 LYS cc_start: 0.8841 (mttt) cc_final: 0.8571 (mtpm) REVERT: B 477 ASP cc_start: 0.8140 (m-30) cc_final: 0.7577 (m-30) REVERT: B 490 ILE cc_start: 0.7670 (mm) cc_final: 0.7358 (mp) REVERT: B 561 ASN cc_start: 0.7392 (m-40) cc_final: 0.6952 (p0) REVERT: B 631 ARG cc_start: 0.7290 (mtm180) cc_final: 0.6993 (mtm110) REVERT: B 635 GLN cc_start: 0.6771 (OUTLIER) cc_final: 0.6463 (mm-40) REVERT: B 642 GLU cc_start: 0.6783 (tp30) cc_final: 0.6551 (tp30) REVERT: C 14 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7566 (mp0) REVERT: C 41 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7212 (ptm-80) REVERT: C 72 LYS cc_start: 0.8092 (ttmt) cc_final: 0.7740 (tmtt) REVERT: C 82 ASP cc_start: 0.7809 (m-30) cc_final: 0.7315 (m-30) REVERT: C 233 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7193 (tt0) REVERT: C 457 MET cc_start: 0.8266 (ttp) cc_final: 0.7848 (ttp) REVERT: C 559 MET cc_start: 0.7830 (mtp) cc_final: 0.7485 (mtp) REVERT: C 596 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.7520 (pttt) REVERT: C 610 SER cc_start: 0.7274 (p) cc_final: 0.6792 (t) REVERT: C 705 LYS cc_start: 0.7451 (mttm) cc_final: 0.6831 (mmtm) REVERT: D 2 ILE cc_start: 0.8861 (OUTLIER) cc_final: 0.8384 (mm) REVERT: D 27 GLU cc_start: 0.8507 (mp0) cc_final: 0.7867 (mm-30) REVERT: D 54 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8171 (mt-10) REVERT: D 82 ASP cc_start: 0.8281 (m-30) cc_final: 0.8031 (m-30) REVERT: D 401 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.8265 (ptm160) REVERT: D 477 ASP cc_start: 0.7586 (m-30) cc_final: 0.7209 (t70) REVERT: D 488 LYS cc_start: 0.7914 (ttmt) cc_final: 0.7445 (tptt) REVERT: D 506 PHE cc_start: 0.7256 (m-80) cc_final: 0.6834 (t80) REVERT: D 530 ARG cc_start: 0.7987 (tpm170) cc_final: 0.7603 (tpm170) REVERT: D 532 MET cc_start: 0.8601 (mtt) cc_final: 0.8344 (mtp) REVERT: D 537 ASN cc_start: 0.8036 (m110) cc_final: 0.6957 (p0) REVERT: D 596 LYS cc_start: 0.7452 (OUTLIER) cc_final: 0.6824 (pttt) REVERT: D 631 ARG cc_start: 0.7030 (mtm180) cc_final: 0.6643 (mtm110) REVERT: D 711 TYR cc_start: 0.6567 (t80) cc_final: 0.6114 (t80) REVERT: D 804 LYS cc_start: 0.6894 (mttm) cc_final: 0.6502 (ttmm) REVERT: E 38 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7682 (mm-30) REVERT: E 40 GLU cc_start: 0.6905 (OUTLIER) cc_final: 0.6452 (mm-30) REVERT: E 401 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7727 (ttm170) REVERT: E 431 ASP cc_start: 0.7032 (OUTLIER) cc_final: 0.6525 (t70) REVERT: E 488 LYS cc_start: 0.7141 (ttmt) cc_final: 0.6912 (tttt) REVERT: E 537 ASN cc_start: 0.7402 (m110) cc_final: 0.6616 (p0) REVERT: E 596 LYS cc_start: 0.6888 (OUTLIER) cc_final: 0.6455 (pttm) REVERT: E 717 ASN cc_start: 0.5613 (OUTLIER) cc_final: 0.5175 (m-40) REVERT: E 765 LYS cc_start: 0.8553 (mtpt) cc_final: 0.8272 (tmmt) REVERT: E 766 MET cc_start: 0.6908 (OUTLIER) cc_final: 0.6309 (mtp) REVERT: E 777 LEU cc_start: 0.7696 (mt) cc_final: 0.7286 (tp) REVERT: E 781 GLN cc_start: 0.7694 (OUTLIER) cc_final: 0.7466 (pm20) REVERT: E 785 MET cc_start: 0.7200 (OUTLIER) cc_final: 0.6527 (tpt) REVERT: E 804 LYS cc_start: 0.6427 (mmtm) cc_final: 0.6184 (mmtm) REVERT: F 37 GLU cc_start: 0.7357 (mm-30) cc_final: 0.6873 (mm-30) REVERT: F 71 LYS cc_start: 0.8044 (mttt) cc_final: 0.7549 (mptt) REVERT: F 82 ASP cc_start: 0.7637 (m-30) cc_final: 0.7333 (m-30) REVERT: F 248 LYS cc_start: 0.7665 (mmmt) cc_final: 0.6820 (tmmt) REVERT: F 401 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.8060 (mtp-110) REVERT: F 557 LYS cc_start: 0.8126 (mtpt) cc_final: 0.7649 (mtmm) REVERT: F 678 VAL cc_start: 0.4956 (OUTLIER) cc_final: 0.4605 (p) REVERT: F 705 LYS cc_start: 0.7699 (mttm) cc_final: 0.7109 (mttp) REVERT: F 766 MET cc_start: 0.6530 (OUTLIER) cc_final: 0.6219 (ttt) REVERT: F 785 MET cc_start: 0.6804 (tpt) cc_final: 0.6173 (tmm) outliers start: 127 outliers final: 40 residues processed: 516 average time/residue: 0.7179 time to fit residues: 450.7790 Evaluate side-chains 454 residues out of total 4554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 387 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LYS Chi-restraints excluded: chain A residue 212 ARG Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 401 ARG Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 589 LYS Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain A residue 635 GLN Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain B residue 41 ARG Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 635 GLN Chi-restraints excluded: chain B residue 678 VAL Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 41 ARG Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 589 LYS Chi-restraints excluded: chain C residue 596 LYS Chi-restraints excluded: chain C residue 620 ILE Chi-restraints excluded: chain C residue 678 VAL Chi-restraints excluded: chain C residue 767 LYS Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 285 MET Chi-restraints excluded: chain D residue 401 ARG Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 456 GLU Chi-restraints excluded: chain D residue 518 ILE Chi-restraints excluded: chain D residue 589 LYS Chi-restraints excluded: chain D residue 596 LYS Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 401 ARG Chi-restraints excluded: chain E residue 407 THR Chi-restraints excluded: chain E residue 431 ASP Chi-restraints excluded: chain E residue 545 VAL Chi-restraints excluded: chain E residue 596 LYS Chi-restraints excluded: chain E residue 611 ASP Chi-restraints excluded: chain E residue 717 ASN Chi-restraints excluded: chain E residue 746 VAL Chi-restraints excluded: chain E residue 766 MET Chi-restraints excluded: chain E residue 781 GLN Chi-restraints excluded: chain E residue 785 MET Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain F residue 344 ASP Chi-restraints excluded: chain F residue 401 ARG Chi-restraints excluded: chain F residue 407 THR Chi-restraints excluded: chain F residue 584 LEU Chi-restraints excluded: chain F residue 589 LYS Chi-restraints excluded: chain F residue 678 VAL Chi-restraints excluded: chain F residue 698 GLU Chi-restraints excluded: chain F residue 766 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: [466, 93, 13, 465, 194, 76, 281, 17, 86, 47, 173] chunk 466 optimal weight: 7.9990 chunk 93 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 465 optimal weight: 0.6980 chunk 194 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 281 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 173 optimal weight: 0.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 291 ASN D 493 ASN F 493 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.182011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.127659 restraints weight = 51129.232| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.77 r_work: 0.3309 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 41394 Z= 0.128 Angle : 0.545 12.559 55794 Z= 0.274 Chirality : 0.041 0.309 6270 Planarity : 0.004 0.040 7128 Dihedral : 5.361 57.899 5496 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.76 % Favored : 97.02 % Rotamer: Outliers : 2.92 % Allowed : 19.87 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.64 (0.12), residues: 4932 helix: 1.65 (0.09), residues: 3312 sheet: 0.28 (0.36), residues: 216 loop : -0.02 (0.17), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 812 TYR 0.025 0.001 TYR E 711 PHE 0.019 0.001 PHE E 597 TRP 0.021 0.002 TRP A 137 HIS 0.005 0.001 HIS F 595 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (41382) covalent geometry : angle 0.54461 / 0.27 (55794) hydrogen bonds : bond 0.03601 / 2.36 ( 2377) hydrogen bonds : angle 3.64598 / 2.62 ( 7005) Misc. bond : bond 0.00209 / 0.13 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9864 Ramachandran restraints generated. 4932 Oldfield, 0 Emsley, 4932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9864 Ramachandran restraints generated. 4932 Oldfield, 0 Emsley, 4932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 4554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 420 time to evaluate : 1.690 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 ILE cc_start: 0.8845 (OUTLIER) cc_final: 0.8331 (mm) REVERT: A 13 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.7837 (mptt) REVERT: A 27 GLU cc_start: 0.8572 (mp0) cc_final: 0.8195 (mm-30) REVERT: A 41 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7703 (mtm-85) REVERT: A 328 LYS cc_start: 0.8907 (mttt) cc_final: 0.8506 (mmpt) REVERT: A 401 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.8000 (ptp-170) REVERT: A 507 THR cc_start: 0.8187 (m) cc_final: 0.7885 (t) REVERT: A 555 LYS cc_start: 0.8011 (pptt) cc_final: 0.7743 (mmtt) REVERT: A 559 MET cc_start: 0.7817 (mtp) cc_final: 0.7495 (mtp) REVERT: A 635 GLN cc_start: 0.7530 (OUTLIER) cc_final: 0.6865 (mp10) REVERT: A 726 ILE cc_start: 0.7563 (OUTLIER) cc_final: 0.7008 (tp) REVERT: B 2 ILE cc_start: 0.8917 (OUTLIER) cc_final: 0.8337 (mm) REVERT: B 27 GLU cc_start: 0.8339 (mp0) cc_final: 0.8048 (mm-30) REVERT: B 41 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7751 (mtm-85) REVERT: B 54 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8263 (mt-10) REVERT: B 114 ASN cc_start: 0.8538 (t0) cc_final: 0.8236 (t0) REVERT: B 244 GLU cc_start: 0.7636 (tt0) cc_final: 0.7278 (tm-30) REVERT: B 261 LYS cc_start: 0.8550 (mtpt) cc_final: 0.8297 (mtmt) REVERT: B 262 GLU cc_start: 0.8487 (pt0) cc_final: 0.8200 (pt0) REVERT: B 328 LYS cc_start: 0.8755 (mttt) cc_final: 0.8547 (mtpm) REVERT: B 401 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.8222 (ptm160) REVERT: B 477 ASP cc_start: 0.8066 (m-30) cc_final: 0.7596 (m-30) REVERT: B 490 ILE cc_start: 0.7797 (mm) cc_final: 0.7481 (mp) REVERT: B 537 ASN cc_start: 0.7824 (m110) cc_final: 0.7153 (p0) REVERT: B 561 ASN cc_start: 0.7391 (m-40) cc_final: 0.6997 (p0) REVERT: B 631 ARG cc_start: 0.7324 (mtm180) cc_final: 0.6935 (mtm110) REVERT: B 642 GLU cc_start: 0.6813 (tp30) cc_final: 0.6595 (tp30) REVERT: C 14 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7673 (mp0) REVERT: C 72 LYS cc_start: 0.8109 (ttmt) cc_final: 0.7852 (tmtt) REVERT: C 82 ASP cc_start: 0.7842 (m-30) cc_final: 0.7424 (m-30) REVERT: C 233 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7413 (mm-30) REVERT: C 285 MET cc_start: 0.8099 (OUTLIER) cc_final: 0.7886 (tpp) REVERT: C 457 MET cc_start: 0.8206 (ttp) cc_final: 0.7891 (ttp) REVERT: C 530 ARG cc_start: 0.8333 (tpm170) cc_final: 0.8119 (tpm170) REVERT: C 559 MET cc_start: 0.7820 (mtp) cc_final: 0.7494 (mtp) REVERT: C 596 LYS cc_start: 0.7891 (OUTLIER) cc_final: 0.7566 (pttt) REVERT: C 610 SER cc_start: 0.7324 (p) cc_final: 0.6822 (t) REVERT: C 705 LYS cc_start: 0.7560 (mttm) cc_final: 0.6902 (mmtm) REVERT: C 726 ILE cc_start: 0.7210 (OUTLIER) cc_final: 0.6925 (tp) REVERT: D 27 GLU cc_start: 0.8440 (mp0) cc_final: 0.7921 (mm-30) REVERT: D 54 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8211 (mt-10) REVERT: D 82 ASP cc_start: 0.8253 (m-30) cc_final: 0.8024 (m-30) REVERT: D 200 LYS cc_start: 0.6892 (OUTLIER) cc_final: 0.6671 (mmtp) REVERT: D 401 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.8240 (ptm160) REVERT: D 477 ASP cc_start: 0.7540 (m-30) cc_final: 0.7222 (t70) REVERT: D 488 LYS cc_start: 0.7967 (ttmt) cc_final: 0.7497 (tptt) REVERT: D 530 ARG cc_start: 0.8065 (tpm170) cc_final: 0.7659 (tpm170) REVERT: D 532 MET cc_start: 0.8647 (mtt) cc_final: 0.8370 (mtp) REVERT: D 596 LYS cc_start: 0.7503 (OUTLIER) cc_final: 0.6871 (pttt) REVERT: D 631 ARG cc_start: 0.7071 (mtm180) cc_final: 0.6684 (mtm110) REVERT: D 711 TYR cc_start: 0.6671 (t80) cc_final: 0.6234 (t80) REVERT: D 726 ILE cc_start: 0.7424 (OUTLIER) cc_final: 0.6915 (tp) REVERT: D 804 LYS cc_start: 0.6890 (mttm) cc_final: 0.6501 (ttmm) REVERT: E 38 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.6861 (tt0) REVERT: E 40 GLU cc_start: 0.6995 (OUTLIER) cc_final: 0.6548 (mm-30) REVERT: E 240 GLU cc_start: 0.6544 (OUTLIER) cc_final: 0.5937 (pp20) REVERT: E 339 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6872 (mt-10) REVERT: E 401 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.7715 (ttm170) REVERT: E 431 ASP cc_start: 0.7063 (OUTLIER) cc_final: 0.6666 (t70) REVERT: E 488 LYS cc_start: 0.7273 (ttmt) cc_final: 0.7045 (tttt) REVERT: E 537 ASN cc_start: 0.7295 (m110) cc_final: 0.6590 (p0) REVERT: E 596 LYS cc_start: 0.6966 (OUTLIER) cc_final: 0.6529 (pttm) REVERT: E 717 ASN cc_start: 0.5591 (OUTLIER) cc_final: 0.5185 (m-40) REVERT: E 765 LYS cc_start: 0.8590 (mtpt) cc_final: 0.8266 (tmmt) REVERT: E 777 LEU cc_start: 0.7713 (mt) cc_final: 0.7303 (tp) REVERT: E 785 MET cc_start: 0.7173 (OUTLIER) cc_final: 0.6496 (tpt) REVERT: E 804 LYS cc_start: 0.6498 (mmtm) cc_final: 0.6243 (mmtm) REVERT: F 37 GLU cc_start: 0.7291 (mm-30) cc_final: 0.6839 (mm-30) REVERT: F 71 LYS cc_start: 0.8119 (mttt) cc_final: 0.7671 (mptt) REVERT: F 82 ASP cc_start: 0.7662 (m-30) cc_final: 0.7373 (m-30) REVERT: F 248 LYS cc_start: 0.7754 (mmmt) cc_final: 0.6911 (tmmt) REVERT: F 401 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7999 (mtp-110) REVERT: F 557 LYS cc_start: 0.8094 (mtpt) cc_final: 0.7712 (mtmm) REVERT: F 678 VAL cc_start: 0.4987 (OUTLIER) cc_final: 0.4626 (p) REVERT: F 705 LYS cc_start: 0.7867 (mttm) cc_final: 0.7238 (mttp) REVERT: F 766 MET cc_start: 0.6642 (OUTLIER) cc_final: 0.6210 (ttt) REVERT: F 785 MET cc_start: 0.6853 (tpt) cc_final: 0.6227 (tmm) outliers start: 133 outliers final: 38 residues processed: 515 average time/residue: 0.6974 time to fit residues: 439.8930 Evaluate side-chains 446 residues out of total 4554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 376 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 13 LYS Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 212 ARG Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 401 ARG Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 581 SER Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain A residue 635 GLN Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 41 ARG Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 401 ARG Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 456 GLU Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 285 MET Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 589 LYS Chi-restraints excluded: chain C residue 596 LYS Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 767 LYS Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 285 MET Chi-restraints excluded: chain D residue 401 ARG Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 518 ILE Chi-restraints excluded: chain D residue 589 LYS Chi-restraints excluded: chain D residue 596 LYS Chi-restraints excluded: chain D residue 717 ASN Chi-restraints excluded: chain D residue 719 VAL Chi-restraints excluded: chain D residue 726 ILE Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain E residue 339 GLU Chi-restraints excluded: chain E residue 401 ARG Chi-restraints excluded: chain E residue 407 THR Chi-restraints excluded: chain E residue 431 ASP Chi-restraints excluded: chain E residue 545 VAL Chi-restraints excluded: chain E residue 596 LYS Chi-restraints excluded: chain E residue 717 ASN Chi-restraints excluded: chain E residue 726 ILE Chi-restraints excluded: chain E residue 746 VAL Chi-restraints excluded: chain E residue 785 MET Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain F residue 344 ASP Chi-restraints excluded: chain F residue 401 ARG Chi-restraints excluded: chain F residue 407 THR Chi-restraints excluded: chain F residue 584 LEU Chi-restraints excluded: chain F residue 678 VAL Chi-restraints excluded: chain F residue 766 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: [362, 280, 105, 251, 245, 190, 289, 24, 456, 277, 16] chunk 362 optimal weight: 0.0000 chunk 280 optimal weight: 0.0050 chunk 105 optimal weight: 8.9990 chunk 251 optimal weight: 5.9990 chunk 245 optimal weight: 7.9990 chunk 190 optimal weight: 0.9990 chunk 289 optimal weight: 0.3980 chunk 24 optimal weight: 0.8980 chunk 456 optimal weight: 1.9990 chunk 277 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 639 GLN B 527 HIS F 493 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.183350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.122772 restraints weight = 52103.471| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.95 r_work: 0.3320 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 41394 Z= 0.102 Angle : 0.519 12.020 55794 Z= 0.261 Chirality : 0.040 0.326 6270 Planarity : 0.003 0.045 7128 Dihedral : 5.093 57.835 5492 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.55 % Favored : 97.28 % Rotamer: Outliers : 2.15 % Allowed : 20.93 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.77 (0.12), residues: 4932 helix: 1.75 (0.09), residues: 3318 sheet: 0.40 (0.37), residues: 216 loop : 0.03 (0.17), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 812 TYR 0.031 0.001 TYR E 711 PHE 0.032 0.001 PHE D 506 TRP 0.017 0.002 TRP D 137 HIS 0.006 0.001 HIS D 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (41382) covalent geometry : angle 0.51869 / 0.26 (55794) hydrogen bonds : bond 0.03224 / 2.11 ( 2377) hydrogen bonds : angle 3.56628 / 2.57 ( 7005) Misc. bond : bond 0.00104 / 0.06 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9864 Ramachandran restraints generated. 4932 Oldfield, 0 Emsley, 4932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9864 Ramachandran restraints generated. 4932 Oldfield, 0 Emsley, 4932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 4554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 430 time to evaluate : 1.678 Fit side-chains revert: symmetry clash REVERT: A 13 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7369 (mptt) REVERT: A 27 GLU cc_start: 0.8611 (mp0) cc_final: 0.7998 (mm-30) REVERT: A 41 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.7526 (mtm-85) REVERT: A 68 GLU cc_start: 0.6339 (pm20) cc_final: 0.6110 (pp20) REVERT: A 114 ASN cc_start: 0.8317 (t0) cc_final: 0.7929 (t0) REVERT: A 401 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.8261 (ttt180) REVERT: A 507 THR cc_start: 0.8085 (m) cc_final: 0.7788 (t) REVERT: A 555 LYS cc_start: 0.7859 (pptt) cc_final: 0.7442 (mmtt) REVERT: A 559 MET cc_start: 0.7730 (mtp) cc_final: 0.7339 (mtp) REVERT: A 635 GLN cc_start: 0.7187 (OUTLIER) cc_final: 0.6544 (mp10) REVERT: A 642 GLU cc_start: 0.7045 (OUTLIER) cc_final: 0.6463 (mp0) REVERT: A 717 ASN cc_start: 0.6610 (OUTLIER) cc_final: 0.6282 (m-40) REVERT: A 726 ILE cc_start: 0.7303 (OUTLIER) cc_final: 0.6795 (tp) REVERT: A 812 ARG cc_start: 0.6785 (ttp-110) cc_final: 0.6412 (ttp80) REVERT: B 2 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8173 (mm) REVERT: B 27 GLU cc_start: 0.8340 (mp0) cc_final: 0.7894 (mm-30) REVERT: B 41 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.7583 (mtm-85) REVERT: B 244 GLU cc_start: 0.7535 (tt0) cc_final: 0.7093 (tm-30) REVERT: B 328 LYS cc_start: 0.8764 (mttt) cc_final: 0.8426 (mtpm) REVERT: B 477 ASP cc_start: 0.8100 (m-30) cc_final: 0.7577 (m-30) REVERT: B 490 ILE cc_start: 0.7470 (mm) cc_final: 0.7144 (mp) REVERT: B 561 ASN cc_start: 0.7293 (m-40) cc_final: 0.6820 (p0) REVERT: B 631 ARG cc_start: 0.7111 (mtm180) cc_final: 0.6754 (mtm110) REVERT: B 642 GLU cc_start: 0.6724 (tp30) cc_final: 0.6431 (tp30) REVERT: C 72 LYS cc_start: 0.7973 (ttmt) cc_final: 0.7574 (tmtt) REVERT: C 82 ASP cc_start: 0.7503 (m-30) cc_final: 0.7085 (m-30) REVERT: C 233 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7187 (tt0) REVERT: C 457 MET cc_start: 0.8062 (ttp) cc_final: 0.7604 (ttp) REVERT: C 557 LYS cc_start: 0.8371 (mtpt) cc_final: 0.7703 (mppt) REVERT: C 559 MET cc_start: 0.7721 (mtp) cc_final: 0.7320 (mtp) REVERT: C 610 SER cc_start: 0.7113 (p) cc_final: 0.6660 (t) REVERT: C 660 ASN cc_start: 0.7132 (t0) cc_final: 0.6863 (t0) REVERT: C 726 ILE cc_start: 0.7024 (OUTLIER) cc_final: 0.6776 (tp) REVERT: D 27 GLU cc_start: 0.8381 (mp0) cc_final: 0.7684 (mm-30) REVERT: D 82 ASP cc_start: 0.8036 (m-30) cc_final: 0.7755 (m-30) REVERT: D 401 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.8021 (ttm170) REVERT: D 477 ASP cc_start: 0.7615 (m-30) cc_final: 0.7219 (t70) REVERT: D 488 LYS cc_start: 0.7740 (ttmt) cc_final: 0.7308 (tptt) REVERT: D 530 ARG cc_start: 0.7785 (tpm170) cc_final: 0.7414 (tpm170) REVERT: D 596 LYS cc_start: 0.7314 (OUTLIER) cc_final: 0.6681 (pttt) REVERT: D 608 ARG cc_start: 0.7292 (ptt180) cc_final: 0.6935 (ptt180) REVERT: D 631 ARG cc_start: 0.6894 (mtm180) cc_final: 0.6491 (mtm110) REVERT: D 711 TYR cc_start: 0.6412 (t80) cc_final: 0.6009 (t80) REVERT: D 804 LYS cc_start: 0.6863 (mttm) cc_final: 0.6436 (ttmm) REVERT: D 812 ARG cc_start: 0.6530 (mtp-110) cc_final: 0.6316 (mtm110) REVERT: E 38 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.6771 (tt0) REVERT: E 431 ASP cc_start: 0.6925 (OUTLIER) cc_final: 0.6419 (t70) REVERT: E 445 GLU cc_start: 0.7889 (tt0) cc_final: 0.7610 (mm-30) REVERT: E 488 LYS cc_start: 0.7266 (ttmt) cc_final: 0.7022 (tttt) REVERT: E 596 LYS cc_start: 0.6819 (OUTLIER) cc_final: 0.6388 (pttm) REVERT: E 717 ASN cc_start: 0.5348 (OUTLIER) cc_final: 0.4973 (m-40) REVERT: E 765 LYS cc_start: 0.8563 (mtpt) cc_final: 0.8194 (tmmt) REVERT: E 766 MET cc_start: 0.6606 (OUTLIER) cc_final: 0.5521 (mtp) REVERT: E 785 MET cc_start: 0.7117 (tpt) cc_final: 0.6359 (tpt) REVERT: E 804 LYS cc_start: 0.6537 (mmtm) cc_final: 0.6080 (ttpp) REVERT: F 37 GLU cc_start: 0.7101 (mm-30) cc_final: 0.6586 (mm-30) REVERT: F 71 LYS cc_start: 0.7769 (mttt) cc_final: 0.7241 (mptt) REVERT: F 82 ASP cc_start: 0.7396 (m-30) cc_final: 0.7103 (m-30) REVERT: F 101 GLU cc_start: 0.7541 (mt-10) cc_final: 0.7171 (mp0) REVERT: F 144 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8011 (tp30) REVERT: F 248 LYS cc_start: 0.7507 (mmmt) cc_final: 0.6568 (tmmt) REVERT: F 530 ARG cc_start: 0.7783 (tpm170) cc_final: 0.7572 (tpm170) REVERT: F 557 LYS cc_start: 0.8105 (mtpt) cc_final: 0.7556 (mtmm) REVERT: F 678 VAL cc_start: 0.4924 (OUTLIER) cc_final: 0.4587 (p) REVERT: F 705 LYS cc_start: 0.7760 (mttm) cc_final: 0.7125 (mttp) REVERT: F 766 MET cc_start: 0.6525 (OUTLIER) cc_final: 0.6123 (ttt) REVERT: F 785 MET cc_start: 0.6844 (tpt) cc_final: 0.6128 (tmm) outliers start: 98 outliers final: 28 residues processed: 500 average time/residue: 0.6708 time to fit residues: 412.9828 Evaluate side-chains 421 residues out of total 4554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 372 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LYS Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 401 ARG Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain A residue 635 GLN Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 41 ARG Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 589 LYS Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 767 LYS Chi-restraints excluded: chain D residue 401 ARG Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 518 ILE Chi-restraints excluded: chain D residue 596 LYS Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 407 THR Chi-restraints excluded: chain E residue 431 ASP Chi-restraints excluded: chain E residue 545 VAL Chi-restraints excluded: chain E residue 596 LYS Chi-restraints excluded: chain E residue 611 ASP Chi-restraints excluded: chain E residue 717 ASN Chi-restraints excluded: chain E residue 766 MET Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain F residue 344 ASP Chi-restraints excluded: chain F residue 407 THR Chi-restraints excluded: chain F residue 584 LEU Chi-restraints excluded: chain F residue 585 THR Chi-restraints excluded: chain F residue 589 LYS Chi-restraints excluded: chain F residue 678 VAL Chi-restraints excluded: chain F residue 719 VAL Chi-restraints excluded: chain F residue 766 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: [0, 75, 375, 65, 56, 418, 259, 489, 209, 313, 262] chunk 0 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 375 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 chunk 418 optimal weight: 0.5980 chunk 259 optimal weight: 1.9990 chunk 489 optimal weight: 5.9990 chunk 209 optimal weight: 4.9990 chunk 313 optimal weight: 8.9990 chunk 262 optimal weight: 2.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 ASN C 103 GLN C 291 ASN ** E 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 224 ASN F 493 ASN F 727 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.179024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.124857 restraints weight = 51098.213| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.70 r_work: 0.3263 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 41394 Z= 0.225 Angle : 0.641 13.030 55794 Z= 0.321 Chirality : 0.045 0.384 6270 Planarity : 0.005 0.051 7128 Dihedral : 5.695 63.384 5492 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.04 % Favored : 96.70 % Rotamer: Outliers : 2.88 % Allowed : 21.10 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.45 (0.12), residues: 4932 helix: 1.50 (0.09), residues: 3324 sheet: 0.21 (0.35), residues: 216 loop : -0.09 (0.17), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 185 TYR 0.028 0.001 TYR A 258 PHE 0.020 0.002 PHE A 597 TRP 0.031 0.003 TRP D 137 HIS 0.005 0.001 HIS A 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00558 / 0.22 (41382) covalent geometry : angle 0.64150 / 0.32 (55794) hydrogen bonds : bond 0.04345 / 2.87 ( 2377) hydrogen bonds : angle 3.82141 / 2.75 ( 7005) Misc. bond : bond 0.00401 / 0.25 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9864 Ramachandran restraints generated. 4932 Oldfield, 0 Emsley, 4932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9864 Ramachandran restraints generated. 4932 Oldfield, 0 Emsley, 4932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 4554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 386 time to evaluate : 1.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ILE cc_start: 0.8935 (OUTLIER) cc_final: 0.8407 (mm) REVERT: A 13 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.7789 (mptt) REVERT: A 27 GLU cc_start: 0.8597 (mp0) cc_final: 0.8161 (mm-30) REVERT: A 41 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7725 (mtm-85) REVERT: A 240 GLU cc_start: 0.6962 (OUTLIER) cc_final: 0.6461 (pp20) REVERT: A 328 LYS cc_start: 0.8970 (mttt) cc_final: 0.8534 (mmpt) REVERT: A 401 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.7961 (ptp-170) REVERT: A 555 LYS cc_start: 0.8032 (pptt) cc_final: 0.7746 (mmtt) REVERT: A 559 MET cc_start: 0.7906 (mtp) cc_final: 0.7467 (mtp) REVERT: A 630 LYS cc_start: 0.8538 (mmtp) cc_final: 0.7769 (mmmt) REVERT: A 635 GLN cc_start: 0.7526 (OUTLIER) cc_final: 0.6782 (mp10) REVERT: A 717 ASN cc_start: 0.7020 (OUTLIER) cc_final: 0.6675 (m-40) REVERT: A 726 ILE cc_start: 0.7615 (OUTLIER) cc_final: 0.7074 (tp) REVERT: B 2 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8460 (mm) REVERT: B 27 GLU cc_start: 0.8310 (mp0) cc_final: 0.7998 (mm-30) REVERT: B 114 ASN cc_start: 0.8603 (t0) cc_final: 0.8251 (t0) REVERT: B 244 GLU cc_start: 0.7648 (tt0) cc_final: 0.7294 (tm-30) REVERT: B 261 LYS cc_start: 0.8540 (mtpt) cc_final: 0.8332 (mtmt) REVERT: B 328 LYS cc_start: 0.8789 (mttt) cc_final: 0.8573 (mtpm) REVERT: B 401 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.8284 (ptm160) REVERT: B 477 ASP cc_start: 0.8158 (m-30) cc_final: 0.7675 (m-30) REVERT: B 537 ASN cc_start: 0.7950 (m110) cc_final: 0.7284 (p0) REVERT: B 561 ASN cc_start: 0.7527 (m-40) cc_final: 0.7095 (p0) REVERT: B 631 ARG cc_start: 0.7306 (mtm180) cc_final: 0.6977 (mtm110) REVERT: B 785 MET cc_start: 0.7600 (OUTLIER) cc_final: 0.6745 (tpt) REVERT: C 72 LYS cc_start: 0.8078 (ttmt) cc_final: 0.7781 (tmtt) REVERT: C 82 ASP cc_start: 0.7984 (m-30) cc_final: 0.7467 (m-30) REVERT: C 233 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7234 (tt0) REVERT: C 530 ARG cc_start: 0.8286 (tpm170) cc_final: 0.8078 (tpm170) REVERT: C 559 MET cc_start: 0.7948 (mtp) cc_final: 0.7619 (mtp) REVERT: C 596 LYS cc_start: 0.7911 (OUTLIER) cc_final: 0.7604 (pttt) REVERT: C 726 ILE cc_start: 0.7234 (OUTLIER) cc_final: 0.6945 (tp) REVERT: C 785 MET cc_start: 0.7705 (mmp) cc_final: 0.7503 (mmm) REVERT: D 13 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7668 (tppt) REVERT: D 27 GLU cc_start: 0.8463 (mp0) cc_final: 0.7915 (mm-30) REVERT: D 54 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8278 (mt-10) REVERT: D 200 LYS cc_start: 0.6940 (OUTLIER) cc_final: 0.6688 (mmtp) REVERT: D 401 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.8195 (ptm160) REVERT: D 477 ASP cc_start: 0.7632 (m-30) cc_final: 0.7298 (t70) REVERT: D 488 LYS cc_start: 0.7943 (ttmt) cc_final: 0.7474 (tttt) REVERT: D 530 ARG cc_start: 0.8140 (tpm170) cc_final: 0.7663 (tpm170) REVERT: D 537 ASN cc_start: 0.8081 (m110) cc_final: 0.7254 (p0) REVERT: D 596 LYS cc_start: 0.7638 (OUTLIER) cc_final: 0.6982 (pttt) REVERT: D 631 ARG cc_start: 0.7061 (mtm180) cc_final: 0.6636 (mtm110) REVERT: D 711 TYR cc_start: 0.6774 (t80) cc_final: 0.6360 (t80) REVERT: D 804 LYS cc_start: 0.6938 (mttm) cc_final: 0.6543 (ttmm) REVERT: E 38 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.6859 (tt0) REVERT: E 240 GLU cc_start: 0.6595 (OUTLIER) cc_final: 0.5936 (pp20) REVERT: E 339 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6877 (mt-10) REVERT: E 401 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.7695 (ttm170) REVERT: E 431 ASP cc_start: 0.7085 (OUTLIER) cc_final: 0.6668 (t70) REVERT: E 445 GLU cc_start: 0.7976 (tt0) cc_final: 0.7755 (mm-30) REVERT: E 488 LYS cc_start: 0.7339 (ttmt) cc_final: 0.7110 (tttt) REVERT: E 596 LYS cc_start: 0.7083 (OUTLIER) cc_final: 0.6637 (pttm) REVERT: E 717 ASN cc_start: 0.5533 (OUTLIER) cc_final: 0.5144 (m-40) REVERT: E 765 LYS cc_start: 0.8610 (mtpt) cc_final: 0.8208 (tmmt) REVERT: E 766 MET cc_start: 0.6837 (OUTLIER) cc_final: 0.5753 (mtp) REVERT: E 785 MET cc_start: 0.7142 (OUTLIER) cc_final: 0.6508 (tpt) REVERT: E 804 LYS cc_start: 0.6687 (mmtm) cc_final: 0.6174 (mtpm) REVERT: F 37 GLU cc_start: 0.7480 (mm-30) cc_final: 0.6998 (mm-30) REVERT: F 71 LYS cc_start: 0.8142 (mttt) cc_final: 0.7657 (mptt) REVERT: F 82 ASP cc_start: 0.7754 (m-30) cc_final: 0.7424 (m-30) REVERT: F 101 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7246 (mp0) REVERT: F 247 GLN cc_start: 0.7603 (OUTLIER) cc_final: 0.5842 (mp10) REVERT: F 248 LYS cc_start: 0.7606 (mmmt) cc_final: 0.6767 (tmmt) REVERT: F 401 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.8163 (mtm110) REVERT: F 530 ARG cc_start: 0.8079 (tpm170) cc_final: 0.7859 (tpm170) REVERT: F 557 LYS cc_start: 0.8183 (mtpt) cc_final: 0.7712 (mtmm) REVERT: F 678 VAL cc_start: 0.4993 (OUTLIER) cc_final: 0.4611 (p) REVERT: F 705 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7221 (mttp) REVERT: F 708 ASP cc_start: 0.7391 (t0) cc_final: 0.6982 (m-30) REVERT: F 766 MET cc_start: 0.6870 (OUTLIER) cc_final: 0.6441 (ttt) REVERT: F 785 MET cc_start: 0.6883 (tpt) cc_final: 0.6252 (tmm) outliers start: 131 outliers final: 51 residues processed: 480 average time/residue: 0.7008 time to fit residues: 410.8740 Evaluate side-chains 449 residues out of total 4554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 365 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 13 LYS Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 212 ARG Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 401 ARG Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 581 SER Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 589 LYS Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain A residue 635 GLN Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 41 ARG Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 401 ARG Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 456 GLU Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 785 MET Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 589 LYS Chi-restraints excluded: chain C residue 596 LYS Chi-restraints excluded: chain C residue 651 LYS Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 767 LYS Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 401 ARG Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 456 GLU Chi-restraints excluded: chain D residue 518 ILE Chi-restraints excluded: chain D residue 589 LYS Chi-restraints excluded: chain D residue 596 LYS Chi-restraints excluded: chain D residue 697 SER Chi-restraints excluded: chain D residue 719 VAL Chi-restraints excluded: chain D residue 726 ILE Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain E residue 339 GLU Chi-restraints excluded: chain E residue 401 ARG Chi-restraints excluded: chain E residue 407 THR Chi-restraints excluded: chain E residue 431 ASP Chi-restraints excluded: chain E residue 532 MET Chi-restraints excluded: chain E residue 545 VAL Chi-restraints excluded: chain E residue 596 LYS Chi-restraints excluded: chain E residue 611 ASP Chi-restraints excluded: chain E residue 717 ASN Chi-restraints excluded: chain E residue 726 ILE Chi-restraints excluded: chain E residue 745 ASP Chi-restraints excluded: chain E residue 766 MET Chi-restraints excluded: chain E residue 785 MET Chi-restraints excluded: chain F residue 247 GLN Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain F residue 344 ASP Chi-restraints excluded: chain F residue 393 ASP Chi-restraints excluded: chain F residue 401 ARG Chi-restraints excluded: chain F residue 407 THR Chi-restraints excluded: chain F residue 456 GLU Chi-restraints excluded: chain F residue 584 LEU Chi-restraints excluded: chain F residue 589 LYS Chi-restraints excluded: chain F residue 635 GLN Chi-restraints excluded: chain F residue 678 VAL Chi-restraints excluded: chain F residue 698 GLU Chi-restraints excluded: chain F residue 705 LYS Chi-restraints excluded: chain F residue 719 VAL Chi-restraints excluded: chain F residue 766 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: [209, 477, 319, 342, 399, 64, 19, 454, 197, 440, 77] chunk 209 optimal weight: 0.7980 chunk 477 optimal weight: 20.0000 chunk 319 optimal weight: 1.9990 chunk 342 optimal weight: 1.9990 chunk 399 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 454 optimal weight: 0.9980 chunk 197 optimal weight: 0.2980 chunk 440 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 291 ASN F 224 ASN F 493 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.181587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.126485 restraints weight = 50991.575| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.81 r_work: 0.3334 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 41394 Z= 0.128 Angle : 0.556 13.827 55794 Z= 0.280 Chirality : 0.041 0.336 6270 Planarity : 0.004 0.064 7128 Dihedral : 5.362 59.929 5492 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.49 % Favored : 97.26 % Rotamer: Outliers : 2.22 % Allowed : 21.78 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.61 (0.12), residues: 4932 helix: 1.65 (0.09), residues: 3318 sheet: 0.43 (0.44), residues: 144 loop : -0.09 (0.17), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 18 TYR 0.022 0.001 TYR A 258 PHE 0.029 0.001 PHE D 506 TRP 0.020 0.002 TRP A 137 HIS 0.005 0.001 HIS F 595 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (41382) covalent geometry : angle 0.55601 / 0.28 (55794) hydrogen bonds : bond 0.03544 / 2.33 ( 2377) hydrogen bonds : angle 3.68053 / 2.66 ( 7005) Misc. bond : bond 0.00186 / 0.11 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9864 Ramachandran restraints generated. 4932 Oldfield, 0 Emsley, 4932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9864 Ramachandran restraints generated. 4932 Oldfield, 0 Emsley, 4932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 4554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 395 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ILE cc_start: 0.8790 (OUTLIER) cc_final: 0.8252 (mm) REVERT: A 13 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.7776 (mptt) REVERT: A 27 GLU cc_start: 0.8548 (mp0) cc_final: 0.8175 (mm-30) REVERT: A 41 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.7748 (mtm-85) REVERT: A 68 GLU cc_start: 0.6500 (pm20) cc_final: 0.6258 (pp20) REVERT: A 240 GLU cc_start: 0.6916 (OUTLIER) cc_final: 0.6474 (pp20) REVERT: A 328 LYS cc_start: 0.8881 (mttt) cc_final: 0.8487 (mmpt) REVERT: A 401 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.7989 (ptp-170) REVERT: A 461 ASN cc_start: 0.8671 (OUTLIER) cc_final: 0.8300 (t0) REVERT: A 555 LYS cc_start: 0.7993 (pptt) cc_final: 0.7725 (mmtt) REVERT: A 559 MET cc_start: 0.7817 (mtp) cc_final: 0.7492 (mtp) REVERT: A 588 GLN cc_start: 0.8132 (mm-40) cc_final: 0.7643 (mm-40) REVERT: A 630 LYS cc_start: 0.8493 (mmtp) cc_final: 0.7744 (mmmt) REVERT: A 635 GLN cc_start: 0.7489 (OUTLIER) cc_final: 0.6738 (mp10) REVERT: A 642 GLU cc_start: 0.7192 (OUTLIER) cc_final: 0.6687 (mp0) REVERT: A 717 ASN cc_start: 0.6962 (OUTLIER) cc_final: 0.6638 (m-40) REVERT: A 726 ILE cc_start: 0.7614 (OUTLIER) cc_final: 0.7063 (tp) REVERT: B 2 ILE cc_start: 0.8837 (OUTLIER) cc_final: 0.8320 (mm) REVERT: B 27 GLU cc_start: 0.8261 (mp0) cc_final: 0.8033 (mm-30) REVERT: B 41 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7721 (mtm-85) REVERT: B 114 ASN cc_start: 0.8553 (t0) cc_final: 0.8259 (t0) REVERT: B 244 GLU cc_start: 0.7660 (tt0) cc_final: 0.7297 (tm-30) REVERT: B 261 LYS cc_start: 0.8521 (mtpt) cc_final: 0.8292 (mtmt) REVERT: B 477 ASP cc_start: 0.8122 (m-30) cc_final: 0.7671 (m-30) REVERT: B 490 ILE cc_start: 0.7801 (mm) cc_final: 0.7470 (mp) REVERT: B 537 ASN cc_start: 0.7798 (m110) cc_final: 0.7235 (p0) REVERT: B 543 GLU cc_start: 0.8440 (mp0) cc_final: 0.8229 (mm-30) REVERT: B 561 ASN cc_start: 0.7394 (m-40) cc_final: 0.6991 (p0) REVERT: B 588 GLN cc_start: 0.7872 (OUTLIER) cc_final: 0.7080 (mt0) REVERT: B 631 ARG cc_start: 0.7317 (mtm180) cc_final: 0.6992 (mtm110) REVERT: B 785 MET cc_start: 0.7596 (OUTLIER) cc_final: 0.6740 (tpt) REVERT: C 72 LYS cc_start: 0.8078 (ttmt) cc_final: 0.7816 (tmtt) REVERT: C 82 ASP cc_start: 0.7894 (m-30) cc_final: 0.7419 (m-30) REVERT: C 233 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.6901 (tt0) REVERT: C 530 ARG cc_start: 0.8252 (tpm170) cc_final: 0.8044 (tpm170) REVERT: C 559 MET cc_start: 0.7889 (mtp) cc_final: 0.7579 (mtp) REVERT: C 596 LYS cc_start: 0.7902 (OUTLIER) cc_final: 0.7588 (pttt) REVERT: C 726 ILE cc_start: 0.7219 (OUTLIER) cc_final: 0.6932 (tp) REVERT: C 785 MET cc_start: 0.7701 (mmp) cc_final: 0.7496 (mmm) REVERT: D 13 LYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7751 (tppt) REVERT: D 27 GLU cc_start: 0.8423 (mp0) cc_final: 0.7916 (mm-30) REVERT: D 200 LYS cc_start: 0.6819 (OUTLIER) cc_final: 0.6618 (mmtp) REVERT: D 240 GLU cc_start: 0.6751 (OUTLIER) cc_final: 0.5833 (pp20) REVERT: D 401 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.8193 (ptm160) REVERT: D 477 ASP cc_start: 0.7612 (m-30) cc_final: 0.7320 (t70) REVERT: D 488 LYS cc_start: 0.7965 (ttmt) cc_final: 0.7512 (tptt) REVERT: D 507 THR cc_start: 0.7983 (t) cc_final: 0.7781 (p) REVERT: D 530 ARG cc_start: 0.8127 (tpm170) cc_final: 0.7689 (tpm170) REVERT: D 596 LYS cc_start: 0.7513 (OUTLIER) cc_final: 0.6881 (pttt) REVERT: D 631 ARG cc_start: 0.7056 (mtm180) cc_final: 0.6633 (mtm110) REVERT: D 711 TYR cc_start: 0.6786 (t80) cc_final: 0.6382 (t80) REVERT: D 726 ILE cc_start: 0.7333 (OUTLIER) cc_final: 0.6892 (tp) REVERT: D 804 LYS cc_start: 0.6910 (mttm) cc_final: 0.6523 (ttmm) REVERT: E 38 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.6819 (tt0) REVERT: E 240 GLU cc_start: 0.6487 (OUTLIER) cc_final: 0.5881 (pp20) REVERT: E 401 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.7708 (ttm170) REVERT: E 511 MET cc_start: 0.7694 (mtt) cc_final: 0.7431 (mtp) REVERT: E 596 LYS cc_start: 0.7059 (OUTLIER) cc_final: 0.6664 (pttm) REVERT: E 765 LYS cc_start: 0.8603 (mtpt) cc_final: 0.8159 (tptp) REVERT: E 766 MET cc_start: 0.6761 (OUTLIER) cc_final: 0.6109 (mtp) REVERT: E 785 MET cc_start: 0.7154 (OUTLIER) cc_final: 0.6501 (tpt) REVERT: F 37 GLU cc_start: 0.7275 (mm-30) cc_final: 0.6801 (mm-30) REVERT: F 71 LYS cc_start: 0.8102 (mttt) cc_final: 0.7642 (mptt) REVERT: F 82 ASP cc_start: 0.7671 (m-30) cc_final: 0.7353 (m-30) REVERT: F 101 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7247 (mp0) REVERT: F 248 LYS cc_start: 0.7491 (mmmt) cc_final: 0.6696 (tmmt) REVERT: F 530 ARG cc_start: 0.8070 (tpm170) cc_final: 0.7860 (tpm170) REVERT: F 557 LYS cc_start: 0.8114 (mtpt) cc_final: 0.7672 (mtmm) REVERT: F 619 ILE cc_start: 0.8580 (pt) cc_final: 0.8260 (pt) REVERT: F 678 VAL cc_start: 0.5022 (OUTLIER) cc_final: 0.4665 (p) REVERT: F 705 LYS cc_start: 0.7836 (mttm) cc_final: 0.7222 (mttp) REVERT: F 708 ASP cc_start: 0.7327 (t0) cc_final: 0.6915 (m-30) REVERT: F 727 ASN cc_start: 0.7247 (m110) cc_final: 0.6782 (m110) REVERT: F 766 MET cc_start: 0.6791 (OUTLIER) cc_final: 0.6342 (ttt) REVERT: F 774 GLU cc_start: 0.7662 (tp30) cc_final: 0.7397 (tp30) REVERT: F 785 MET cc_start: 0.6878 (tpt) cc_final: 0.6219 (tmm) outliers start: 101 outliers final: 39 residues processed: 467 average time/residue: 0.6855 time to fit residues: 392.3299 Evaluate side-chains 441 residues out of total 4554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 371 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 13 LYS Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 401 ARG Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 461 ASN Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 589 LYS Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain A residue 635 GLN Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 41 ARG Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 588 GLN Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 785 MET Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 589 LYS Chi-restraints excluded: chain C residue 596 LYS Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 767 LYS Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 240 GLU Chi-restraints excluded: chain D residue 401 ARG Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 518 ILE Chi-restraints excluded: chain D residue 589 LYS Chi-restraints excluded: chain D residue 596 LYS Chi-restraints excluded: chain D residue 719 VAL Chi-restraints excluded: chain D residue 726 ILE Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain E residue 401 ARG Chi-restraints excluded: chain E residue 407 THR Chi-restraints excluded: chain E residue 545 VAL Chi-restraints excluded: chain E residue 596 LYS Chi-restraints excluded: chain E residue 675 GLN Chi-restraints excluded: chain E residue 726 ILE Chi-restraints excluded: chain E residue 766 MET Chi-restraints excluded: chain E residue 785 MET Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain F residue 344 ASP Chi-restraints excluded: chain F residue 407 THR Chi-restraints excluded: chain F residue 584 LEU Chi-restraints excluded: chain F residue 589 LYS Chi-restraints excluded: chain F residue 678 VAL Chi-restraints excluded: chain F residue 698 GLU Chi-restraints excluded: chain F residue 719 VAL Chi-restraints excluded: chain F residue 766 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: [481, 315, 245, 389, 479, 171, 159, 2, 280, 463, 445] chunk 481 optimal weight: 8.9990 chunk 315 optimal weight: 1.9990 chunk 245 optimal weight: 5.9990 chunk 389 optimal weight: 2.9990 chunk 479 optimal weight: 3.9990 chunk 171 optimal weight: 3.9990 chunk 159 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 280 optimal weight: 0.3980 chunk 463 optimal weight: 0.4980 chunk 445 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 224 ASN F 493 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.179865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.124857 restraints weight = 51171.143| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.83 r_work: 0.3295 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 41394 Z= 0.174 Angle : 0.608 16.931 55794 Z= 0.304 Chirality : 0.043 0.349 6270 Planarity : 0.004 0.077 7128 Dihedral : 5.530 59.907 5492 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.04 % Favored : 96.70 % Rotamer: Outliers : 2.26 % Allowed : 22.09 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.51 (0.12), residues: 4932 helix: 1.56 (0.09), residues: 3318 sheet: 0.28 (0.39), residues: 180 loop : -0.09 (0.17), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 812 TYR 0.049 0.001 TYR E 711 PHE 0.020 0.002 PHE A 597 TRP 0.022 0.002 TRP D 137 HIS 0.004 0.001 HIS F 595 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.17 (41382) covalent geometry : angle 0.60841 / 0.30 (55794) hydrogen bonds : bond 0.03955 / 2.60 ( 2377) hydrogen bonds : angle 3.76019 / 2.71 ( 7005) Misc. bond : bond 0.00304 / 0.19 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9864 Ramachandran restraints generated. 4932 Oldfield, 0 Emsley, 4932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9864 Ramachandran restraints generated. 4932 Oldfield, 0 Emsley, 4932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 4554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 382 time to evaluate : 1.650 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 ILE cc_start: 0.8908 (OUTLIER) cc_final: 0.8344 (mm) REVERT: A 13 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.7782 (mptt) REVERT: A 27 GLU cc_start: 0.8563 (mp0) cc_final: 0.8149 (mm-30) REVERT: A 41 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7741 (mtm-85) REVERT: A 240 GLU cc_start: 0.6982 (OUTLIER) cc_final: 0.6519 (pp20) REVERT: A 328 LYS cc_start: 0.8921 (mttt) cc_final: 0.8490 (mmpt) REVERT: A 401 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.7966 (ptp-170) REVERT: A 461 ASN cc_start: 0.8713 (OUTLIER) cc_final: 0.8342 (t0) REVERT: A 555 LYS cc_start: 0.7974 (pptt) cc_final: 0.7683 (mmtt) REVERT: A 559 MET cc_start: 0.7841 (mtp) cc_final: 0.7478 (mtp) REVERT: A 630 LYS cc_start: 0.8498 (mmtp) cc_final: 0.7822 (mmmt) REVERT: A 635 GLN cc_start: 0.7488 (OUTLIER) cc_final: 0.6744 (mp10) REVERT: A 717 ASN cc_start: 0.6951 (OUTLIER) cc_final: 0.6629 (m-40) REVERT: A 726 ILE cc_start: 0.7572 (OUTLIER) cc_final: 0.7030 (tp) REVERT: B 2 ILE cc_start: 0.8966 (OUTLIER) cc_final: 0.8421 (mm) REVERT: B 27 GLU cc_start: 0.8286 (mp0) cc_final: 0.8011 (mm-30) REVERT: B 41 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7737 (mtm-85) REVERT: B 114 ASN cc_start: 0.8579 (t0) cc_final: 0.8234 (t0) REVERT: B 244 GLU cc_start: 0.7641 (tt0) cc_final: 0.7273 (tm-30) REVERT: B 261 LYS cc_start: 0.8530 (mtpt) cc_final: 0.8305 (mtmt) REVERT: B 328 LYS cc_start: 0.8822 (mtpm) cc_final: 0.8457 (mtmt) REVERT: B 401 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.8270 (ptm160) REVERT: B 477 ASP cc_start: 0.8160 (m-30) cc_final: 0.7703 (m-30) REVERT: B 537 ASN cc_start: 0.7885 (m110) cc_final: 0.7250 (p0) REVERT: B 561 ASN cc_start: 0.7414 (m-40) cc_final: 0.6994 (p0) REVERT: B 631 ARG cc_start: 0.7303 (mtm180) cc_final: 0.6955 (mtm110) REVERT: B 785 MET cc_start: 0.7564 (OUTLIER) cc_final: 0.6738 (tpt) REVERT: C 72 LYS cc_start: 0.8103 (ttmt) cc_final: 0.7806 (tmtt) REVERT: C 82 ASP cc_start: 0.7917 (m-30) cc_final: 0.7423 (m-30) REVERT: C 233 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.6944 (tt0) REVERT: C 530 ARG cc_start: 0.8240 (tpm170) cc_final: 0.8014 (tpm170) REVERT: C 559 MET cc_start: 0.7915 (mtp) cc_final: 0.7586 (mtp) REVERT: C 596 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7552 (pttt) REVERT: C 726 ILE cc_start: 0.7247 (OUTLIER) cc_final: 0.6943 (tp) REVERT: C 785 MET cc_start: 0.7656 (mmp) cc_final: 0.7445 (mmm) REVERT: D 13 LYS cc_start: 0.7956 (OUTLIER) cc_final: 0.7665 (tppt) REVERT: D 27 GLU cc_start: 0.8450 (mp0) cc_final: 0.7918 (mm-30) REVERT: D 54 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8215 (mt-10) REVERT: D 200 LYS cc_start: 0.6878 (OUTLIER) cc_final: 0.6650 (mmtp) REVERT: D 240 GLU cc_start: 0.6799 (OUTLIER) cc_final: 0.5857 (pp20) REVERT: D 401 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.8196 (ptm160) REVERT: D 477 ASP cc_start: 0.7731 (m-30) cc_final: 0.7344 (t70) REVERT: D 488 LYS cc_start: 0.7961 (ttmt) cc_final: 0.7498 (tttt) REVERT: D 507 THR cc_start: 0.7994 (t) cc_final: 0.7780 (p) REVERT: D 530 ARG cc_start: 0.8135 (tpm170) cc_final: 0.7656 (tpm170) REVERT: D 596 LYS cc_start: 0.7602 (OUTLIER) cc_final: 0.6950 (pttt) REVERT: D 631 ARG cc_start: 0.6965 (mtm180) cc_final: 0.6567 (mtm110) REVERT: D 711 TYR cc_start: 0.6766 (t80) cc_final: 0.6375 (t80) REVERT: D 804 LYS cc_start: 0.6930 (mttm) cc_final: 0.6544 (ttmm) REVERT: D 812 ARG cc_start: 0.6614 (mtp-110) cc_final: 0.6341 (mtm110) REVERT: E 38 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.6802 (tt0) REVERT: E 206 TYR cc_start: 0.8005 (t80) cc_final: 0.7770 (t80) REVERT: E 240 GLU cc_start: 0.6511 (OUTLIER) cc_final: 0.5860 (pp20) REVERT: E 339 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6847 (mt-10) REVERT: E 401 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7683 (ttm170) REVERT: E 596 LYS cc_start: 0.7007 (OUTLIER) cc_final: 0.6632 (pttm) REVERT: E 672 ILE cc_start: 0.6798 (tp) cc_final: 0.6479 (tt) REVERT: E 717 ASN cc_start: 0.5446 (OUTLIER) cc_final: 0.5054 (m-40) REVERT: E 765 LYS cc_start: 0.8589 (mtpt) cc_final: 0.8188 (tmmt) REVERT: E 766 MET cc_start: 0.6768 (OUTLIER) cc_final: 0.5613 (mtp) REVERT: E 785 MET cc_start: 0.7166 (OUTLIER) cc_final: 0.6514 (tpt) REVERT: F 37 GLU cc_start: 0.7394 (mm-30) cc_final: 0.6884 (mm-30) REVERT: F 71 LYS cc_start: 0.8104 (mttt) cc_final: 0.7624 (mptt) REVERT: F 82 ASP cc_start: 0.7713 (m-30) cc_final: 0.7382 (m-30) REVERT: F 101 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7256 (mp0) REVERT: F 247 GLN cc_start: 0.7479 (OUTLIER) cc_final: 0.5516 (mp10) REVERT: F 248 LYS cc_start: 0.7518 (mmmt) cc_final: 0.6691 (tmmt) REVERT: F 557 LYS cc_start: 0.8164 (mtpt) cc_final: 0.7720 (mtmm) REVERT: F 619 ILE cc_start: 0.8583 (pt) cc_final: 0.8283 (pt) REVERT: F 678 VAL cc_start: 0.5077 (OUTLIER) cc_final: 0.4713 (p) REVERT: F 705 LYS cc_start: 0.7805 (mttm) cc_final: 0.7201 (mttp) REVERT: F 727 ASN cc_start: 0.7216 (m110) cc_final: 0.6761 (m110) REVERT: F 766 MET cc_start: 0.6856 (OUTLIER) cc_final: 0.6395 (ttt) REVERT: F 774 GLU cc_start: 0.7746 (tp30) cc_final: 0.7470 (tp30) REVERT: F 785 MET cc_start: 0.6876 (tpt) cc_final: 0.6209 (tmm) outliers start: 103 outliers final: 46 residues processed: 458 average time/residue: 0.7057 time to fit residues: 395.1852 Evaluate side-chains 447 residues out of total 4554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 368 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 13 LYS Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 212 ARG Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 401 ARG Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 461 ASN Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 589 LYS Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain A residue 635 GLN Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 41 ARG Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 401 ARG Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 456 GLU Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 785 MET Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 285 MET Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 589 LYS Chi-restraints excluded: chain C residue 596 LYS Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 240 GLU Chi-restraints excluded: chain D residue 401 ARG Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 456 GLU Chi-restraints excluded: chain D residue 518 ILE Chi-restraints excluded: chain D residue 589 LYS Chi-restraints excluded: chain D residue 596 LYS Chi-restraints excluded: chain D residue 719 VAL Chi-restraints excluded: chain D residue 726 ILE Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain E residue 339 GLU Chi-restraints excluded: chain E residue 401 ARG Chi-restraints excluded: chain E residue 407 THR Chi-restraints excluded: chain E residue 545 VAL Chi-restraints excluded: chain E residue 596 LYS Chi-restraints excluded: chain E residue 675 GLN Chi-restraints excluded: chain E residue 691 THR Chi-restraints excluded: chain E residue 717 ASN Chi-restraints excluded: chain E residue 726 ILE Chi-restraints excluded: chain E residue 766 MET Chi-restraints excluded: chain E residue 785 MET Chi-restraints excluded: chain F residue 224 ASN Chi-restraints excluded: chain F residue 247 GLN Chi-restraints excluded: chain F residue 344 ASP Chi-restraints excluded: chain F residue 407 THR Chi-restraints excluded: chain F residue 456 GLU Chi-restraints excluded: chain F residue 584 LEU Chi-restraints excluded: chain F residue 589 LYS Chi-restraints excluded: chain F residue 678 VAL Chi-restraints excluded: chain F residue 698 GLU Chi-restraints excluded: chain F residue 719 VAL Chi-restraints excluded: chain F residue 766 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: [35, 101, 407, 227, 168, 402, 275, 257, 335, 452, 343] chunk 35 optimal weight: 0.5980 chunk 101 optimal weight: 3.9990 chunk 407 optimal weight: 6.9990 chunk 227 optimal weight: 5.9990 chunk 168 optimal weight: 0.8980 chunk 402 optimal weight: 10.0000 chunk 275 optimal weight: 0.9980 chunk 257 optimal weight: 1.9990 chunk 335 optimal weight: 4.9990 chunk 452 optimal weight: 0.0010 chunk 343 optimal weight: 2.9990 overall best weight: 0.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 291 ASN F 493 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.181748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.126548 restraints weight = 50921.627| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.83 r_work: 0.3332 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 41394 Z= 0.123 Angle : 0.569 16.676 55794 Z= 0.286 Chirality : 0.042 0.328 6270 Planarity : 0.004 0.041 7128 Dihedral : 5.327 59.290 5492 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.55 % Favored : 97.22 % Rotamer: Outliers : 1.67 % Allowed : 22.66 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.63 (0.12), residues: 4932 helix: 1.67 (0.09), residues: 3312 sheet: 0.41 (0.44), residues: 144 loop : -0.08 (0.17), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 812 TYR 0.055 0.001 TYR E 711 PHE 0.031 0.001 PHE D 506 TRP 0.018 0.002 TRP A 137 HIS 0.005 0.001 HIS F 595 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 (41382) covalent geometry : angle 0.56921 / 0.29 (55794) hydrogen bonds : bond 0.03512 / 2.31 ( 2377) hydrogen bonds : angle 3.69918 / 2.67 ( 7005) Misc. bond : bond 0.00173 / 0.11 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9864 Ramachandran restraints generated. 4932 Oldfield, 0 Emsley, 4932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9864 Ramachandran restraints generated. 4932 Oldfield, 0 Emsley, 4932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 4554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 385 time to evaluate : 1.493 Fit side-chains revert: symmetry clash REVERT: A 2 ILE cc_start: 0.8794 (OUTLIER) cc_final: 0.8263 (mm) REVERT: A 13 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.7853 (mptt) REVERT: A 27 GLU cc_start: 0.8542 (mp0) cc_final: 0.8165 (mm-30) REVERT: A 41 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7766 (mtm-85) REVERT: A 68 GLU cc_start: 0.6590 (pm20) cc_final: 0.6340 (pp20) REVERT: A 240 GLU cc_start: 0.6885 (OUTLIER) cc_final: 0.6501 (pp20) REVERT: A 401 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.7973 (ptp-170) REVERT: A 461 ASN cc_start: 0.8678 (OUTLIER) cc_final: 0.8283 (t0) REVERT: A 507 THR cc_start: 0.8264 (m) cc_final: 0.7895 (t) REVERT: A 555 LYS cc_start: 0.7969 (pptt) cc_final: 0.7682 (mmtt) REVERT: A 559 MET cc_start: 0.7775 (mtp) cc_final: 0.7485 (mtp) REVERT: A 630 LYS cc_start: 0.8490 (mmtp) cc_final: 0.7706 (mmmt) REVERT: A 635 GLN cc_start: 0.7462 (OUTLIER) cc_final: 0.6719 (mp10) REVERT: A 717 ASN cc_start: 0.6908 (OUTLIER) cc_final: 0.6613 (m-40) REVERT: A 726 ILE cc_start: 0.7592 (OUTLIER) cc_final: 0.7043 (tp) REVERT: B 2 ILE cc_start: 0.8827 (OUTLIER) cc_final: 0.8320 (mm) REVERT: B 27 GLU cc_start: 0.8244 (mp0) cc_final: 0.8029 (mm-30) REVERT: B 41 ARG cc_start: 0.7970 (OUTLIER) cc_final: 0.7729 (mtm-85) REVERT: B 114 ASN cc_start: 0.8553 (t0) cc_final: 0.8240 (t0) REVERT: B 244 GLU cc_start: 0.7675 (tt0) cc_final: 0.7285 (tm-30) REVERT: B 261 LYS cc_start: 0.8518 (mtpt) cc_final: 0.8289 (mtmt) REVERT: B 328 LYS cc_start: 0.8796 (mtpm) cc_final: 0.8439 (mtmt) REVERT: B 477 ASP cc_start: 0.8137 (m-30) cc_final: 0.7684 (m-30) REVERT: B 490 ILE cc_start: 0.7804 (mm) cc_final: 0.7475 (mp) REVERT: B 537 ASN cc_start: 0.7910 (m110) cc_final: 0.7265 (p0) REVERT: B 561 ASN cc_start: 0.7390 (m-40) cc_final: 0.6979 (p0) REVERT: B 631 ARG cc_start: 0.7285 (mtm180) cc_final: 0.6934 (mtm110) REVERT: B 785 MET cc_start: 0.7560 (OUTLIER) cc_final: 0.6729 (tpt) REVERT: C 72 LYS cc_start: 0.8076 (ttmt) cc_final: 0.7807 (tmtt) REVERT: C 82 ASP cc_start: 0.7808 (m-30) cc_final: 0.7399 (m-30) REVERT: C 233 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7144 (tt0) REVERT: C 530 ARG cc_start: 0.8274 (tpm170) cc_final: 0.8064 (tpm170) REVERT: C 557 LYS cc_start: 0.8287 (mtpt) cc_final: 0.7764 (mppt) REVERT: C 559 MET cc_start: 0.7848 (mtp) cc_final: 0.7539 (mtp) REVERT: C 596 LYS cc_start: 0.7901 (OUTLIER) cc_final: 0.7607 (pttt) REVERT: C 609 LEU cc_start: 0.7937 (mt) cc_final: 0.7655 (mp) REVERT: C 660 ASN cc_start: 0.7404 (t0) cc_final: 0.7188 (t0) REVERT: C 726 ILE cc_start: 0.7189 (OUTLIER) cc_final: 0.6878 (tp) REVERT: C 785 MET cc_start: 0.7659 (mmp) cc_final: 0.7445 (mmm) REVERT: D 27 GLU cc_start: 0.8407 (mp0) cc_final: 0.7840 (mm-30) REVERT: D 54 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8186 (mt-10) REVERT: D 240 GLU cc_start: 0.6772 (OUTLIER) cc_final: 0.5845 (pp20) REVERT: D 401 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.8054 (ttm170) REVERT: D 426 ILE cc_start: 0.8485 (tt) cc_final: 0.8192 (tp) REVERT: D 477 ASP cc_start: 0.7700 (m-30) cc_final: 0.7327 (t70) REVERT: D 488 LYS cc_start: 0.7929 (ttmt) cc_final: 0.7476 (tptt) REVERT: D 530 ARG cc_start: 0.8143 (tpm170) cc_final: 0.7687 (tpm170) REVERT: D 596 LYS cc_start: 0.7484 (OUTLIER) cc_final: 0.6857 (pttt) REVERT: D 631 ARG cc_start: 0.6993 (mtm180) cc_final: 0.6560 (mtm110) REVERT: D 711 TYR cc_start: 0.6793 (t80) cc_final: 0.6373 (t80) REVERT: D 726 ILE cc_start: 0.7323 (OUTLIER) cc_final: 0.6884 (tp) REVERT: D 804 LYS cc_start: 0.6950 (mttm) cc_final: 0.6558 (ttmm) REVERT: D 812 ARG cc_start: 0.6616 (mtp-110) cc_final: 0.6336 (mtm110) REVERT: E 38 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.6771 (tt0) REVERT: E 240 GLU cc_start: 0.6469 (OUTLIER) cc_final: 0.5836 (pp20) REVERT: E 339 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6852 (mt-10) REVERT: E 401 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7697 (ttm170) REVERT: E 596 LYS cc_start: 0.7099 (OUTLIER) cc_final: 0.6751 (pttm) REVERT: E 672 ILE cc_start: 0.6815 (tp) cc_final: 0.6523 (tt) REVERT: E 717 ASN cc_start: 0.5401 (OUTLIER) cc_final: 0.5042 (m-40) REVERT: E 765 LYS cc_start: 0.8584 (mtpt) cc_final: 0.8186 (tmmt) REVERT: E 766 MET cc_start: 0.6686 (OUTLIER) cc_final: 0.5714 (mtp) REVERT: E 785 MET cc_start: 0.7144 (OUTLIER) cc_final: 0.6477 (tpt) REVERT: F 37 GLU cc_start: 0.7280 (mm-30) cc_final: 0.6769 (mm-30) REVERT: F 71 LYS cc_start: 0.8097 (mttt) cc_final: 0.7625 (mptt) REVERT: F 82 ASP cc_start: 0.7662 (m-30) cc_final: 0.7340 (m-30) REVERT: F 101 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7192 (mp0) REVERT: F 247 GLN cc_start: 0.7456 (OUTLIER) cc_final: 0.5493 (mp10) REVERT: F 248 LYS cc_start: 0.7481 (mmmt) cc_final: 0.6681 (tmmt) REVERT: F 557 LYS cc_start: 0.8181 (mtpt) cc_final: 0.7741 (mtmm) REVERT: F 619 ILE cc_start: 0.8585 (pt) cc_final: 0.8275 (pt) REVERT: F 678 VAL cc_start: 0.5005 (OUTLIER) cc_final: 0.4656 (p) REVERT: F 705 LYS cc_start: 0.7811 (mttm) cc_final: 0.7229 (mttp) REVERT: F 727 ASN cc_start: 0.7216 (m110) cc_final: 0.6778 (m110) REVERT: F 766 MET cc_start: 0.6783 (OUTLIER) cc_final: 0.6275 (ttt) REVERT: F 774 GLU cc_start: 0.7723 (tp30) cc_final: 0.7444 (tp30) REVERT: F 785 MET cc_start: 0.6855 (tpt) cc_final: 0.6142 (tmm) outliers start: 76 outliers final: 36 residues processed: 442 average time/residue: 0.7096 time to fit residues: 383.7734 Evaluate side-chains 436 residues out of total 4554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 369 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 13 LYS Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 401 ARG Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 461 ASN Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain A residue 635 GLN Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 41 ARG Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 456 GLU Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 785 MET Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 285 MET Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 589 LYS Chi-restraints excluded: chain C residue 596 LYS Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 240 GLU Chi-restraints excluded: chain D residue 401 ARG Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 456 GLU Chi-restraints excluded: chain D residue 589 LYS Chi-restraints excluded: chain D residue 596 LYS Chi-restraints excluded: chain D residue 697 SER Chi-restraints excluded: chain D residue 719 VAL Chi-restraints excluded: chain D residue 726 ILE Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain E residue 339 GLU Chi-restraints excluded: chain E residue 401 ARG Chi-restraints excluded: chain E residue 407 THR Chi-restraints excluded: chain E residue 545 VAL Chi-restraints excluded: chain E residue 596 LYS Chi-restraints excluded: chain E residue 717 ASN Chi-restraints excluded: chain E residue 726 ILE Chi-restraints excluded: chain E residue 766 MET Chi-restraints excluded: chain E residue 785 MET Chi-restraints excluded: chain F residue 247 GLN Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain F residue 344 ASP Chi-restraints excluded: chain F residue 407 THR Chi-restraints excluded: chain F residue 584 LEU Chi-restraints excluded: chain F residue 589 LYS Chi-restraints excluded: chain F residue 678 VAL Chi-restraints excluded: chain F residue 719 VAL Chi-restraints excluded: chain F residue 766 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: [113, 278, 13, 200, 254, 253, 78, 471, 295, 175, 293] chunk 113 optimal weight: 0.0370 chunk 278 optimal weight: 0.7980 chunk 13 optimal weight: 0.2980 chunk 200 optimal weight: 0.9990 chunk 254 optimal weight: 0.1980 chunk 253 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 chunk 471 optimal weight: 1.9990 chunk 295 optimal weight: 6.9990 chunk 175 optimal weight: 3.9990 chunk 293 optimal weight: 2.9990 overall best weight: 0.4660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 493 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.183164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.122480 restraints weight = 51843.769| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.85 r_work: 0.3320 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 41394 Z= 0.107 Angle : 0.549 15.603 55794 Z= 0.275 Chirality : 0.041 0.281 6270 Planarity : 0.003 0.041 7128 Dihedral : 5.038 55.438 5492 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.84 % Favored : 96.98 % Rotamer: Outliers : 1.45 % Allowed : 22.97 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.73 (0.12), residues: 4932 helix: 1.73 (0.09), residues: 3318 sheet: 0.04 (0.40), residues: 192 loop : 0.03 (0.17), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 812 TYR 0.025 0.001 TYR E 711 PHE 0.017 0.001 PHE A 597 TRP 0.019 0.002 TRP B 137 HIS 0.006 0.001 HIS D 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (41382) covalent geometry : angle 0.54901 / 0.28 (55794) hydrogen bonds : bond 0.03199 / 2.09 ( 2377) hydrogen bonds : angle 3.62815 / 2.62 ( 7005) Misc. bond : bond 0.00112 / 0.07 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19667.84 seconds wall clock time: 333 minutes 50.90 seconds (20030.90 seconds total)