Starting phenix.real_space_refine on Tue Sep 24 08:29:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7alw_11820/09_2024/7alw_11820.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7alw_11820/09_2024/7alw_11820.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7alw_11820/09_2024/7alw_11820.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7alw_11820/09_2024/7alw_11820.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7alw_11820/09_2024/7alw_11820.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7alw_11820/09_2024/7alw_11820.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 162 5.16 5 C 31968 2.51 5 N 8442 2.21 5 O 9576 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 396 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 50148 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2786 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 331} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J, M, L, O, N, Q, P, R Time building chain proxies: 9.03, per 1000 atoms: 0.18 Number of scatterers: 50148 At special positions: 0 Unit cell: (188.238, 189.882, 132.342, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 162 16.00 O 9576 8.00 N 8442 7.00 C 31968 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=0, symmetry=0 Time building additional restraints: 9.57 Conformation dependent library (CDL) restraints added in 4.7 seconds 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11592 Finding SS restraints... Secondary structure from input PDB file: 270 helices and 72 sheets defined 45.6% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.26 Creating SS restraints... Processing helix chain 'A' and resid 393 through 406 removed outlier: 3.621A pdb=" N VAL A 397 " --> pdb=" O GLU A 393 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP A 404 " --> pdb=" O ALA A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 458 Processing helix chain 'A' and resid 476 through 487 removed outlier: 4.071A pdb=" N GLU A 481 " --> pdb=" O VAL A 477 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ARG A 482 " --> pdb=" O GLU A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 508 removed outlier: 3.654A pdb=" N LEU A 497 " --> pdb=" O HIS A 493 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N HIS A 500 " --> pdb=" O VAL A 496 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG A 506 " --> pdb=" O SER A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 525 removed outlier: 3.557A pdb=" N ARG A 519 " --> pdb=" O ILE A 515 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR A 520 " --> pdb=" O GLN A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 540 removed outlier: 3.655A pdb=" N ILE A 533 " --> pdb=" O TYR A 529 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ARG A 538 " --> pdb=" O LYS A 534 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE A 539 " --> pdb=" O GLU A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 555 removed outlier: 3.876A pdb=" N ARG A 551 " --> pdb=" O GLU A 547 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU A 555 " --> pdb=" O ARG A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 573 removed outlier: 3.674A pdb=" N ALA A 568 " --> pdb=" O SER A 564 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TRP A 572 " --> pdb=" O ALA A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 588 removed outlier: 3.532A pdb=" N SER A 588 " --> pdb=" O GLU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 598 removed outlier: 4.262A pdb=" N TYR A 596 " --> pdb=" O ARG A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 618 removed outlier: 3.733A pdb=" N GLU A 615 " --> pdb=" O ASP A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 621 No H-bonds generated for 'chain 'A' and resid 619 through 621' Processing helix chain 'A' and resid 637 through 649 Processing helix chain 'A' and resid 664 through 666 No H-bonds generated for 'chain 'A' and resid 664 through 666' Processing helix chain 'A' and resid 667 through 676 removed outlier: 3.528A pdb=" N ARG A 672 " --> pdb=" O ARG A 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 406 removed outlier: 3.620A pdb=" N VAL B 397 " --> pdb=" O GLU B 393 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP B 404 " --> pdb=" O ALA B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 458 Processing helix chain 'B' and resid 476 through 487 removed outlier: 4.071A pdb=" N GLU B 481 " --> pdb=" O VAL B 477 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ARG B 482 " --> pdb=" O GLU B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 508 removed outlier: 3.653A pdb=" N LEU B 497 " --> pdb=" O HIS B 493 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N HIS B 500 " --> pdb=" O VAL B 496 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG B 506 " --> pdb=" O SER B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 525 removed outlier: 3.557A pdb=" N ARG B 519 " --> pdb=" O ILE B 515 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR B 520 " --> pdb=" O GLN B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 540 removed outlier: 3.654A pdb=" N ILE B 533 " --> pdb=" O TYR B 529 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG B 538 " --> pdb=" O LYS B 534 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE B 539 " --> pdb=" O GLU B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 555 removed outlier: 3.876A pdb=" N ARG B 551 " --> pdb=" O GLU B 547 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU B 555 " --> pdb=" O ARG B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 573 removed outlier: 3.673A pdb=" N ALA B 568 " --> pdb=" O SER B 564 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TRP B 572 " --> pdb=" O ALA B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 588 removed outlier: 3.533A pdb=" N SER B 588 " --> pdb=" O GLU B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 598 removed outlier: 4.262A pdb=" N TYR B 596 " --> pdb=" O ARG B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 618 removed outlier: 3.733A pdb=" N GLU B 615 " --> pdb=" O ASP B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 621 No H-bonds generated for 'chain 'B' and resid 619 through 621' Processing helix chain 'B' and resid 637 through 649 Processing helix chain 'B' and resid 664 through 666 No H-bonds generated for 'chain 'B' and resid 664 through 666' Processing helix chain 'B' and resid 667 through 676 removed outlier: 3.528A pdb=" N ARG B 672 " --> pdb=" O ARG B 668 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 406 removed outlier: 3.620A pdb=" N VAL C 397 " --> pdb=" O GLU C 393 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP C 404 " --> pdb=" O ALA C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 458 Processing helix chain 'C' and resid 476 through 487 removed outlier: 4.071A pdb=" N GLU C 481 " --> pdb=" O VAL C 477 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ARG C 482 " --> pdb=" O GLU C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 508 removed outlier: 3.654A pdb=" N LEU C 497 " --> pdb=" O HIS C 493 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N HIS C 500 " --> pdb=" O VAL C 496 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG C 506 " --> pdb=" O SER C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 525 removed outlier: 3.557A pdb=" N ARG C 519 " --> pdb=" O ILE C 515 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR C 520 " --> pdb=" O GLN C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 540 removed outlier: 3.654A pdb=" N ILE C 533 " --> pdb=" O TYR C 529 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG C 538 " --> pdb=" O LYS C 534 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE C 539 " --> pdb=" O GLU C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 555 removed outlier: 3.876A pdb=" N ARG C 551 " --> pdb=" O GLU C 547 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU C 555 " --> pdb=" O ARG C 551 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 573 removed outlier: 3.674A pdb=" N ALA C 568 " --> pdb=" O SER C 564 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TRP C 572 " --> pdb=" O ALA C 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 588 removed outlier: 3.532A pdb=" N SER C 588 " --> pdb=" O GLU C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 598 removed outlier: 4.261A pdb=" N TYR C 596 " --> pdb=" O ARG C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 611 through 618 removed outlier: 3.733A pdb=" N GLU C 615 " --> pdb=" O ASP C 611 " (cutoff:3.500A) Processing helix chain 'C' and resid 619 through 621 No H-bonds generated for 'chain 'C' and resid 619 through 621' Processing helix chain 'C' and resid 637 through 649 Processing helix chain 'C' and resid 664 through 666 No H-bonds generated for 'chain 'C' and resid 664 through 666' Processing helix chain 'C' and resid 667 through 676 removed outlier: 3.528A pdb=" N ARG C 672 " --> pdb=" O ARG C 668 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 406 removed outlier: 3.620A pdb=" N VAL D 397 " --> pdb=" O GLU D 393 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP D 404 " --> pdb=" O ALA D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 476 through 487 removed outlier: 4.071A pdb=" N GLU D 481 " --> pdb=" O VAL D 477 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ARG D 482 " --> pdb=" O GLU D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 508 removed outlier: 3.653A pdb=" N LEU D 497 " --> pdb=" O HIS D 493 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N HIS D 500 " --> pdb=" O VAL D 496 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG D 506 " --> pdb=" O SER D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 525 removed outlier: 3.557A pdb=" N ARG D 519 " --> pdb=" O ILE D 515 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR D 520 " --> pdb=" O GLN D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 540 removed outlier: 3.654A pdb=" N ILE D 533 " --> pdb=" O TYR D 529 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ARG D 538 " --> pdb=" O LYS D 534 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE D 539 " --> pdb=" O GLU D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 555 removed outlier: 3.876A pdb=" N ARG D 551 " --> pdb=" O GLU D 547 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU D 555 " --> pdb=" O ARG D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 573 removed outlier: 3.673A pdb=" N ALA D 568 " --> pdb=" O SER D 564 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TRP D 572 " --> pdb=" O ALA D 568 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 588 removed outlier: 3.532A pdb=" N SER D 588 " --> pdb=" O GLU D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 598 removed outlier: 4.261A pdb=" N TYR D 596 " --> pdb=" O ARG D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 611 through 618 removed outlier: 3.733A pdb=" N GLU D 615 " --> pdb=" O ASP D 611 " (cutoff:3.500A) Processing helix chain 'D' and resid 619 through 621 No H-bonds generated for 'chain 'D' and resid 619 through 621' Processing helix chain 'D' and resid 637 through 649 Processing helix chain 'D' and resid 664 through 666 No H-bonds generated for 'chain 'D' and resid 664 through 666' Processing helix chain 'D' and resid 667 through 676 removed outlier: 3.527A pdb=" N ARG D 672 " --> pdb=" O ARG D 668 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 406 removed outlier: 3.621A pdb=" N VAL E 397 " --> pdb=" O GLU E 393 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP E 404 " --> pdb=" O ALA E 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 458 Processing helix chain 'E' and resid 476 through 487 removed outlier: 4.072A pdb=" N GLU E 481 " --> pdb=" O VAL E 477 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ARG E 482 " --> pdb=" O GLU E 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 492 through 508 removed outlier: 3.654A pdb=" N LEU E 497 " --> pdb=" O HIS E 493 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N HIS E 500 " --> pdb=" O VAL E 496 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG E 506 " --> pdb=" O SER E 502 " (cutoff:3.500A) Processing helix chain 'E' and resid 514 through 525 removed outlier: 3.558A pdb=" N ARG E 519 " --> pdb=" O ILE E 515 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR E 520 " --> pdb=" O GLN E 516 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 540 removed outlier: 3.654A pdb=" N ILE E 533 " --> pdb=" O TYR E 529 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG E 538 " --> pdb=" O LYS E 534 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE E 539 " --> pdb=" O GLU E 535 " (cutoff:3.500A) Processing helix chain 'E' and resid 541 through 555 removed outlier: 3.876A pdb=" N ARG E 551 " --> pdb=" O GLU E 547 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU E 555 " --> pdb=" O ARG E 551 " (cutoff:3.500A) Processing helix chain 'E' and resid 562 through 573 removed outlier: 3.674A pdb=" N ALA E 568 " --> pdb=" O SER E 564 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TRP E 572 " --> pdb=" O ALA E 568 " (cutoff:3.500A) Processing helix chain 'E' and resid 578 through 588 removed outlier: 3.532A pdb=" N SER E 588 " --> pdb=" O GLU E 584 " (cutoff:3.500A) Processing helix chain 'E' and resid 590 through 598 removed outlier: 4.261A pdb=" N TYR E 596 " --> pdb=" O ARG E 592 " (cutoff:3.500A) Processing helix chain 'E' and resid 611 through 618 removed outlier: 3.734A pdb=" N GLU E 615 " --> pdb=" O ASP E 611 " (cutoff:3.500A) Processing helix chain 'E' and resid 619 through 621 No H-bonds generated for 'chain 'E' and resid 619 through 621' Processing helix chain 'E' and resid 637 through 649 Processing helix chain 'E' and resid 664 through 666 No H-bonds generated for 'chain 'E' and resid 664 through 666' Processing helix chain 'E' and resid 667 through 676 removed outlier: 3.528A pdb=" N ARG E 672 " --> pdb=" O ARG E 668 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 406 removed outlier: 3.621A pdb=" N VAL F 397 " --> pdb=" O GLU F 393 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP F 404 " --> pdb=" O ALA F 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 458 Processing helix chain 'F' and resid 476 through 487 removed outlier: 4.072A pdb=" N GLU F 481 " --> pdb=" O VAL F 477 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ARG F 482 " --> pdb=" O GLU F 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 492 through 508 removed outlier: 3.654A pdb=" N LEU F 497 " --> pdb=" O HIS F 493 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N HIS F 500 " --> pdb=" O VAL F 496 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG F 506 " --> pdb=" O SER F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 514 through 525 removed outlier: 3.557A pdb=" N ARG F 519 " --> pdb=" O ILE F 515 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR F 520 " --> pdb=" O GLN F 516 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 540 removed outlier: 3.654A pdb=" N ILE F 533 " --> pdb=" O TYR F 529 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG F 538 " --> pdb=" O LYS F 534 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE F 539 " --> pdb=" O GLU F 535 " (cutoff:3.500A) Processing helix chain 'F' and resid 541 through 555 removed outlier: 3.875A pdb=" N ARG F 551 " --> pdb=" O GLU F 547 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU F 555 " --> pdb=" O ARG F 551 " (cutoff:3.500A) Processing helix chain 'F' and resid 562 through 573 removed outlier: 3.673A pdb=" N ALA F 568 " --> pdb=" O SER F 564 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TRP F 572 " --> pdb=" O ALA F 568 " (cutoff:3.500A) Processing helix chain 'F' and resid 578 through 588 removed outlier: 3.532A pdb=" N SER F 588 " --> pdb=" O GLU F 584 " (cutoff:3.500A) Processing helix chain 'F' and resid 590 through 598 removed outlier: 4.261A pdb=" N TYR F 596 " --> pdb=" O ARG F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 611 through 618 removed outlier: 3.733A pdb=" N GLU F 615 " --> pdb=" O ASP F 611 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 621 No H-bonds generated for 'chain 'F' and resid 619 through 621' Processing helix chain 'F' and resid 637 through 649 Processing helix chain 'F' and resid 664 through 666 No H-bonds generated for 'chain 'F' and resid 664 through 666' Processing helix chain 'F' and resid 667 through 676 removed outlier: 3.528A pdb=" N ARG F 672 " --> pdb=" O ARG F 668 " (cutoff:3.500A) Processing helix chain 'G' and resid 393 through 406 removed outlier: 3.621A pdb=" N VAL G 397 " --> pdb=" O GLU G 393 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP G 404 " --> pdb=" O ALA G 400 " (cutoff:3.500A) Processing helix chain 'G' and resid 453 through 458 Processing helix chain 'G' and resid 476 through 487 removed outlier: 4.071A pdb=" N GLU G 481 " --> pdb=" O VAL G 477 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ARG G 482 " --> pdb=" O GLU G 478 " (cutoff:3.500A) Processing helix chain 'G' and resid 492 through 508 removed outlier: 3.653A pdb=" N LEU G 497 " --> pdb=" O HIS G 493 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N HIS G 500 " --> pdb=" O VAL G 496 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG G 506 " --> pdb=" O SER G 502 " (cutoff:3.500A) Processing helix chain 'G' and resid 514 through 525 removed outlier: 3.557A pdb=" N ARG G 519 " --> pdb=" O ILE G 515 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR G 520 " --> pdb=" O GLN G 516 " (cutoff:3.500A) Processing helix chain 'G' and resid 529 through 540 removed outlier: 3.653A pdb=" N ILE G 533 " --> pdb=" O TYR G 529 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG G 538 " --> pdb=" O LYS G 534 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE G 539 " --> pdb=" O GLU G 535 " (cutoff:3.500A) Processing helix chain 'G' and resid 541 through 555 removed outlier: 3.876A pdb=" N ARG G 551 " --> pdb=" O GLU G 547 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU G 555 " --> pdb=" O ARG G 551 " (cutoff:3.500A) Processing helix chain 'G' and resid 562 through 573 removed outlier: 3.673A pdb=" N ALA G 568 " --> pdb=" O SER G 564 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TRP G 572 " --> pdb=" O ALA G 568 " (cutoff:3.500A) Processing helix chain 'G' and resid 578 through 588 removed outlier: 3.532A pdb=" N SER G 588 " --> pdb=" O GLU G 584 " (cutoff:3.500A) Processing helix chain 'G' and resid 590 through 598 removed outlier: 4.262A pdb=" N TYR G 596 " --> pdb=" O ARG G 592 " (cutoff:3.500A) Processing helix chain 'G' and resid 611 through 618 removed outlier: 3.733A pdb=" N GLU G 615 " --> pdb=" O ASP G 611 " (cutoff:3.500A) Processing helix chain 'G' and resid 619 through 621 No H-bonds generated for 'chain 'G' and resid 619 through 621' Processing helix chain 'G' and resid 637 through 649 Processing helix chain 'G' and resid 664 through 666 No H-bonds generated for 'chain 'G' and resid 664 through 666' Processing helix chain 'G' and resid 667 through 676 removed outlier: 3.528A pdb=" N ARG G 672 " --> pdb=" O ARG G 668 " (cutoff:3.500A) Processing helix chain 'H' and resid 393 through 406 removed outlier: 3.621A pdb=" N VAL H 397 " --> pdb=" O GLU H 393 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP H 404 " --> pdb=" O ALA H 400 " (cutoff:3.500A) Processing helix chain 'H' and resid 453 through 458 Processing helix chain 'H' and resid 476 through 487 removed outlier: 4.071A pdb=" N GLU H 481 " --> pdb=" O VAL H 477 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ARG H 482 " --> pdb=" O GLU H 478 " (cutoff:3.500A) Processing helix chain 'H' and resid 492 through 508 removed outlier: 3.653A pdb=" N LEU H 497 " --> pdb=" O HIS H 493 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N HIS H 500 " --> pdb=" O VAL H 496 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG H 506 " --> pdb=" O SER H 502 " (cutoff:3.500A) Processing helix chain 'H' and resid 514 through 525 removed outlier: 3.557A pdb=" N ARG H 519 " --> pdb=" O ILE H 515 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR H 520 " --> pdb=" O GLN H 516 " (cutoff:3.500A) Processing helix chain 'H' and resid 529 through 540 removed outlier: 3.655A pdb=" N ILE H 533 " --> pdb=" O TYR H 529 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG H 538 " --> pdb=" O LYS H 534 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE H 539 " --> pdb=" O GLU H 535 " (cutoff:3.500A) Processing helix chain 'H' and resid 541 through 555 removed outlier: 3.876A pdb=" N ARG H 551 " --> pdb=" O GLU H 547 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU H 555 " --> pdb=" O ARG H 551 " (cutoff:3.500A) Processing helix chain 'H' and resid 562 through 573 removed outlier: 3.674A pdb=" N ALA H 568 " --> pdb=" O SER H 564 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TRP H 572 " --> pdb=" O ALA H 568 " (cutoff:3.500A) Processing helix chain 'H' and resid 578 through 588 removed outlier: 3.532A pdb=" N SER H 588 " --> pdb=" O GLU H 584 " (cutoff:3.500A) Processing helix chain 'H' and resid 590 through 598 removed outlier: 4.262A pdb=" N TYR H 596 " --> pdb=" O ARG H 592 " (cutoff:3.500A) Processing helix chain 'H' and resid 611 through 618 removed outlier: 3.733A pdb=" N GLU H 615 " --> pdb=" O ASP H 611 " (cutoff:3.500A) Processing helix chain 'H' and resid 619 through 621 No H-bonds generated for 'chain 'H' and resid 619 through 621' Processing helix chain 'H' and resid 637 through 649 Processing helix chain 'H' and resid 664 through 666 No H-bonds generated for 'chain 'H' and resid 664 through 666' Processing helix chain 'H' and resid 667 through 676 removed outlier: 3.528A pdb=" N ARG H 672 " --> pdb=" O ARG H 668 " (cutoff:3.500A) Processing helix chain 'I' and resid 393 through 406 removed outlier: 3.620A pdb=" N VAL I 397 " --> pdb=" O GLU I 393 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP I 404 " --> pdb=" O ALA I 400 " (cutoff:3.500A) Processing helix chain 'I' and resid 453 through 458 Processing helix chain 'I' and resid 476 through 487 removed outlier: 4.071A pdb=" N GLU I 481 " --> pdb=" O VAL I 477 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ARG I 482 " --> pdb=" O GLU I 478 " (cutoff:3.500A) Processing helix chain 'I' and resid 492 through 508 removed outlier: 3.653A pdb=" N LEU I 497 " --> pdb=" O HIS I 493 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N HIS I 500 " --> pdb=" O VAL I 496 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG I 506 " --> pdb=" O SER I 502 " (cutoff:3.500A) Processing helix chain 'I' and resid 514 through 525 removed outlier: 3.557A pdb=" N ARG I 519 " --> pdb=" O ILE I 515 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR I 520 " --> pdb=" O GLN I 516 " (cutoff:3.500A) Processing helix chain 'I' and resid 529 through 540 removed outlier: 3.654A pdb=" N ILE I 533 " --> pdb=" O TYR I 529 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG I 538 " --> pdb=" O LYS I 534 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE I 539 " --> pdb=" O GLU I 535 " (cutoff:3.500A) Processing helix chain 'I' and resid 541 through 555 removed outlier: 3.876A pdb=" N ARG I 551 " --> pdb=" O GLU I 547 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU I 555 " --> pdb=" O ARG I 551 " (cutoff:3.500A) Processing helix chain 'I' and resid 562 through 573 removed outlier: 3.674A pdb=" N ALA I 568 " --> pdb=" O SER I 564 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TRP I 572 " --> pdb=" O ALA I 568 " (cutoff:3.500A) Processing helix chain 'I' and resid 578 through 588 removed outlier: 3.532A pdb=" N SER I 588 " --> pdb=" O GLU I 584 " (cutoff:3.500A) Processing helix chain 'I' and resid 590 through 598 removed outlier: 4.262A pdb=" N TYR I 596 " --> pdb=" O ARG I 592 " (cutoff:3.500A) Processing helix chain 'I' and resid 611 through 618 removed outlier: 3.733A pdb=" N GLU I 615 " --> pdb=" O ASP I 611 " (cutoff:3.500A) Processing helix chain 'I' and resid 619 through 621 No H-bonds generated for 'chain 'I' and resid 619 through 621' Processing helix chain 'I' and resid 637 through 649 Processing helix chain 'I' and resid 664 through 666 No H-bonds generated for 'chain 'I' and resid 664 through 666' Processing helix chain 'I' and resid 667 through 676 removed outlier: 3.528A pdb=" N ARG I 672 " --> pdb=" O ARG I 668 " (cutoff:3.500A) Processing helix chain 'J' and resid 393 through 406 removed outlier: 3.621A pdb=" N VAL J 397 " --> pdb=" O GLU J 393 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP J 404 " --> pdb=" O ALA J 400 " (cutoff:3.500A) Processing helix chain 'J' and resid 453 through 458 Processing helix chain 'J' and resid 476 through 487 removed outlier: 4.071A pdb=" N GLU J 481 " --> pdb=" O VAL J 477 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ARG J 482 " --> pdb=" O GLU J 478 " (cutoff:3.500A) Processing helix chain 'J' and resid 492 through 508 removed outlier: 3.654A pdb=" N LEU J 497 " --> pdb=" O HIS J 493 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N HIS J 500 " --> pdb=" O VAL J 496 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG J 506 " --> pdb=" O SER J 502 " (cutoff:3.500A) Processing helix chain 'J' and resid 514 through 525 removed outlier: 3.557A pdb=" N ARG J 519 " --> pdb=" O ILE J 515 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR J 520 " --> pdb=" O GLN J 516 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 540 removed outlier: 3.654A pdb=" N ILE J 533 " --> pdb=" O TYR J 529 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG J 538 " --> pdb=" O LYS J 534 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE J 539 " --> pdb=" O GLU J 535 " (cutoff:3.500A) Processing helix chain 'J' and resid 541 through 555 removed outlier: 3.876A pdb=" N ARG J 551 " --> pdb=" O GLU J 547 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU J 555 " --> pdb=" O ARG J 551 " (cutoff:3.500A) Processing helix chain 'J' and resid 562 through 573 removed outlier: 3.673A pdb=" N ALA J 568 " --> pdb=" O SER J 564 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TRP J 572 " --> pdb=" O ALA J 568 " (cutoff:3.500A) Processing helix chain 'J' and resid 578 through 588 removed outlier: 3.532A pdb=" N SER J 588 " --> pdb=" O GLU J 584 " (cutoff:3.500A) Processing helix chain 'J' and resid 590 through 598 removed outlier: 4.262A pdb=" N TYR J 596 " --> pdb=" O ARG J 592 " (cutoff:3.500A) Processing helix chain 'J' and resid 611 through 618 removed outlier: 3.733A pdb=" N GLU J 615 " --> pdb=" O ASP J 611 " (cutoff:3.500A) Processing helix chain 'J' and resid 619 through 621 No H-bonds generated for 'chain 'J' and resid 619 through 621' Processing helix chain 'J' and resid 637 through 649 Processing helix chain 'J' and resid 664 through 666 No H-bonds generated for 'chain 'J' and resid 664 through 666' Processing helix chain 'J' and resid 667 through 676 removed outlier: 3.528A pdb=" N ARG J 672 " --> pdb=" O ARG J 668 " (cutoff:3.500A) Processing helix chain 'K' and resid 393 through 406 removed outlier: 3.621A pdb=" N VAL K 397 " --> pdb=" O GLU K 393 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP K 404 " --> pdb=" O ALA K 400 " (cutoff:3.500A) Processing helix chain 'K' and resid 453 through 458 Processing helix chain 'K' and resid 476 through 487 removed outlier: 4.071A pdb=" N GLU K 481 " --> pdb=" O VAL K 477 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ARG K 482 " --> pdb=" O GLU K 478 " (cutoff:3.500A) Processing helix chain 'K' and resid 492 through 508 removed outlier: 3.653A pdb=" N LEU K 497 " --> pdb=" O HIS K 493 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N HIS K 500 " --> pdb=" O VAL K 496 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG K 506 " --> pdb=" O SER K 502 " (cutoff:3.500A) Processing helix chain 'K' and resid 514 through 525 removed outlier: 3.556A pdb=" N ARG K 519 " --> pdb=" O ILE K 515 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR K 520 " --> pdb=" O GLN K 516 " (cutoff:3.500A) Processing helix chain 'K' and resid 529 through 540 removed outlier: 3.655A pdb=" N ILE K 533 " --> pdb=" O TYR K 529 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG K 538 " --> pdb=" O LYS K 534 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE K 539 " --> pdb=" O GLU K 535 " (cutoff:3.500A) Processing helix chain 'K' and resid 541 through 555 removed outlier: 3.875A pdb=" N ARG K 551 " --> pdb=" O GLU K 547 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU K 555 " --> pdb=" O ARG K 551 " (cutoff:3.500A) Processing helix chain 'K' and resid 562 through 573 removed outlier: 3.674A pdb=" N ALA K 568 " --> pdb=" O SER K 564 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TRP K 572 " --> pdb=" O ALA K 568 " (cutoff:3.500A) Processing helix chain 'K' and resid 578 through 588 removed outlier: 3.532A pdb=" N SER K 588 " --> pdb=" O GLU K 584 " (cutoff:3.500A) Processing helix chain 'K' and resid 590 through 598 removed outlier: 4.262A pdb=" N TYR K 596 " --> pdb=" O ARG K 592 " (cutoff:3.500A) Processing helix chain 'K' and resid 611 through 618 removed outlier: 3.734A pdb=" N GLU K 615 " --> pdb=" O ASP K 611 " (cutoff:3.500A) Processing helix chain 'K' and resid 619 through 621 No H-bonds generated for 'chain 'K' and resid 619 through 621' Processing helix chain 'K' and resid 637 through 649 Processing helix chain 'K' and resid 664 through 666 No H-bonds generated for 'chain 'K' and resid 664 through 666' Processing helix chain 'K' and resid 667 through 676 removed outlier: 3.528A pdb=" N ARG K 672 " --> pdb=" O ARG K 668 " (cutoff:3.500A) Processing helix chain 'L' and resid 393 through 406 removed outlier: 3.621A pdb=" N VAL L 397 " --> pdb=" O GLU L 393 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP L 404 " --> pdb=" O ALA L 400 " (cutoff:3.500A) Processing helix chain 'L' and resid 453 through 458 Processing helix chain 'L' and resid 476 through 487 removed outlier: 4.071A pdb=" N GLU L 481 " --> pdb=" O VAL L 477 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ARG L 482 " --> pdb=" O GLU L 478 " (cutoff:3.500A) Processing helix chain 'L' and resid 492 through 508 removed outlier: 3.653A pdb=" N LEU L 497 " --> pdb=" O HIS L 493 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N HIS L 500 " --> pdb=" O VAL L 496 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG L 506 " --> pdb=" O SER L 502 " (cutoff:3.500A) Processing helix chain 'L' and resid 514 through 525 removed outlier: 3.557A pdb=" N ARG L 519 " --> pdb=" O ILE L 515 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR L 520 " --> pdb=" O GLN L 516 " (cutoff:3.500A) Processing helix chain 'L' and resid 529 through 540 removed outlier: 3.653A pdb=" N ILE L 533 " --> pdb=" O TYR L 529 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG L 538 " --> pdb=" O LYS L 534 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE L 539 " --> pdb=" O GLU L 535 " (cutoff:3.500A) Processing helix chain 'L' and resid 541 through 555 removed outlier: 3.876A pdb=" N ARG L 551 " --> pdb=" O GLU L 547 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU L 555 " --> pdb=" O ARG L 551 " (cutoff:3.500A) Processing helix chain 'L' and resid 562 through 573 removed outlier: 3.674A pdb=" N ALA L 568 " --> pdb=" O SER L 564 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TRP L 572 " --> pdb=" O ALA L 568 " (cutoff:3.500A) Processing helix chain 'L' and resid 578 through 588 removed outlier: 3.532A pdb=" N SER L 588 " --> pdb=" O GLU L 584 " (cutoff:3.500A) Processing helix chain 'L' and resid 590 through 598 removed outlier: 4.261A pdb=" N TYR L 596 " --> pdb=" O ARG L 592 " (cutoff:3.500A) Processing helix chain 'L' and resid 611 through 618 removed outlier: 3.734A pdb=" N GLU L 615 " --> pdb=" O ASP L 611 " (cutoff:3.500A) Processing helix chain 'L' and resid 619 through 621 No H-bonds generated for 'chain 'L' and resid 619 through 621' Processing helix chain 'L' and resid 637 through 649 Processing helix chain 'L' and resid 664 through 666 No H-bonds generated for 'chain 'L' and resid 664 through 666' Processing helix chain 'L' and resid 667 through 676 removed outlier: 3.528A pdb=" N ARG L 672 " --> pdb=" O ARG L 668 " (cutoff:3.500A) Processing helix chain 'M' and resid 393 through 406 removed outlier: 3.621A pdb=" N VAL M 397 " --> pdb=" O GLU M 393 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP M 404 " --> pdb=" O ALA M 400 " (cutoff:3.500A) Processing helix chain 'M' and resid 453 through 458 Processing helix chain 'M' and resid 476 through 487 removed outlier: 4.071A pdb=" N GLU M 481 " --> pdb=" O VAL M 477 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ARG M 482 " --> pdb=" O GLU M 478 " (cutoff:3.500A) Processing helix chain 'M' and resid 492 through 508 removed outlier: 3.654A pdb=" N LEU M 497 " --> pdb=" O HIS M 493 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N HIS M 500 " --> pdb=" O VAL M 496 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG M 506 " --> pdb=" O SER M 502 " (cutoff:3.500A) Processing helix chain 'M' and resid 514 through 525 removed outlier: 3.556A pdb=" N ARG M 519 " --> pdb=" O ILE M 515 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR M 520 " --> pdb=" O GLN M 516 " (cutoff:3.500A) Processing helix chain 'M' and resid 529 through 540 removed outlier: 3.654A pdb=" N ILE M 533 " --> pdb=" O TYR M 529 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ARG M 538 " --> pdb=" O LYS M 534 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE M 539 " --> pdb=" O GLU M 535 " (cutoff:3.500A) Processing helix chain 'M' and resid 541 through 555 removed outlier: 3.876A pdb=" N ARG M 551 " --> pdb=" O GLU M 547 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU M 555 " --> pdb=" O ARG M 551 " (cutoff:3.500A) Processing helix chain 'M' and resid 562 through 573 removed outlier: 3.674A pdb=" N ALA M 568 " --> pdb=" O SER M 564 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TRP M 572 " --> pdb=" O ALA M 568 " (cutoff:3.500A) Processing helix chain 'M' and resid 578 through 588 removed outlier: 3.532A pdb=" N SER M 588 " --> pdb=" O GLU M 584 " (cutoff:3.500A) Processing helix chain 'M' and resid 590 through 598 removed outlier: 4.262A pdb=" N TYR M 596 " --> pdb=" O ARG M 592 " (cutoff:3.500A) Processing helix chain 'M' and resid 611 through 618 removed outlier: 3.732A pdb=" N GLU M 615 " --> pdb=" O ASP M 611 " (cutoff:3.500A) Processing helix chain 'M' and resid 619 through 621 No H-bonds generated for 'chain 'M' and resid 619 through 621' Processing helix chain 'M' and resid 637 through 649 Processing helix chain 'M' and resid 664 through 666 No H-bonds generated for 'chain 'M' and resid 664 through 666' Processing helix chain 'M' and resid 667 through 676 removed outlier: 3.528A pdb=" N ARG M 672 " --> pdb=" O ARG M 668 " (cutoff:3.500A) Processing helix chain 'N' and resid 393 through 406 removed outlier: 3.622A pdb=" N VAL N 397 " --> pdb=" O GLU N 393 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP N 404 " --> pdb=" O ALA N 400 " (cutoff:3.500A) Processing helix chain 'N' and resid 453 through 458 Processing helix chain 'N' and resid 476 through 487 removed outlier: 4.071A pdb=" N GLU N 481 " --> pdb=" O VAL N 477 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ARG N 482 " --> pdb=" O GLU N 478 " (cutoff:3.500A) Processing helix chain 'N' and resid 492 through 508 removed outlier: 3.653A pdb=" N LEU N 497 " --> pdb=" O HIS N 493 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N HIS N 500 " --> pdb=" O VAL N 496 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG N 506 " --> pdb=" O SER N 502 " (cutoff:3.500A) Processing helix chain 'N' and resid 514 through 525 removed outlier: 3.558A pdb=" N ARG N 519 " --> pdb=" O ILE N 515 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR N 520 " --> pdb=" O GLN N 516 " (cutoff:3.500A) Processing helix chain 'N' and resid 529 through 540 removed outlier: 3.655A pdb=" N ILE N 533 " --> pdb=" O TYR N 529 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ARG N 538 " --> pdb=" O LYS N 534 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE N 539 " --> pdb=" O GLU N 535 " (cutoff:3.500A) Processing helix chain 'N' and resid 541 through 555 removed outlier: 3.876A pdb=" N ARG N 551 " --> pdb=" O GLU N 547 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU N 555 " --> pdb=" O ARG N 551 " (cutoff:3.500A) Processing helix chain 'N' and resid 562 through 573 removed outlier: 3.674A pdb=" N ALA N 568 " --> pdb=" O SER N 564 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TRP N 572 " --> pdb=" O ALA N 568 " (cutoff:3.500A) Processing helix chain 'N' and resid 578 through 588 removed outlier: 3.531A pdb=" N SER N 588 " --> pdb=" O GLU N 584 " (cutoff:3.500A) Processing helix chain 'N' and resid 590 through 598 removed outlier: 4.262A pdb=" N TYR N 596 " --> pdb=" O ARG N 592 " (cutoff:3.500A) Processing helix chain 'N' and resid 611 through 618 removed outlier: 3.733A pdb=" N GLU N 615 " --> pdb=" O ASP N 611 " (cutoff:3.500A) Processing helix chain 'N' and resid 619 through 621 No H-bonds generated for 'chain 'N' and resid 619 through 621' Processing helix chain 'N' and resid 637 through 649 Processing helix chain 'N' and resid 664 through 666 No H-bonds generated for 'chain 'N' and resid 664 through 666' Processing helix chain 'N' and resid 667 through 676 removed outlier: 3.528A pdb=" N ARG N 672 " --> pdb=" O ARG N 668 " (cutoff:3.500A) Processing helix chain 'O' and resid 393 through 406 removed outlier: 3.620A pdb=" N VAL O 397 " --> pdb=" O GLU O 393 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP O 404 " --> pdb=" O ALA O 400 " (cutoff:3.500A) Processing helix chain 'O' and resid 453 through 458 Processing helix chain 'O' and resid 476 through 487 removed outlier: 4.072A pdb=" N GLU O 481 " --> pdb=" O VAL O 477 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ARG O 482 " --> pdb=" O GLU O 478 " (cutoff:3.500A) Processing helix chain 'O' and resid 492 through 508 removed outlier: 3.653A pdb=" N LEU O 497 " --> pdb=" O HIS O 493 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N HIS O 500 " --> pdb=" O VAL O 496 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG O 506 " --> pdb=" O SER O 502 " (cutoff:3.500A) Processing helix chain 'O' and resid 514 through 525 removed outlier: 3.556A pdb=" N ARG O 519 " --> pdb=" O ILE O 515 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR O 520 " --> pdb=" O GLN O 516 " (cutoff:3.500A) Processing helix chain 'O' and resid 529 through 540 removed outlier: 3.653A pdb=" N ILE O 533 " --> pdb=" O TYR O 529 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ARG O 538 " --> pdb=" O LYS O 534 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE O 539 " --> pdb=" O GLU O 535 " (cutoff:3.500A) Processing helix chain 'O' and resid 541 through 555 removed outlier: 3.876A pdb=" N ARG O 551 " --> pdb=" O GLU O 547 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU O 555 " --> pdb=" O ARG O 551 " (cutoff:3.500A) Processing helix chain 'O' and resid 562 through 573 removed outlier: 3.673A pdb=" N ALA O 568 " --> pdb=" O SER O 564 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TRP O 572 " --> pdb=" O ALA O 568 " (cutoff:3.500A) Processing helix chain 'O' and resid 578 through 588 removed outlier: 3.533A pdb=" N SER O 588 " --> pdb=" O GLU O 584 " (cutoff:3.500A) Processing helix chain 'O' and resid 590 through 598 removed outlier: 4.261A pdb=" N TYR O 596 " --> pdb=" O ARG O 592 " (cutoff:3.500A) Processing helix chain 'O' and resid 611 through 618 removed outlier: 3.733A pdb=" N GLU O 615 " --> pdb=" O ASP O 611 " (cutoff:3.500A) Processing helix chain 'O' and resid 619 through 621 No H-bonds generated for 'chain 'O' and resid 619 through 621' Processing helix chain 'O' and resid 637 through 649 Processing helix chain 'O' and resid 664 through 666 No H-bonds generated for 'chain 'O' and resid 664 through 666' Processing helix chain 'O' and resid 667 through 676 removed outlier: 3.528A pdb=" N ARG O 672 " --> pdb=" O ARG O 668 " (cutoff:3.500A) Processing helix chain 'P' and resid 393 through 406 removed outlier: 3.621A pdb=" N VAL P 397 " --> pdb=" O GLU P 393 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP P 404 " --> pdb=" O ALA P 400 " (cutoff:3.500A) Processing helix chain 'P' and resid 453 through 458 Processing helix chain 'P' and resid 476 through 487 removed outlier: 4.072A pdb=" N GLU P 481 " --> pdb=" O VAL P 477 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ARG P 482 " --> pdb=" O GLU P 478 " (cutoff:3.500A) Processing helix chain 'P' and resid 492 through 508 removed outlier: 3.654A pdb=" N LEU P 497 " --> pdb=" O HIS P 493 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N HIS P 500 " --> pdb=" O VAL P 496 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG P 506 " --> pdb=" O SER P 502 " (cutoff:3.500A) Processing helix chain 'P' and resid 514 through 525 removed outlier: 3.557A pdb=" N ARG P 519 " --> pdb=" O ILE P 515 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR P 520 " --> pdb=" O GLN P 516 " (cutoff:3.500A) Processing helix chain 'P' and resid 529 through 540 removed outlier: 3.654A pdb=" N ILE P 533 " --> pdb=" O TYR P 529 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG P 538 " --> pdb=" O LYS P 534 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE P 539 " --> pdb=" O GLU P 535 " (cutoff:3.500A) Processing helix chain 'P' and resid 541 through 555 removed outlier: 3.876A pdb=" N ARG P 551 " --> pdb=" O GLU P 547 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU P 555 " --> pdb=" O ARG P 551 " (cutoff:3.500A) Processing helix chain 'P' and resid 562 through 573 removed outlier: 3.674A pdb=" N ALA P 568 " --> pdb=" O SER P 564 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TRP P 572 " --> pdb=" O ALA P 568 " (cutoff:3.500A) Processing helix chain 'P' and resid 578 through 588 removed outlier: 3.533A pdb=" N SER P 588 " --> pdb=" O GLU P 584 " (cutoff:3.500A) Processing helix chain 'P' and resid 590 through 598 removed outlier: 4.261A pdb=" N TYR P 596 " --> pdb=" O ARG P 592 " (cutoff:3.500A) Processing helix chain 'P' and resid 611 through 618 removed outlier: 3.733A pdb=" N GLU P 615 " --> pdb=" O ASP P 611 " (cutoff:3.500A) Processing helix chain 'P' and resid 619 through 621 No H-bonds generated for 'chain 'P' and resid 619 through 621' Processing helix chain 'P' and resid 637 through 649 Processing helix chain 'P' and resid 664 through 666 No H-bonds generated for 'chain 'P' and resid 664 through 666' Processing helix chain 'P' and resid 667 through 676 removed outlier: 3.528A pdb=" N ARG P 672 " --> pdb=" O ARG P 668 " (cutoff:3.500A) Processing helix chain 'Q' and resid 393 through 406 removed outlier: 3.621A pdb=" N VAL Q 397 " --> pdb=" O GLU Q 393 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP Q 404 " --> pdb=" O ALA Q 400 " (cutoff:3.500A) Processing helix chain 'Q' and resid 453 through 458 Processing helix chain 'Q' and resid 476 through 487 removed outlier: 4.071A pdb=" N GLU Q 481 " --> pdb=" O VAL Q 477 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ARG Q 482 " --> pdb=" O GLU Q 478 " (cutoff:3.500A) Processing helix chain 'Q' and resid 492 through 508 removed outlier: 3.652A pdb=" N LEU Q 497 " --> pdb=" O HIS Q 493 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N HIS Q 500 " --> pdb=" O VAL Q 496 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG Q 506 " --> pdb=" O SER Q 502 " (cutoff:3.500A) Processing helix chain 'Q' and resid 514 through 525 removed outlier: 3.558A pdb=" N ARG Q 519 " --> pdb=" O ILE Q 515 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR Q 520 " --> pdb=" O GLN Q 516 " (cutoff:3.500A) Processing helix chain 'Q' and resid 529 through 540 removed outlier: 3.654A pdb=" N ILE Q 533 " --> pdb=" O TYR Q 529 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG Q 538 " --> pdb=" O LYS Q 534 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE Q 539 " --> pdb=" O GLU Q 535 " (cutoff:3.500A) Processing helix chain 'Q' and resid 541 through 555 removed outlier: 3.876A pdb=" N ARG Q 551 " --> pdb=" O GLU Q 547 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU Q 555 " --> pdb=" O ARG Q 551 " (cutoff:3.500A) Processing helix chain 'Q' and resid 562 through 573 removed outlier: 3.674A pdb=" N ALA Q 568 " --> pdb=" O SER Q 564 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TRP Q 572 " --> pdb=" O ALA Q 568 " (cutoff:3.500A) Processing helix chain 'Q' and resid 578 through 588 removed outlier: 3.532A pdb=" N SER Q 588 " --> pdb=" O GLU Q 584 " (cutoff:3.500A) Processing helix chain 'Q' and resid 590 through 598 removed outlier: 4.262A pdb=" N TYR Q 596 " --> pdb=" O ARG Q 592 " (cutoff:3.500A) Processing helix chain 'Q' and resid 611 through 618 removed outlier: 3.734A pdb=" N GLU Q 615 " --> pdb=" O ASP Q 611 " (cutoff:3.500A) Processing helix chain 'Q' and resid 619 through 621 No H-bonds generated for 'chain 'Q' and resid 619 through 621' Processing helix chain 'Q' and resid 637 through 649 Processing helix chain 'Q' and resid 664 through 666 No H-bonds generated for 'chain 'Q' and resid 664 through 666' Processing helix chain 'Q' and resid 667 through 676 removed outlier: 3.528A pdb=" N ARG Q 672 " --> pdb=" O ARG Q 668 " (cutoff:3.500A) Processing helix chain 'R' and resid 393 through 406 removed outlier: 3.620A pdb=" N VAL R 397 " --> pdb=" O GLU R 393 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP R 404 " --> pdb=" O ALA R 400 " (cutoff:3.500A) Processing helix chain 'R' and resid 453 through 458 Processing helix chain 'R' and resid 476 through 487 removed outlier: 4.072A pdb=" N GLU R 481 " --> pdb=" O VAL R 477 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ARG R 482 " --> pdb=" O GLU R 478 " (cutoff:3.500A) Processing helix chain 'R' and resid 492 through 508 removed outlier: 3.653A pdb=" N LEU R 497 " --> pdb=" O HIS R 493 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N HIS R 500 " --> pdb=" O VAL R 496 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG R 506 " --> pdb=" O SER R 502 " (cutoff:3.500A) Processing helix chain 'R' and resid 514 through 525 removed outlier: 3.557A pdb=" N ARG R 519 " --> pdb=" O ILE R 515 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR R 520 " --> pdb=" O GLN R 516 " (cutoff:3.500A) Processing helix chain 'R' and resid 529 through 540 removed outlier: 3.654A pdb=" N ILE R 533 " --> pdb=" O TYR R 529 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG R 538 " --> pdb=" O LYS R 534 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE R 539 " --> pdb=" O GLU R 535 " (cutoff:3.500A) Processing helix chain 'R' and resid 541 through 555 removed outlier: 3.876A pdb=" N ARG R 551 " --> pdb=" O GLU R 547 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU R 555 " --> pdb=" O ARG R 551 " (cutoff:3.500A) Processing helix chain 'R' and resid 562 through 573 removed outlier: 3.673A pdb=" N ALA R 568 " --> pdb=" O SER R 564 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TRP R 572 " --> pdb=" O ALA R 568 " (cutoff:3.500A) Processing helix chain 'R' and resid 578 through 588 removed outlier: 3.532A pdb=" N SER R 588 " --> pdb=" O GLU R 584 " (cutoff:3.500A) Processing helix chain 'R' and resid 590 through 598 removed outlier: 4.261A pdb=" N TYR R 596 " --> pdb=" O ARG R 592 " (cutoff:3.500A) Processing helix chain 'R' and resid 611 through 618 removed outlier: 3.733A pdb=" N GLU R 615 " --> pdb=" O ASP R 611 " (cutoff:3.500A) Processing helix chain 'R' and resid 619 through 621 No H-bonds generated for 'chain 'R' and resid 619 through 621' Processing helix chain 'R' and resid 637 through 649 Processing helix chain 'R' and resid 664 through 666 No H-bonds generated for 'chain 'R' and resid 664 through 666' Processing helix chain 'R' and resid 667 through 676 removed outlier: 3.528A pdb=" N ARG R 672 " --> pdb=" O ARG R 668 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 412 through 417 removed outlier: 7.021A pdb=" N LEU A 373 " --> pdb=" O HIS A 413 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ARG A 415 " --> pdb=" O LEU A 373 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE A 375 " --> pdb=" O ARG A 415 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASN A 417 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N VAL A 377 " --> pdb=" O ASN A 417 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N GLU A 424 " --> pdb=" O ASP A 378 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TYR A 425 " --> pdb=" O ARG A 436 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ARG A 436 " --> pdb=" O TYR A 425 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE A 427 " --> pdb=" O VAL A 434 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.692A pdb=" N ARG A 447 " --> pdb=" O PHE A 491 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE A 491 " --> pdb=" O ARG A 447 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 604 through 605 Processing sheet with id=AA4, first strand: chain 'A' and resid 661 through 662 removed outlier: 6.968A pdb=" N LEU A 661 " --> pdb=" O LEU A 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 412 through 417 removed outlier: 7.021A pdb=" N LEU B 373 " --> pdb=" O HIS B 413 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ARG B 415 " --> pdb=" O LEU B 373 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE B 375 " --> pdb=" O ARG B 415 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASN B 417 " --> pdb=" O ILE B 375 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N VAL B 377 " --> pdb=" O ASN B 417 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLU B 424 " --> pdb=" O ASP B 378 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TYR B 425 " --> pdb=" O ARG B 436 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ARG B 436 " --> pdb=" O TYR B 425 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE B 427 " --> pdb=" O VAL B 434 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.691A pdb=" N ARG B 447 " --> pdb=" O PHE B 491 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE B 491 " --> pdb=" O ARG B 447 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 604 through 605 Processing sheet with id=AA8, first strand: chain 'B' and resid 661 through 662 removed outlier: 6.968A pdb=" N LEU B 661 " --> pdb=" O LEU B 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 412 through 417 removed outlier: 7.020A pdb=" N LEU C 373 " --> pdb=" O HIS C 413 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ARG C 415 " --> pdb=" O LEU C 373 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE C 375 " --> pdb=" O ARG C 415 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASN C 417 " --> pdb=" O ILE C 375 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N VAL C 377 " --> pdb=" O ASN C 417 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLU C 424 " --> pdb=" O ASP C 378 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TYR C 425 " --> pdb=" O ARG C 436 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ARG C 436 " --> pdb=" O TYR C 425 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE C 427 " --> pdb=" O VAL C 434 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.692A pdb=" N ARG C 447 " --> pdb=" O PHE C 491 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE C 491 " --> pdb=" O ARG C 447 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 604 through 605 Processing sheet with id=AB3, first strand: chain 'C' and resid 661 through 662 removed outlier: 6.969A pdb=" N LEU C 661 " --> pdb=" O LEU C 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 412 through 417 removed outlier: 7.021A pdb=" N LEU D 373 " --> pdb=" O HIS D 413 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ARG D 415 " --> pdb=" O LEU D 373 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE D 375 " --> pdb=" O ARG D 415 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASN D 417 " --> pdb=" O ILE D 375 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N VAL D 377 " --> pdb=" O ASN D 417 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLU D 424 " --> pdb=" O ASP D 378 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TYR D 425 " --> pdb=" O ARG D 436 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG D 436 " --> pdb=" O TYR D 425 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE D 427 " --> pdb=" O VAL D 434 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 473 through 474 removed outlier: 3.692A pdb=" N ARG D 447 " --> pdb=" O PHE D 491 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE D 491 " --> pdb=" O ARG D 447 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 604 through 605 Processing sheet with id=AB7, first strand: chain 'D' and resid 661 through 662 removed outlier: 6.967A pdb=" N LEU D 661 " --> pdb=" O LEU D 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'E' and resid 412 through 417 removed outlier: 7.021A pdb=" N LEU E 373 " --> pdb=" O HIS E 413 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ARG E 415 " --> pdb=" O LEU E 373 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE E 375 " --> pdb=" O ARG E 415 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASN E 417 " --> pdb=" O ILE E 375 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N VAL E 377 " --> pdb=" O ASN E 417 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLU E 424 " --> pdb=" O ASP E 378 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TYR E 425 " --> pdb=" O ARG E 436 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ARG E 436 " --> pdb=" O TYR E 425 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE E 427 " --> pdb=" O VAL E 434 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 473 through 474 removed outlier: 3.691A pdb=" N ARG E 447 " --> pdb=" O PHE E 491 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE E 491 " --> pdb=" O ARG E 447 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 604 through 605 Processing sheet with id=AC2, first strand: chain 'E' and resid 661 through 662 removed outlier: 6.968A pdb=" N LEU E 661 " --> pdb=" O LEU E 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'F' and resid 412 through 417 removed outlier: 7.021A pdb=" N LEU F 373 " --> pdb=" O HIS F 413 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ARG F 415 " --> pdb=" O LEU F 373 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE F 375 " --> pdb=" O ARG F 415 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASN F 417 " --> pdb=" O ILE F 375 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N VAL F 377 " --> pdb=" O ASN F 417 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N GLU F 424 " --> pdb=" O ASP F 378 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TYR F 425 " --> pdb=" O ARG F 436 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG F 436 " --> pdb=" O TYR F 425 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE F 427 " --> pdb=" O VAL F 434 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 473 through 474 removed outlier: 3.691A pdb=" N ARG F 447 " --> pdb=" O PHE F 491 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE F 491 " --> pdb=" O ARG F 447 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 604 through 605 Processing sheet with id=AC6, first strand: chain 'F' and resid 661 through 662 removed outlier: 6.968A pdb=" N LEU F 661 " --> pdb=" O LEU F 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'G' and resid 412 through 417 removed outlier: 7.021A pdb=" N LEU G 373 " --> pdb=" O HIS G 413 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ARG G 415 " --> pdb=" O LEU G 373 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE G 375 " --> pdb=" O ARG G 415 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASN G 417 " --> pdb=" O ILE G 375 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N VAL G 377 " --> pdb=" O ASN G 417 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLU G 424 " --> pdb=" O ASP G 378 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TYR G 425 " --> pdb=" O ARG G 436 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ARG G 436 " --> pdb=" O TYR G 425 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE G 427 " --> pdb=" O VAL G 434 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 473 through 474 removed outlier: 3.692A pdb=" N ARG G 447 " --> pdb=" O PHE G 491 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE G 491 " --> pdb=" O ARG G 447 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 604 through 605 Processing sheet with id=AD1, first strand: chain 'G' and resid 661 through 662 removed outlier: 6.969A pdb=" N LEU G 661 " --> pdb=" O LEU G 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'H' and resid 412 through 417 removed outlier: 7.021A pdb=" N LEU H 373 " --> pdb=" O HIS H 413 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ARG H 415 " --> pdb=" O LEU H 373 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ILE H 375 " --> pdb=" O ARG H 415 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASN H 417 " --> pdb=" O ILE H 375 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N VAL H 377 " --> pdb=" O ASN H 417 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLU H 424 " --> pdb=" O ASP H 378 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TYR H 425 " --> pdb=" O ARG H 436 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG H 436 " --> pdb=" O TYR H 425 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE H 427 " --> pdb=" O VAL H 434 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 473 through 474 removed outlier: 3.691A pdb=" N ARG H 447 " --> pdb=" O PHE H 491 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE H 491 " --> pdb=" O ARG H 447 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 604 through 605 Processing sheet with id=AD5, first strand: chain 'H' and resid 661 through 662 removed outlier: 6.968A pdb=" N LEU H 661 " --> pdb=" O LEU H 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'I' and resid 412 through 417 removed outlier: 7.020A pdb=" N LEU I 373 " --> pdb=" O HIS I 413 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ARG I 415 " --> pdb=" O LEU I 373 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ILE I 375 " --> pdb=" O ARG I 415 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASN I 417 " --> pdb=" O ILE I 375 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N VAL I 377 " --> pdb=" O ASN I 417 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLU I 424 " --> pdb=" O ASP I 378 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TYR I 425 " --> pdb=" O ARG I 436 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG I 436 " --> pdb=" O TYR I 425 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE I 427 " --> pdb=" O VAL I 434 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 473 through 474 removed outlier: 3.692A pdb=" N ARG I 447 " --> pdb=" O PHE I 491 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE I 491 " --> pdb=" O ARG I 447 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 604 through 605 Processing sheet with id=AD9, first strand: chain 'I' and resid 661 through 662 removed outlier: 6.968A pdb=" N LEU I 661 " --> pdb=" O LEU I 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'J' and resid 412 through 417 removed outlier: 7.021A pdb=" N LEU J 373 " --> pdb=" O HIS J 413 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ARG J 415 " --> pdb=" O LEU J 373 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE J 375 " --> pdb=" O ARG J 415 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASN J 417 " --> pdb=" O ILE J 375 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N VAL J 377 " --> pdb=" O ASN J 417 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N GLU J 424 " --> pdb=" O ASP J 378 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TYR J 425 " --> pdb=" O ARG J 436 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG J 436 " --> pdb=" O TYR J 425 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE J 427 " --> pdb=" O VAL J 434 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 473 through 474 removed outlier: 3.691A pdb=" N ARG J 447 " --> pdb=" O PHE J 491 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE J 491 " --> pdb=" O ARG J 447 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 604 through 605 Processing sheet with id=AE4, first strand: chain 'J' and resid 661 through 662 removed outlier: 6.968A pdb=" N LEU J 661 " --> pdb=" O LEU J 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'K' and resid 412 through 417 removed outlier: 7.021A pdb=" N LEU K 373 " --> pdb=" O HIS K 413 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ARG K 415 " --> pdb=" O LEU K 373 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ILE K 375 " --> pdb=" O ARG K 415 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASN K 417 " --> pdb=" O ILE K 375 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N VAL K 377 " --> pdb=" O ASN K 417 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N GLU K 424 " --> pdb=" O ASP K 378 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TYR K 425 " --> pdb=" O ARG K 436 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG K 436 " --> pdb=" O TYR K 425 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE K 427 " --> pdb=" O VAL K 434 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 473 through 474 removed outlier: 3.691A pdb=" N ARG K 447 " --> pdb=" O PHE K 491 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE K 491 " --> pdb=" O ARG K 447 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 604 through 605 Processing sheet with id=AE8, first strand: chain 'K' and resid 661 through 662 removed outlier: 6.968A pdb=" N LEU K 661 " --> pdb=" O LEU K 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'L' and resid 412 through 417 removed outlier: 7.021A pdb=" N LEU L 373 " --> pdb=" O HIS L 413 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ARG L 415 " --> pdb=" O LEU L 373 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ILE L 375 " --> pdb=" O ARG L 415 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASN L 417 " --> pdb=" O ILE L 375 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N VAL L 377 " --> pdb=" O ASN L 417 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLU L 424 " --> pdb=" O ASP L 378 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TYR L 425 " --> pdb=" O ARG L 436 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG L 436 " --> pdb=" O TYR L 425 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE L 427 " --> pdb=" O VAL L 434 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 473 through 474 removed outlier: 3.691A pdb=" N ARG L 447 " --> pdb=" O PHE L 491 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE L 491 " --> pdb=" O ARG L 447 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 604 through 605 Processing sheet with id=AF3, first strand: chain 'L' and resid 661 through 662 removed outlier: 6.967A pdb=" N LEU L 661 " --> pdb=" O LEU L 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'M' and resid 412 through 417 removed outlier: 7.021A pdb=" N LEU M 373 " --> pdb=" O HIS M 413 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ARG M 415 " --> pdb=" O LEU M 373 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ILE M 375 " --> pdb=" O ARG M 415 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASN M 417 " --> pdb=" O ILE M 375 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N VAL M 377 " --> pdb=" O ASN M 417 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLU M 424 " --> pdb=" O ASP M 378 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TYR M 425 " --> pdb=" O ARG M 436 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ARG M 436 " --> pdb=" O TYR M 425 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE M 427 " --> pdb=" O VAL M 434 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'M' and resid 473 through 474 removed outlier: 3.692A pdb=" N ARG M 447 " --> pdb=" O PHE M 491 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE M 491 " --> pdb=" O ARG M 447 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'M' and resid 604 through 605 Processing sheet with id=AF7, first strand: chain 'M' and resid 661 through 662 removed outlier: 6.968A pdb=" N LEU M 661 " --> pdb=" O LEU M 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'N' and resid 412 through 417 removed outlier: 7.020A pdb=" N LEU N 373 " --> pdb=" O HIS N 413 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ARG N 415 " --> pdb=" O LEU N 373 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE N 375 " --> pdb=" O ARG N 415 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASN N 417 " --> pdb=" O ILE N 375 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N VAL N 377 " --> pdb=" O ASN N 417 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLU N 424 " --> pdb=" O ASP N 378 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TYR N 425 " --> pdb=" O ARG N 436 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG N 436 " --> pdb=" O TYR N 425 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE N 427 " --> pdb=" O VAL N 434 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'N' and resid 473 through 474 removed outlier: 3.691A pdb=" N ARG N 447 " --> pdb=" O PHE N 491 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE N 491 " --> pdb=" O ARG N 447 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'N' and resid 604 through 605 Processing sheet with id=AG2, first strand: chain 'N' and resid 661 through 662 removed outlier: 6.968A pdb=" N LEU N 661 " --> pdb=" O LEU N 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'O' and resid 412 through 417 removed outlier: 7.020A pdb=" N LEU O 373 " --> pdb=" O HIS O 413 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ARG O 415 " --> pdb=" O LEU O 373 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE O 375 " --> pdb=" O ARG O 415 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASN O 417 " --> pdb=" O ILE O 375 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N VAL O 377 " --> pdb=" O ASN O 417 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLU O 424 " --> pdb=" O ASP O 378 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TYR O 425 " --> pdb=" O ARG O 436 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ARG O 436 " --> pdb=" O TYR O 425 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE O 427 " --> pdb=" O VAL O 434 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'O' and resid 473 through 474 removed outlier: 3.691A pdb=" N ARG O 447 " --> pdb=" O PHE O 491 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE O 491 " --> pdb=" O ARG O 447 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'O' and resid 604 through 605 Processing sheet with id=AG6, first strand: chain 'O' and resid 661 through 662 removed outlier: 6.968A pdb=" N LEU O 661 " --> pdb=" O LEU O 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 Processing sheet with id=AG7, first strand: chain 'P' and resid 412 through 417 removed outlier: 7.021A pdb=" N LEU P 373 " --> pdb=" O HIS P 413 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ARG P 415 " --> pdb=" O LEU P 373 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ILE P 375 " --> pdb=" O ARG P 415 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASN P 417 " --> pdb=" O ILE P 375 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N VAL P 377 " --> pdb=" O ASN P 417 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLU P 424 " --> pdb=" O ASP P 378 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TYR P 425 " --> pdb=" O ARG P 436 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG P 436 " --> pdb=" O TYR P 425 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE P 427 " --> pdb=" O VAL P 434 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'P' and resid 473 through 474 removed outlier: 3.691A pdb=" N ARG P 447 " --> pdb=" O PHE P 491 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE P 491 " --> pdb=" O ARG P 447 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'P' and resid 604 through 605 Processing sheet with id=AH1, first strand: chain 'P' and resid 661 through 662 removed outlier: 6.969A pdb=" N LEU P 661 " --> pdb=" O LEU P 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH1 Processing sheet with id=AH2, first strand: chain 'Q' and resid 412 through 417 removed outlier: 7.022A pdb=" N LEU Q 373 " --> pdb=" O HIS Q 413 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ARG Q 415 " --> pdb=" O LEU Q 373 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE Q 375 " --> pdb=" O ARG Q 415 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASN Q 417 " --> pdb=" O ILE Q 375 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N VAL Q 377 " --> pdb=" O ASN Q 417 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N GLU Q 424 " --> pdb=" O ASP Q 378 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TYR Q 425 " --> pdb=" O ARG Q 436 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG Q 436 " --> pdb=" O TYR Q 425 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE Q 427 " --> pdb=" O VAL Q 434 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Q' and resid 473 through 474 removed outlier: 3.691A pdb=" N ARG Q 447 " --> pdb=" O PHE Q 491 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE Q 491 " --> pdb=" O ARG Q 447 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'Q' and resid 604 through 605 Processing sheet with id=AH5, first strand: chain 'Q' and resid 661 through 662 removed outlier: 6.968A pdb=" N LEU Q 661 " --> pdb=" O LEU Q 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH5 Processing sheet with id=AH6, first strand: chain 'R' and resid 412 through 417 removed outlier: 7.020A pdb=" N LEU R 373 " --> pdb=" O HIS R 413 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ARG R 415 " --> pdb=" O LEU R 373 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE R 375 " --> pdb=" O ARG R 415 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASN R 417 " --> pdb=" O ILE R 375 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N VAL R 377 " --> pdb=" O ASN R 417 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N GLU R 424 " --> pdb=" O ASP R 378 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TYR R 425 " --> pdb=" O ARG R 436 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG R 436 " --> pdb=" O TYR R 425 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE R 427 " --> pdb=" O VAL R 434 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'R' and resid 473 through 474 removed outlier: 3.691A pdb=" N ARG R 447 " --> pdb=" O PHE R 491 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE R 491 " --> pdb=" O ARG R 447 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'R' and resid 604 through 605 Processing sheet with id=AH9, first strand: chain 'R' and resid 661 through 662 removed outlier: 6.969A pdb=" N LEU R 661 " --> pdb=" O LEU R 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH9 1584 hydrogen bonds defined for protein. 4698 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: 15.46 Time building geometry restraints manager: 11.57 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: 16786 1.34 - 1.46: 9349 1.46 - 1.57: 24589 1.57 - 1.69: 0 1.69 - 1.81: 288 Bond restraints: 51012 Sorted by residual: bond pdb=" CB VAL Q 553 " pdb=" CG2 VAL Q 553 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.84e+00 bond pdb=" CB VAL E 553 " pdb=" CG2 VAL E 553 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.79e+00 bond pdb=" CB VAL D 553 " pdb=" CG2 VAL D 553 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.79e+00 bond pdb=" CB VAL A 553 " pdb=" CG2 VAL A 553 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.78e+00 bond pdb=" CB VAL M 553 " pdb=" CG2 VAL M 553 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.76e+00 ... (remaining 51007 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 66116 2.09 - 4.17: 2494 4.17 - 6.26: 348 6.26 - 8.35: 0 8.35 - 10.43: 36 Bond angle restraints: 68994 Sorted by residual: angle pdb=" N ALA D 441 " pdb=" CA ALA D 441 " pdb=" C ALA D 441 " ideal model delta sigma weight residual 113.15 107.90 5.25 1.19e+00 7.06e-01 1.95e+01 angle pdb=" N ALA N 441 " pdb=" CA ALA N 441 " pdb=" C ALA N 441 " ideal model delta sigma weight residual 113.15 107.90 5.25 1.19e+00 7.06e-01 1.95e+01 angle pdb=" N ALA B 441 " pdb=" CA ALA B 441 " pdb=" C ALA B 441 " ideal model delta sigma weight residual 113.15 107.91 5.24 1.19e+00 7.06e-01 1.94e+01 angle pdb=" N ALA P 441 " pdb=" CA ALA P 441 " pdb=" C ALA P 441 " ideal model delta sigma weight residual 113.15 107.92 5.23 1.19e+00 7.06e-01 1.93e+01 angle pdb=" N ALA C 441 " pdb=" CA ALA C 441 " pdb=" C ALA C 441 " ideal model delta sigma weight residual 113.15 107.92 5.23 1.19e+00 7.06e-01 1.93e+01 ... (remaining 68989 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.90: 27073 16.90 - 33.80: 3238 33.80 - 50.69: 618 50.69 - 67.59: 139 67.59 - 84.49: 90 Dihedral angle restraints: 31158 sinusoidal: 13068 harmonic: 18090 Sorted by residual: dihedral pdb=" CA LEU J 385 " pdb=" C LEU J 385 " pdb=" N GLU J 386 " pdb=" CA GLU J 386 " ideal model delta harmonic sigma weight residual 180.00 137.64 42.36 0 5.00e+00 4.00e-02 7.18e+01 dihedral pdb=" CA LEU K 385 " pdb=" C LEU K 385 " pdb=" N GLU K 386 " pdb=" CA GLU K 386 " ideal model delta harmonic sigma weight residual 180.00 137.64 42.36 0 5.00e+00 4.00e-02 7.18e+01 dihedral pdb=" CA LEU A 385 " pdb=" C LEU A 385 " pdb=" N GLU A 386 " pdb=" CA GLU A 386 " ideal model delta harmonic sigma weight residual 180.00 137.66 42.34 0 5.00e+00 4.00e-02 7.17e+01 ... (remaining 31155 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 4416 0.041 - 0.083: 2567 0.083 - 0.124: 601 0.124 - 0.165: 138 0.165 - 0.207: 36 Chirality restraints: 7758 Sorted by residual: chirality pdb=" CA ILE M 458 " pdb=" N ILE M 458 " pdb=" C ILE M 458 " pdb=" CB ILE M 458 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA ILE Q 458 " pdb=" N ILE Q 458 " pdb=" C ILE Q 458 " pdb=" CB ILE Q 458 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA ILE D 458 " pdb=" N ILE D 458 " pdb=" C ILE D 458 " pdb=" CB ILE D 458 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 7755 not shown) Planarity restraints: 8928 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU D 639 " -0.007 2.00e-02 2.50e+03 1.46e-02 2.13e+00 pdb=" CD GLU D 639 " 0.025 2.00e-02 2.50e+03 pdb=" OE1 GLU D 639 " -0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU D 639 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU K 639 " -0.007 2.00e-02 2.50e+03 1.45e-02 2.11e+00 pdb=" CD GLU K 639 " 0.025 2.00e-02 2.50e+03 pdb=" OE1 GLU K 639 " -0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU K 639 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 639 " 0.007 2.00e-02 2.50e+03 1.44e-02 2.09e+00 pdb=" CD GLU C 639 " -0.025 2.00e-02 2.50e+03 pdb=" OE1 GLU C 639 " 0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU C 639 " 0.009 2.00e-02 2.50e+03 ... (remaining 8925 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 3031 2.70 - 3.25: 53341 3.25 - 3.80: 78002 3.80 - 4.35: 100259 4.35 - 4.90: 165771 Nonbonded interactions: 400404 Sorted by model distance: nonbonded pdb=" O LEU B 385 " pdb=" N ALA B 387 " model vdw 2.150 3.120 nonbonded pdb=" O LEU D 385 " pdb=" N ALA D 387 " model vdw 2.150 3.120 nonbonded pdb=" O LEU I 385 " pdb=" N ALA I 387 " model vdw 2.150 3.120 nonbonded pdb=" O LEU L 385 " pdb=" N ALA L 387 " model vdw 2.150 3.120 nonbonded pdb=" O LEU N 385 " pdb=" N ALA N 387 " model vdw 2.151 3.120 ... (remaining 400399 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.500 Check model and map are aligned: 0.300 Set scattering table: 0.360 Process input model: 71.450 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.170 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:2.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 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 : 0.010 0.056 51012 Z= 0.638 Angle : 0.960 10.433 68994 Z= 0.529 Chirality : 0.052 0.207 7758 Planarity : 0.004 0.036 8928 Dihedral : 15.639 84.488 19566 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.29 % Allowed : 17.33 % Favored : 82.37 % Rotamer: Outliers : 0.98 % Allowed : 7.52 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 16.67 % Twisted General : 0.60 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.45 (0.07), residues: 6156 helix: -4.69 (0.05), residues: 2736 sheet: -3.48 (0.17), residues: 558 loop : -3.96 (0.09), residues: 2862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP P 474 HIS 0.006 0.002 HIS P 493 PHE 0.014 0.003 PHE N 490 TYR 0.013 0.002 TYR D 529 ARG 0.007 0.001 ARG H 447 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 885 residues out of total 5526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 831 time to evaluate : 4.354 Fit side-chains REVERT: A 474 TRP cc_start: 0.7414 (m100) cc_final: 0.7184 (m100) REVERT: A 480 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7785 (pt0) REVERT: A 503 HIS cc_start: 0.8419 (OUTLIER) cc_final: 0.8150 (t-90) REVERT: B 393 GLU cc_start: 0.7794 (tp30) cc_final: 0.7092 (tp30) REVERT: B 474 TRP cc_start: 0.7385 (m100) cc_final: 0.7140 (m100) REVERT: B 480 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7974 (pt0) REVERT: B 503 HIS cc_start: 0.8433 (OUTLIER) cc_final: 0.8132 (t-90) REVERT: C 474 TRP cc_start: 0.7348 (m100) cc_final: 0.7035 (m100) REVERT: C 480 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7861 (pt0) REVERT: D 480 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7892 (pt0) REVERT: D 503 HIS cc_start: 0.8443 (OUTLIER) cc_final: 0.8176 (t-90) REVERT: E 480 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7830 (pt0) REVERT: E 503 HIS cc_start: 0.8396 (OUTLIER) cc_final: 0.8126 (t-90) REVERT: F 480 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7839 (pt0) REVERT: F 503 HIS cc_start: 0.8444 (OUTLIER) cc_final: 0.8150 (t-90) REVERT: F 525 MET cc_start: 0.9111 (mtp) cc_final: 0.8872 (mtp) REVERT: G 480 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.8078 (pt0) REVERT: H 393 GLU cc_start: 0.7769 (tp30) cc_final: 0.7216 (tp30) REVERT: H 474 TRP cc_start: 0.7396 (m100) cc_final: 0.6711 (m100) REVERT: H 480 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7848 (pt0) REVERT: H 503 HIS cc_start: 0.8495 (OUTLIER) cc_final: 0.8210 (t-90) REVERT: I 474 TRP cc_start: 0.7419 (m100) cc_final: 0.6734 (m100) REVERT: I 480 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7807 (pt0) REVERT: I 503 HIS cc_start: 0.8424 (OUTLIER) cc_final: 0.8172 (t-90) REVERT: J 480 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7905 (pt0) REVERT: J 503 HIS cc_start: 0.8405 (OUTLIER) cc_final: 0.8151 (t-90) REVERT: K 393 GLU cc_start: 0.7768 (tp30) cc_final: 0.7212 (tp30) REVERT: K 474 TRP cc_start: 0.7399 (m100) cc_final: 0.6756 (m100) REVERT: K 480 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7847 (pt0) REVERT: K 503 HIS cc_start: 0.8493 (OUTLIER) cc_final: 0.8211 (t-90) REVERT: L 474 TRP cc_start: 0.7425 (m100) cc_final: 0.6684 (m100) REVERT: L 480 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7809 (pt0) REVERT: L 503 HIS cc_start: 0.8432 (OUTLIER) cc_final: 0.8180 (t-90) REVERT: M 474 TRP cc_start: 0.7424 (m100) cc_final: 0.7188 (m100) REVERT: M 480 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7760 (pt0) REVERT: M 503 HIS cc_start: 0.8428 (OUTLIER) cc_final: 0.8157 (t-90) REVERT: N 393 GLU cc_start: 0.7788 (tp30) cc_final: 0.7079 (tp30) REVERT: N 474 TRP cc_start: 0.7388 (m100) cc_final: 0.7136 (m100) REVERT: N 480 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7973 (pt0) REVERT: N 503 HIS cc_start: 0.8435 (OUTLIER) cc_final: 0.8136 (t-90) REVERT: O 474 TRP cc_start: 0.7348 (m100) cc_final: 0.7038 (m100) REVERT: O 480 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7856 (pt0) REVERT: P 503 HIS cc_start: 0.8429 (OUTLIER) cc_final: 0.8134 (t-90) REVERT: Q 474 TRP cc_start: 0.7423 (m100) cc_final: 0.7209 (m100) REVERT: Q 480 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7834 (pt0) REVERT: Q 503 HIS cc_start: 0.8400 (OUTLIER) cc_final: 0.8133 (t-90) REVERT: R 480 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.8002 (pt0) REVERT: R 503 HIS cc_start: 0.8477 (OUTLIER) cc_final: 0.8183 (t-90) REVERT: R 525 MET cc_start: 0.9061 (mtp) cc_final: 0.8838 (mtp) outliers start: 54 outliers final: 0 residues processed: 850 average time/residue: 0.4908 time to fit residues: 692.0703 Evaluate side-chains 563 residues out of total 5526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 531 time to evaluate : 4.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 503 HIS Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain D residue 503 HIS Chi-restraints excluded: chain E residue 480 GLU Chi-restraints excluded: chain E residue 503 HIS Chi-restraints excluded: chain F residue 480 GLU Chi-restraints excluded: chain F residue 503 HIS Chi-restraints excluded: chain G residue 480 GLU Chi-restraints excluded: chain H residue 480 GLU Chi-restraints excluded: chain H residue 503 HIS Chi-restraints excluded: chain I residue 480 GLU Chi-restraints excluded: chain I residue 503 HIS Chi-restraints excluded: chain J residue 480 GLU Chi-restraints excluded: chain J residue 503 HIS Chi-restraints excluded: chain K residue 480 GLU Chi-restraints excluded: chain K residue 503 HIS Chi-restraints excluded: chain L residue 480 GLU Chi-restraints excluded: chain L residue 503 HIS Chi-restraints excluded: chain M residue 480 GLU Chi-restraints excluded: chain M residue 503 HIS Chi-restraints excluded: chain N residue 480 GLU Chi-restraints excluded: chain N residue 503 HIS Chi-restraints excluded: chain O residue 480 GLU Chi-restraints excluded: chain P residue 503 HIS Chi-restraints excluded: chain Q residue 480 GLU Chi-restraints excluded: chain Q residue 503 HIS Chi-restraints excluded: chain R residue 480 GLU Chi-restraints excluded: chain R residue 503 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 516 optimal weight: 0.9980 chunk 463 optimal weight: 3.9990 chunk 257 optimal weight: 0.7980 chunk 158 optimal weight: 0.9980 chunk 312 optimal weight: 3.9990 chunk 247 optimal weight: 5.9990 chunk 479 optimal weight: 0.7980 chunk 185 optimal weight: 0.8980 chunk 291 optimal weight: 0.9990 chunk 357 optimal weight: 0.7980 chunk 555 optimal weight: 10.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 HIS B 465 HIS C 465 HIS D 465 HIS E 465 HIS F 465 HIS G 465 HIS H 465 HIS I 465 HIS J 465 HIS K 465 HIS L 465 HIS M 465 HIS N 465 HIS O 465 HIS P 465 HIS Q 465 HIS R 465 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 51012 Z= 0.207 Angle : 0.728 11.936 68994 Z= 0.367 Chirality : 0.046 0.213 7758 Planarity : 0.004 0.029 8928 Dihedral : 7.524 45.408 6993 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.29 % Allowed : 10.36 % Favored : 89.34 % Rotamer: Outliers : 2.00 % Allowed : 11.00 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 11.57 % Twisted General : 0.60 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.05 (0.09), residues: 6156 helix: -3.02 (0.08), residues: 2862 sheet: -2.96 (0.14), residues: 810 loop : -3.74 (0.11), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP J 474 HIS 0.002 0.001 HIS G 503 PHE 0.010 0.001 PHE R 610 TYR 0.013 0.001 TYR E 460 ARG 0.007 0.001 ARG G 447 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 817 residues out of total 5526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 707 time to evaluate : 4.345 Fit side-chains REVERT: A 473 PHE cc_start: 0.7783 (m-80) cc_final: 0.7495 (m-80) REVERT: A 689 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8120 (mt-10) REVERT: B 473 PHE cc_start: 0.7758 (m-80) cc_final: 0.7257 (m-80) REVERT: B 689 GLU cc_start: 0.8372 (mt-10) cc_final: 0.8069 (mt-10) REVERT: C 473 PHE cc_start: 0.7718 (m-80) cc_final: 0.7067 (m-80) REVERT: C 689 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8126 (mt-10) REVERT: D 473 PHE cc_start: 0.7854 (m-80) cc_final: 0.7562 (m-80) REVERT: D 474 TRP cc_start: 0.7002 (m100) cc_final: 0.6735 (m100) REVERT: D 689 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8214 (mt-10) REVERT: E 689 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8123 (mt-10) REVERT: F 473 PHE cc_start: 0.7854 (m-80) cc_final: 0.7320 (m-80) REVERT: F 480 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7450 (tm-30) REVERT: F 689 GLU cc_start: 0.8483 (mt-10) cc_final: 0.7863 (mt-10) REVERT: G 474 TRP cc_start: 0.6862 (m100) cc_final: 0.6507 (m100) REVERT: G 689 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8143 (mt-10) REVERT: H 393 GLU cc_start: 0.7749 (tp30) cc_final: 0.7379 (tp30) REVERT: H 473 PHE cc_start: 0.7889 (m-80) cc_final: 0.7527 (m-80) REVERT: H 689 GLU cc_start: 0.8430 (mt-10) cc_final: 0.7816 (mt-10) REVERT: I 473 PHE cc_start: 0.7800 (m-80) cc_final: 0.7313 (m-80) REVERT: I 689 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8121 (mt-10) REVERT: J 473 PHE cc_start: 0.7891 (m-80) cc_final: 0.7362 (m-80) REVERT: J 689 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8146 (mt-10) REVERT: K 393 GLU cc_start: 0.7753 (tp30) cc_final: 0.7322 (tp30) REVERT: K 473 PHE cc_start: 0.7898 (m-80) cc_final: 0.7532 (m-80) REVERT: K 689 GLU cc_start: 0.8429 (mt-10) cc_final: 0.7783 (mt-10) REVERT: L 473 PHE cc_start: 0.7803 (m-80) cc_final: 0.7314 (m-80) REVERT: L 689 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8124 (mt-10) REVERT: M 473 PHE cc_start: 0.7804 (m-80) cc_final: 0.7503 (m-80) REVERT: M 689 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8105 (mt-10) REVERT: N 473 PHE cc_start: 0.7749 (m-80) cc_final: 0.7257 (m-80) REVERT: N 689 GLU cc_start: 0.8358 (mt-10) cc_final: 0.8068 (mt-10) REVERT: O 473 PHE cc_start: 0.7725 (m-80) cc_final: 0.7069 (m-80) REVERT: O 480 GLU cc_start: 0.8054 (tm-30) cc_final: 0.7409 (tm-30) REVERT: O 689 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8142 (mt-10) REVERT: P 689 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8228 (mt-10) REVERT: Q 689 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8120 (mt-10) REVERT: R 417 ASN cc_start: 0.8068 (m-40) cc_final: 0.7830 (m-40) REVERT: R 473 PHE cc_start: 0.7838 (m-80) cc_final: 0.7277 (m-80) REVERT: R 480 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7806 (pt0) REVERT: R 689 GLU cc_start: 0.8492 (mt-10) cc_final: 0.7860 (mt-10) outliers start: 110 outliers final: 82 residues processed: 805 average time/residue: 0.4513 time to fit residues: 626.1179 Evaluate side-chains 602 residues out of total 5526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 520 time to evaluate : 4.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 472 THR Chi-restraints excluded: chain B residue 493 HIS Chi-restraints excluded: chain B residue 503 HIS Chi-restraints excluded: chain B residue 665 MET Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain C residue 503 HIS Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 503 HIS Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 493 HIS Chi-restraints excluded: chain E residue 503 HIS Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 432 VAL Chi-restraints excluded: chain F residue 472 THR Chi-restraints excluded: chain F residue 503 HIS Chi-restraints excluded: chain F residue 665 MET Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 432 VAL Chi-restraints excluded: chain G residue 493 HIS Chi-restraints excluded: chain G residue 503 HIS Chi-restraints excluded: chain H residue 390 LEU Chi-restraints excluded: chain H residue 432 VAL Chi-restraints excluded: chain H residue 472 THR Chi-restraints excluded: chain H residue 503 HIS Chi-restraints excluded: chain I residue 390 LEU Chi-restraints excluded: chain I residue 432 VAL Chi-restraints excluded: chain I residue 472 THR Chi-restraints excluded: chain I residue 503 HIS Chi-restraints excluded: chain I residue 665 MET Chi-restraints excluded: chain J residue 390 LEU Chi-restraints excluded: chain J residue 432 VAL Chi-restraints excluded: chain J residue 472 THR Chi-restraints excluded: chain J residue 503 HIS Chi-restraints excluded: chain K residue 390 LEU Chi-restraints excluded: chain K residue 432 VAL Chi-restraints excluded: chain K residue 472 THR Chi-restraints excluded: chain K residue 503 HIS Chi-restraints excluded: chain L residue 390 LEU Chi-restraints excluded: chain L residue 432 VAL Chi-restraints excluded: chain L residue 472 THR Chi-restraints excluded: chain L residue 503 HIS Chi-restraints excluded: chain L residue 665 MET Chi-restraints excluded: chain M residue 390 LEU Chi-restraints excluded: chain M residue 432 VAL Chi-restraints excluded: chain M residue 472 THR Chi-restraints excluded: chain M residue 503 HIS Chi-restraints excluded: chain M residue 696 ILE Chi-restraints excluded: chain N residue 390 LEU Chi-restraints excluded: chain N residue 432 VAL Chi-restraints excluded: chain N residue 472 THR Chi-restraints excluded: chain N residue 493 HIS Chi-restraints excluded: chain N residue 503 HIS Chi-restraints excluded: chain N residue 665 MET Chi-restraints excluded: chain O residue 390 LEU Chi-restraints excluded: chain O residue 432 VAL Chi-restraints excluded: chain O residue 472 THR Chi-restraints excluded: chain O residue 503 HIS Chi-restraints excluded: chain P residue 390 LEU Chi-restraints excluded: chain P residue 432 VAL Chi-restraints excluded: chain P residue 472 THR Chi-restraints excluded: chain P residue 503 HIS Chi-restraints excluded: chain Q residue 390 LEU Chi-restraints excluded: chain Q residue 432 VAL Chi-restraints excluded: chain Q residue 472 THR Chi-restraints excluded: chain Q residue 493 HIS Chi-restraints excluded: chain Q residue 503 HIS Chi-restraints excluded: chain R residue 390 LEU Chi-restraints excluded: chain R residue 432 VAL Chi-restraints excluded: chain R residue 472 THR Chi-restraints excluded: chain R residue 503 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 308 optimal weight: 6.9990 chunk 172 optimal weight: 6.9990 chunk 462 optimal weight: 1.9990 chunk 378 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 556 optimal weight: 9.9990 chunk 601 optimal weight: 0.6980 chunk 495 optimal weight: 0.1980 chunk 552 optimal weight: 2.9990 chunk 189 optimal weight: 0.9990 chunk 446 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN B 452 GLN C 452 GLN D 452 GLN E 452 GLN F 452 GLN G 452 GLN H 452 GLN I 452 GLN I 500 HIS J 452 GLN K 452 GLN L 452 GLN L 500 HIS M 452 GLN N 452 GLN O 452 GLN P 452 GLN Q 452 GLN R 452 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 51012 Z= 0.231 Angle : 0.693 11.314 68994 Z= 0.348 Chirality : 0.047 0.184 7758 Planarity : 0.004 0.046 8928 Dihedral : 6.669 47.569 6942 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.29 % Allowed : 10.40 % Favored : 89.31 % Rotamer: Outliers : 3.20 % Allowed : 13.76 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 12.04 % Twisted General : 0.60 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.06 (0.10), residues: 6156 helix: -2.33 (0.08), residues: 2862 sheet: -2.41 (0.19), residues: 486 loop : -3.11 (0.11), residues: 2808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 474 HIS 0.006 0.001 HIS O 503 PHE 0.013 0.001 PHE G 473 TYR 0.026 0.001 TYR Q 460 ARG 0.005 0.000 ARG B 506 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 852 residues out of total 5526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 676 time to evaluate : 4.347 Fit side-chains REVERT: A 473 PHE cc_start: 0.7595 (m-80) cc_final: 0.7353 (m-80) REVERT: A 503 HIS cc_start: 0.8403 (OUTLIER) cc_final: 0.7923 (t-90) REVERT: A 689 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8165 (mt-10) REVERT: B 473 PHE cc_start: 0.7619 (m-80) cc_final: 0.7108 (m-80) REVERT: B 503 HIS cc_start: 0.8443 (OUTLIER) cc_final: 0.7998 (t-90) REVERT: B 562 MET cc_start: 0.8668 (tpt) cc_final: 0.8356 (tpt) REVERT: B 639 GLU cc_start: 0.8005 (tp30) cc_final: 0.7756 (tp30) REVERT: B 689 GLU cc_start: 0.8366 (mt-10) cc_final: 0.8090 (mt-10) REVERT: C 473 PHE cc_start: 0.7541 (m-80) cc_final: 0.6860 (m-80) REVERT: C 639 GLU cc_start: 0.8004 (tp30) cc_final: 0.7779 (tp30) REVERT: C 689 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8137 (mt-10) REVERT: D 473 PHE cc_start: 0.7843 (m-80) cc_final: 0.7632 (m-80) REVERT: D 689 GLU cc_start: 0.8410 (mt-10) cc_final: 0.8159 (mt-10) REVERT: E 503 HIS cc_start: 0.8381 (OUTLIER) cc_final: 0.7484 (t-90) REVERT: E 507 GLU cc_start: 0.7077 (mt-10) cc_final: 0.6538 (mt-10) REVERT: E 689 GLU cc_start: 0.8342 (mt-10) cc_final: 0.8123 (mt-10) REVERT: F 473 PHE cc_start: 0.7764 (m-80) cc_final: 0.7142 (m-80) REVERT: F 480 GLU cc_start: 0.7982 (tm-30) cc_final: 0.7390 (tm-30) REVERT: F 503 HIS cc_start: 0.8467 (OUTLIER) cc_final: 0.8028 (t-90) REVERT: F 689 GLU cc_start: 0.8351 (mt-10) cc_final: 0.8126 (mt-10) REVERT: G 417 ASN cc_start: 0.8022 (m-40) cc_final: 0.7749 (m-40) REVERT: G 473 PHE cc_start: 0.7737 (m-80) cc_final: 0.7236 (m-80) REVERT: G 689 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8183 (mt-10) REVERT: H 393 GLU cc_start: 0.7729 (tp30) cc_final: 0.7339 (tp30) REVERT: H 473 PHE cc_start: 0.7688 (m-80) cc_final: 0.7263 (m-80) REVERT: H 639 GLU cc_start: 0.7994 (tp30) cc_final: 0.7729 (tp30) REVERT: H 689 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8209 (mt-10) REVERT: I 473 PHE cc_start: 0.7683 (m-80) cc_final: 0.7186 (m-80) REVERT: I 503 HIS cc_start: 0.8451 (OUTLIER) cc_final: 0.8043 (t-90) REVERT: I 689 GLU cc_start: 0.8393 (mt-10) cc_final: 0.8143 (mt-10) REVERT: J 473 PHE cc_start: 0.7623 (m-80) cc_final: 0.7165 (m-80) REVERT: J 639 GLU cc_start: 0.8001 (tp30) cc_final: 0.7801 (tp30) REVERT: J 689 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8154 (mt-10) REVERT: K 393 GLU cc_start: 0.7722 (tp30) cc_final: 0.7323 (tp30) REVERT: K 473 PHE cc_start: 0.7703 (m-80) cc_final: 0.7278 (m-80) REVERT: K 639 GLU cc_start: 0.7991 (tp30) cc_final: 0.7733 (tp30) REVERT: K 689 GLU cc_start: 0.8428 (mt-10) cc_final: 0.8188 (mt-10) REVERT: L 473 PHE cc_start: 0.7685 (m-80) cc_final: 0.7188 (m-80) REVERT: L 503 HIS cc_start: 0.8454 (OUTLIER) cc_final: 0.8053 (t-90) REVERT: L 689 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8144 (mt-10) REVERT: M 473 PHE cc_start: 0.7624 (m-80) cc_final: 0.7367 (m-80) REVERT: M 503 HIS cc_start: 0.8405 (OUTLIER) cc_final: 0.7925 (t-90) REVERT: M 689 GLU cc_start: 0.8393 (mt-10) cc_final: 0.8155 (mt-10) REVERT: N 473 PHE cc_start: 0.7618 (m-80) cc_final: 0.7108 (m-80) REVERT: N 503 HIS cc_start: 0.8440 (OUTLIER) cc_final: 0.8002 (t-90) REVERT: N 562 MET cc_start: 0.8654 (tpt) cc_final: 0.8367 (tpt) REVERT: N 639 GLU cc_start: 0.7997 (tp30) cc_final: 0.7752 (tp30) REVERT: N 689 GLU cc_start: 0.8337 (mt-10) cc_final: 0.8074 (mt-10) REVERT: O 473 PHE cc_start: 0.7552 (m-80) cc_final: 0.6862 (m-80) REVERT: O 639 GLU cc_start: 0.8014 (tp30) cc_final: 0.7791 (tp30) REVERT: O 689 GLU cc_start: 0.8352 (mt-10) cc_final: 0.8122 (mt-10) REVERT: P 474 TRP cc_start: 0.6840 (m100) cc_final: 0.6583 (m100) REVERT: P 480 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7397 (pt0) REVERT: P 562 MET cc_start: 0.8491 (tpt) cc_final: 0.8122 (tpt) REVERT: P 639 GLU cc_start: 0.8021 (tp30) cc_final: 0.7772 (tp30) REVERT: P 689 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8159 (mt-10) REVERT: Q 503 HIS cc_start: 0.8369 (OUTLIER) cc_final: 0.7485 (t-90) REVERT: Q 507 GLU cc_start: 0.7086 (mt-10) cc_final: 0.6549 (mt-10) REVERT: Q 689 GLU cc_start: 0.8346 (mt-10) cc_final: 0.8134 (mt-10) REVERT: R 473 PHE cc_start: 0.7704 (m-80) cc_final: 0.7082 (m-80) REVERT: R 480 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7725 (pt0) REVERT: R 503 HIS cc_start: 0.8504 (OUTLIER) cc_final: 0.8059 (t-90) REVERT: R 689 GLU cc_start: 0.8426 (mt-10) cc_final: 0.8201 (mt-10) outliers start: 176 outliers final: 94 residues processed: 842 average time/residue: 0.4503 time to fit residues: 653.5158 Evaluate side-chains 606 residues out of total 5526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 501 time to evaluate : 4.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 472 THR Chi-restraints excluded: chain B residue 503 HIS Chi-restraints excluded: chain B residue 525 MET Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 665 MET Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 503 HIS Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 503 HIS Chi-restraints excluded: chain E residue 540 VAL Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 432 VAL Chi-restraints excluded: chain F residue 472 THR Chi-restraints excluded: chain F residue 503 HIS Chi-restraints excluded: chain F residue 540 VAL Chi-restraints excluded: chain F residue 665 MET Chi-restraints excluded: chain F residue 690 LEU Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 432 VAL Chi-restraints excluded: chain G residue 480 GLU Chi-restraints excluded: chain G residue 493 HIS Chi-restraints excluded: chain G residue 503 HIS Chi-restraints excluded: chain G residue 540 VAL Chi-restraints excluded: chain H residue 390 LEU Chi-restraints excluded: chain H residue 432 VAL Chi-restraints excluded: chain H residue 472 THR Chi-restraints excluded: chain H residue 493 HIS Chi-restraints excluded: chain H residue 503 HIS Chi-restraints excluded: chain H residue 540 VAL Chi-restraints excluded: chain I residue 390 LEU Chi-restraints excluded: chain I residue 432 VAL Chi-restraints excluded: chain I residue 472 THR Chi-restraints excluded: chain I residue 503 HIS Chi-restraints excluded: chain I residue 525 MET Chi-restraints excluded: chain I residue 540 VAL Chi-restraints excluded: chain J residue 390 LEU Chi-restraints excluded: chain J residue 432 VAL Chi-restraints excluded: chain J residue 472 THR Chi-restraints excluded: chain J residue 493 HIS Chi-restraints excluded: chain J residue 503 HIS Chi-restraints excluded: chain K residue 390 LEU Chi-restraints excluded: chain K residue 432 VAL Chi-restraints excluded: chain K residue 472 THR Chi-restraints excluded: chain K residue 493 HIS Chi-restraints excluded: chain K residue 503 HIS Chi-restraints excluded: chain K residue 540 VAL Chi-restraints excluded: chain L residue 390 LEU Chi-restraints excluded: chain L residue 432 VAL Chi-restraints excluded: chain L residue 472 THR Chi-restraints excluded: chain L residue 503 HIS Chi-restraints excluded: chain L residue 525 MET Chi-restraints excluded: chain L residue 540 VAL Chi-restraints excluded: chain M residue 390 LEU Chi-restraints excluded: chain M residue 432 VAL Chi-restraints excluded: chain M residue 472 THR Chi-restraints excluded: chain M residue 503 HIS Chi-restraints excluded: chain M residue 540 VAL Chi-restraints excluded: chain M residue 690 LEU Chi-restraints excluded: chain M residue 696 ILE Chi-restraints excluded: chain N residue 390 LEU Chi-restraints excluded: chain N residue 432 VAL Chi-restraints excluded: chain N residue 472 THR Chi-restraints excluded: chain N residue 503 HIS Chi-restraints excluded: chain N residue 525 MET Chi-restraints excluded: chain N residue 622 VAL Chi-restraints excluded: chain N residue 665 MET Chi-restraints excluded: chain O residue 390 LEU Chi-restraints excluded: chain O residue 432 VAL Chi-restraints excluded: chain O residue 472 THR Chi-restraints excluded: chain O residue 493 HIS Chi-restraints excluded: chain O residue 540 VAL Chi-restraints excluded: chain P residue 390 LEU Chi-restraints excluded: chain P residue 432 VAL Chi-restraints excluded: chain P residue 472 THR Chi-restraints excluded: chain P residue 480 GLU Chi-restraints excluded: chain P residue 503 HIS Chi-restraints excluded: chain P residue 540 VAL Chi-restraints excluded: chain Q residue 390 LEU Chi-restraints excluded: chain Q residue 432 VAL Chi-restraints excluded: chain Q residue 472 THR Chi-restraints excluded: chain Q residue 503 HIS Chi-restraints excluded: chain Q residue 540 VAL Chi-restraints excluded: chain R residue 390 LEU Chi-restraints excluded: chain R residue 432 VAL Chi-restraints excluded: chain R residue 472 THR Chi-restraints excluded: chain R residue 503 HIS Chi-restraints excluded: chain R residue 665 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 550 optimal weight: 6.9990 chunk 418 optimal weight: 5.9990 chunk 288 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 265 optimal weight: 3.9990 chunk 373 optimal weight: 5.9990 chunk 558 optimal weight: 3.9990 chunk 591 optimal weight: 0.7980 chunk 291 optimal weight: 1.9990 chunk 529 optimal weight: 0.4980 chunk 159 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN B 452 GLN B 500 HIS C 452 GLN D 452 GLN D 500 HIS ** E 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 500 HIS F 452 GLN G 452 GLN H 452 GLN H 500 HIS I 452 GLN J 452 GLN K 452 GLN K 500 HIS L 452 GLN M 452 GLN N 452 GLN N 500 HIS O 452 GLN P 452 GLN P 500 HIS ** Q 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 500 HIS R 452 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 51012 Z= 0.198 Angle : 0.698 11.423 68994 Z= 0.345 Chirality : 0.046 0.219 7758 Planarity : 0.003 0.050 8928 Dihedral : 6.398 47.668 6942 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.67 % Favored : 90.04 % Rotamer: Outliers : 2.96 % Allowed : 15.58 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.31 % Twisted General : 0.60 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.89 (0.10), residues: 6156 helix: -1.82 (0.09), residues: 2808 sheet: -1.93 (0.18), residues: 666 loop : -3.60 (0.11), residues: 2682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 474 HIS 0.004 0.001 HIS C 503 PHE 0.008 0.001 PHE M 473 TYR 0.024 0.001 TYR Q 460 ARG 0.007 0.000 ARG H 506 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 5526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 566 time to evaluate : 4.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 503 HIS cc_start: 0.8350 (OUTLIER) cc_final: 0.7958 (t-90) REVERT: A 689 GLU cc_start: 0.8340 (mt-10) cc_final: 0.7718 (mt-10) REVERT: B 473 PHE cc_start: 0.7602 (m-80) cc_final: 0.7106 (m-80) REVERT: B 503 HIS cc_start: 0.8401 (OUTLIER) cc_final: 0.8059 (t-90) REVERT: B 562 MET cc_start: 0.8640 (tpt) cc_final: 0.8297 (tpt) REVERT: B 639 GLU cc_start: 0.8025 (tp30) cc_final: 0.7817 (tp30) REVERT: B 689 GLU cc_start: 0.8347 (mt-10) cc_final: 0.8093 (mt-10) REVERT: C 473 PHE cc_start: 0.7636 (m-80) cc_final: 0.7038 (m-80) REVERT: C 689 GLU cc_start: 0.8333 (mt-10) cc_final: 0.7984 (mt-10) REVERT: D 473 PHE cc_start: 0.7802 (m-80) cc_final: 0.7511 (m-80) REVERT: D 503 HIS cc_start: 0.8426 (OUTLIER) cc_final: 0.8147 (t-90) REVERT: D 562 MET cc_start: 0.8442 (tpt) cc_final: 0.8066 (tpt) REVERT: E 503 HIS cc_start: 0.8278 (OUTLIER) cc_final: 0.8033 (t-90) REVERT: E 689 GLU cc_start: 0.8285 (mt-10) cc_final: 0.8075 (mt-10) REVERT: F 473 PHE cc_start: 0.7797 (m-80) cc_final: 0.7411 (m-80) REVERT: F 480 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7280 (tm-30) REVERT: F 503 HIS cc_start: 0.8417 (OUTLIER) cc_final: 0.8050 (t-90) REVERT: G 473 PHE cc_start: 0.7641 (m-80) cc_final: 0.7215 (m-80) REVERT: G 507 GLU cc_start: 0.7212 (mt-10) cc_final: 0.6936 (mt-10) REVERT: G 689 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8141 (mt-10) REVERT: H 393 GLU cc_start: 0.7574 (tp30) cc_final: 0.7198 (tp30) REVERT: H 473 PHE cc_start: 0.7722 (m-80) cc_final: 0.7346 (m-10) REVERT: H 503 HIS cc_start: 0.8423 (OUTLIER) cc_final: 0.8100 (t-90) REVERT: H 639 GLU cc_start: 0.8041 (tp30) cc_final: 0.7783 (tp30) REVERT: H 689 GLU cc_start: 0.8448 (mt-10) cc_final: 0.8214 (mt-10) REVERT: I 473 PHE cc_start: 0.7696 (m-80) cc_final: 0.7174 (m-80) REVERT: I 503 HIS cc_start: 0.8306 (OUTLIER) cc_final: 0.8026 (t-90) REVERT: I 689 GLU cc_start: 0.8365 (mt-10) cc_final: 0.8129 (mt-10) REVERT: J 473 PHE cc_start: 0.7647 (m-80) cc_final: 0.7218 (m-80) REVERT: J 503 HIS cc_start: 0.8251 (OUTLIER) cc_final: 0.7908 (t-90) REVERT: J 689 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8171 (mt-10) REVERT: K 393 GLU cc_start: 0.7558 (tp30) cc_final: 0.7189 (tp30) REVERT: K 473 PHE cc_start: 0.7730 (m-80) cc_final: 0.7347 (m-10) REVERT: K 503 HIS cc_start: 0.8425 (OUTLIER) cc_final: 0.8105 (t-90) REVERT: K 639 GLU cc_start: 0.8037 (tp30) cc_final: 0.7787 (tp30) REVERT: K 689 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8202 (mt-10) REVERT: L 473 PHE cc_start: 0.7704 (m-80) cc_final: 0.7181 (m-80) REVERT: L 503 HIS cc_start: 0.8309 (OUTLIER) cc_final: 0.7998 (t-90) REVERT: L 689 GLU cc_start: 0.8362 (mt-10) cc_final: 0.8130 (mt-10) REVERT: M 503 HIS cc_start: 0.8356 (OUTLIER) cc_final: 0.7411 (t-90) REVERT: M 507 GLU cc_start: 0.7152 (mt-10) cc_final: 0.6612 (mt-10) REVERT: M 689 GLU cc_start: 0.8337 (mt-10) cc_final: 0.7709 (mt-10) REVERT: N 473 PHE cc_start: 0.7601 (m-80) cc_final: 0.7108 (m-80) REVERT: N 503 HIS cc_start: 0.8382 (OUTLIER) cc_final: 0.8038 (t-90) REVERT: N 562 MET cc_start: 0.8631 (tpt) cc_final: 0.8322 (tpt) REVERT: N 639 GLU cc_start: 0.8018 (tp30) cc_final: 0.7816 (tp30) REVERT: N 689 GLU cc_start: 0.8333 (mt-10) cc_final: 0.8097 (mt-10) REVERT: O 473 PHE cc_start: 0.7657 (m-80) cc_final: 0.7048 (m-80) REVERT: O 689 GLU cc_start: 0.8330 (mt-10) cc_final: 0.8119 (mt-10) REVERT: P 480 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7362 (pt0) REVERT: P 503 HIS cc_start: 0.8397 (OUTLIER) cc_final: 0.8097 (t-90) REVERT: P 562 MET cc_start: 0.8500 (tpt) cc_final: 0.8122 (tpt) REVERT: P 639 GLU cc_start: 0.8009 (tp30) cc_final: 0.7802 (tp30) REVERT: Q 503 HIS cc_start: 0.8261 (OUTLIER) cc_final: 0.8015 (t-90) REVERT: R 473 PHE cc_start: 0.7730 (m-80) cc_final: 0.7326 (m-80) REVERT: R 480 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7670 (pt0) REVERT: R 503 HIS cc_start: 0.8430 (OUTLIER) cc_final: 0.8062 (t-90) REVERT: R 689 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8179 (mt-10) outliers start: 163 outliers final: 87 residues processed: 702 average time/residue: 0.4689 time to fit residues: 557.3423 Evaluate side-chains 595 residues out of total 5526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 492 time to evaluate : 4.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 472 THR Chi-restraints excluded: chain B residue 493 HIS Chi-restraints excluded: chain B residue 503 HIS Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 493 HIS Chi-restraints excluded: chain D residue 503 HIS Chi-restraints excluded: chain D residue 622 VAL Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 493 HIS Chi-restraints excluded: chain E residue 503 HIS Chi-restraints excluded: chain E residue 622 VAL Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 432 VAL Chi-restraints excluded: chain F residue 503 HIS Chi-restraints excluded: chain F residue 622 VAL Chi-restraints excluded: chain F residue 665 MET Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 420 MET Chi-restraints excluded: chain G residue 432 VAL Chi-restraints excluded: chain G residue 480 GLU Chi-restraints excluded: chain G residue 493 HIS Chi-restraints excluded: chain G residue 622 VAL Chi-restraints excluded: chain H residue 390 LEU Chi-restraints excluded: chain H residue 432 VAL Chi-restraints excluded: chain H residue 472 THR Chi-restraints excluded: chain H residue 493 HIS Chi-restraints excluded: chain H residue 503 HIS Chi-restraints excluded: chain H residue 622 VAL Chi-restraints excluded: chain I residue 432 VAL Chi-restraints excluded: chain I residue 472 THR Chi-restraints excluded: chain I residue 503 HIS Chi-restraints excluded: chain I residue 622 VAL Chi-restraints excluded: chain I residue 665 MET Chi-restraints excluded: chain J residue 390 LEU Chi-restraints excluded: chain J residue 432 VAL Chi-restraints excluded: chain J residue 493 HIS Chi-restraints excluded: chain J residue 503 HIS Chi-restraints excluded: chain J residue 540 VAL Chi-restraints excluded: chain J residue 622 VAL Chi-restraints excluded: chain K residue 390 LEU Chi-restraints excluded: chain K residue 432 VAL Chi-restraints excluded: chain K residue 472 THR Chi-restraints excluded: chain K residue 493 HIS Chi-restraints excluded: chain K residue 503 HIS Chi-restraints excluded: chain K residue 622 VAL Chi-restraints excluded: chain L residue 432 VAL Chi-restraints excluded: chain L residue 472 THR Chi-restraints excluded: chain L residue 503 HIS Chi-restraints excluded: chain L residue 622 VAL Chi-restraints excluded: chain L residue 665 MET Chi-restraints excluded: chain M residue 390 LEU Chi-restraints excluded: chain M residue 432 VAL Chi-restraints excluded: chain M residue 503 HIS Chi-restraints excluded: chain M residue 622 VAL Chi-restraints excluded: chain M residue 665 MET Chi-restraints excluded: chain M residue 696 ILE Chi-restraints excluded: chain N residue 390 LEU Chi-restraints excluded: chain N residue 392 ASP Chi-restraints excluded: chain N residue 432 VAL Chi-restraints excluded: chain N residue 472 THR Chi-restraints excluded: chain N residue 493 HIS Chi-restraints excluded: chain N residue 503 HIS Chi-restraints excluded: chain N residue 540 VAL Chi-restraints excluded: chain N residue 622 VAL Chi-restraints excluded: chain O residue 432 VAL Chi-restraints excluded: chain O residue 493 HIS Chi-restraints excluded: chain O residue 622 VAL Chi-restraints excluded: chain P residue 390 LEU Chi-restraints excluded: chain P residue 432 VAL Chi-restraints excluded: chain P residue 472 THR Chi-restraints excluded: chain P residue 480 GLU Chi-restraints excluded: chain P residue 493 HIS Chi-restraints excluded: chain P residue 503 HIS Chi-restraints excluded: chain P residue 622 VAL Chi-restraints excluded: chain Q residue 390 LEU Chi-restraints excluded: chain Q residue 432 VAL Chi-restraints excluded: chain Q residue 472 THR Chi-restraints excluded: chain Q residue 493 HIS Chi-restraints excluded: chain Q residue 503 HIS Chi-restraints excluded: chain Q residue 622 VAL Chi-restraints excluded: chain R residue 390 LEU Chi-restraints excluded: chain R residue 432 VAL Chi-restraints excluded: chain R residue 503 HIS Chi-restraints excluded: chain R residue 540 VAL Chi-restraints excluded: chain R residue 622 VAL Chi-restraints excluded: chain R residue 665 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 492 optimal weight: 2.9990 chunk 335 optimal weight: 8.9990 chunk 8 optimal weight: 1.9990 chunk 440 optimal weight: 0.7980 chunk 244 optimal weight: 7.9990 chunk 504 optimal weight: 6.9990 chunk 408 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 302 optimal weight: 0.9980 chunk 530 optimal weight: 1.9990 chunk 149 optimal weight: 7.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 HIS B 465 HIS C 465 HIS D 465 HIS E 452 GLN F 465 HIS G 465 HIS H 465 HIS ** I 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 465 HIS ** L 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 465 HIS O 465 HIS P 465 HIS Q 452 GLN Q 465 HIS R 465 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 51012 Z= 0.265 Angle : 0.694 11.113 68994 Z= 0.345 Chirality : 0.048 0.256 7758 Planarity : 0.003 0.065 8928 Dihedral : 6.392 49.334 6942 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.29 % Allowed : 10.25 % Favored : 89.46 % Rotamer: Outliers : 3.85 % Allowed : 15.18 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % Twisted General : 0.60 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.57 (0.10), residues: 6156 helix: -1.55 (0.09), residues: 2826 sheet: -1.44 (0.22), residues: 486 loop : -3.46 (0.10), residues: 2844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 474 HIS 0.005 0.001 HIS J 465 PHE 0.011 0.001 PHE J 473 TYR 0.017 0.001 TYR Q 460 ARG 0.007 0.000 ARG J 447 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 757 residues out of total 5526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 545 time to evaluate : 4.367 Fit side-chains REVERT: A 503 HIS cc_start: 0.8354 (OUTLIER) cc_final: 0.7991 (t-90) REVERT: A 689 GLU cc_start: 0.8354 (mt-10) cc_final: 0.7774 (mt-10) REVERT: B 473 PHE cc_start: 0.7739 (m-80) cc_final: 0.7291 (m-80) REVERT: B 503 HIS cc_start: 0.8349 (OUTLIER) cc_final: 0.7964 (t-90) REVERT: B 689 GLU cc_start: 0.8331 (mt-10) cc_final: 0.8100 (mt-10) REVERT: C 473 PHE cc_start: 0.7802 (m-80) cc_final: 0.7177 (m-80) REVERT: C 480 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7300 (tm-30) REVERT: C 689 GLU cc_start: 0.8319 (mt-10) cc_final: 0.8075 (mt-10) REVERT: D 503 HIS cc_start: 0.8344 (OUTLIER) cc_final: 0.7989 (t-90) REVERT: E 417 ASN cc_start: 0.7992 (m-40) cc_final: 0.7581 (m-40) REVERT: E 503 HIS cc_start: 0.8215 (OUTLIER) cc_final: 0.7909 (t-90) REVERT: F 473 PHE cc_start: 0.7809 (m-80) cc_final: 0.7244 (m-80) REVERT: F 480 GLU cc_start: 0.7876 (tm-30) cc_final: 0.7247 (tm-30) REVERT: F 503 HIS cc_start: 0.8326 (OUTLIER) cc_final: 0.8018 (t-90) REVERT: G 473 PHE cc_start: 0.7782 (m-80) cc_final: 0.7388 (m-80) REVERT: G 689 GLU cc_start: 0.8379 (mt-10) cc_final: 0.8138 (mt-10) REVERT: H 393 GLU cc_start: 0.7571 (tp30) cc_final: 0.7232 (tp30) REVERT: H 473 PHE cc_start: 0.7666 (m-80) cc_final: 0.7404 (m-80) REVERT: H 503 HIS cc_start: 0.8384 (OUTLIER) cc_final: 0.7991 (t-90) REVERT: H 547 GLU cc_start: 0.7776 (tt0) cc_final: 0.7504 (tt0) REVERT: H 639 GLU cc_start: 0.8112 (tp30) cc_final: 0.7869 (tp30) REVERT: H 689 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8212 (mt-10) REVERT: I 473 PHE cc_start: 0.7850 (m-80) cc_final: 0.7326 (m-80) REVERT: I 503 HIS cc_start: 0.8366 (OUTLIER) cc_final: 0.7949 (t-90) REVERT: I 689 GLU cc_start: 0.8349 (mt-10) cc_final: 0.8112 (mt-10) REVERT: J 473 PHE cc_start: 0.7512 (m-80) cc_final: 0.7110 (m-80) REVERT: J 503 HIS cc_start: 0.8316 (OUTLIER) cc_final: 0.7934 (t-90) REVERT: J 689 GLU cc_start: 0.8353 (mt-10) cc_final: 0.8113 (mt-10) REVERT: K 393 GLU cc_start: 0.7541 (tp30) cc_final: 0.7180 (tp30) REVERT: K 473 PHE cc_start: 0.7673 (m-80) cc_final: 0.7407 (m-80) REVERT: K 503 HIS cc_start: 0.8399 (OUTLIER) cc_final: 0.7993 (t-90) REVERT: K 639 GLU cc_start: 0.8110 (tp30) cc_final: 0.7878 (tp30) REVERT: K 689 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8175 (mt-10) REVERT: L 473 PHE cc_start: 0.7853 (m-80) cc_final: 0.7328 (m-80) REVERT: L 503 HIS cc_start: 0.8340 (OUTLIER) cc_final: 0.7936 (t-90) REVERT: L 689 GLU cc_start: 0.8337 (mt-10) cc_final: 0.8102 (mt-10) REVERT: M 503 HIS cc_start: 0.8358 (OUTLIER) cc_final: 0.7992 (t-90) REVERT: N 473 PHE cc_start: 0.7731 (m-80) cc_final: 0.7282 (m-80) REVERT: N 503 HIS cc_start: 0.8346 (OUTLIER) cc_final: 0.7977 (t-90) REVERT: N 639 GLU cc_start: 0.8088 (tp30) cc_final: 0.7887 (tp30) REVERT: N 689 GLU cc_start: 0.8324 (mt-10) cc_final: 0.8093 (mt-10) REVERT: O 473 PHE cc_start: 0.7840 (m-80) cc_final: 0.7230 (m-80) REVERT: O 480 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7285 (tm-30) REVERT: P 480 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8049 (pt0) REVERT: P 503 HIS cc_start: 0.8273 (OUTLIER) cc_final: 0.7955 (t-90) REVERT: Q 417 ASN cc_start: 0.7986 (m-40) cc_final: 0.7572 (m-40) REVERT: Q 503 HIS cc_start: 0.8208 (OUTLIER) cc_final: 0.7900 (t-90) REVERT: R 473 PHE cc_start: 0.7755 (m-80) cc_final: 0.7291 (m-80) REVERT: R 480 GLU cc_start: 0.7908 (tm-30) cc_final: 0.7612 (pt0) REVERT: R 503 HIS cc_start: 0.8317 (OUTLIER) cc_final: 0.7987 (t-90) outliers start: 212 outliers final: 107 residues processed: 723 average time/residue: 0.4264 time to fit residues: 554.8700 Evaluate side-chains 617 residues out of total 5526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 494 time to evaluate : 4.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 493 HIS Chi-restraints excluded: chain B residue 503 HIS Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 665 MET Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 493 HIS Chi-restraints excluded: chain D residue 503 HIS Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 559 ILE Chi-restraints excluded: chain D residue 622 VAL Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain E residue 493 HIS Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 503 HIS Chi-restraints excluded: chain E residue 540 VAL Chi-restraints excluded: chain E residue 559 ILE Chi-restraints excluded: chain E residue 622 VAL Chi-restraints excluded: chain F residue 432 VAL Chi-restraints excluded: chain F residue 503 HIS Chi-restraints excluded: chain F residue 540 VAL Chi-restraints excluded: chain F residue 622 VAL Chi-restraints excluded: chain F residue 665 MET Chi-restraints excluded: chain F residue 690 LEU Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 420 MET Chi-restraints excluded: chain G residue 432 VAL Chi-restraints excluded: chain G residue 480 GLU Chi-restraints excluded: chain G residue 493 HIS Chi-restraints excluded: chain G residue 498 THR Chi-restraints excluded: chain G residue 540 VAL Chi-restraints excluded: chain G residue 622 VAL Chi-restraints excluded: chain H residue 390 LEU Chi-restraints excluded: chain H residue 432 VAL Chi-restraints excluded: chain H residue 503 HIS Chi-restraints excluded: chain H residue 540 VAL Chi-restraints excluded: chain H residue 622 VAL Chi-restraints excluded: chain I residue 390 LEU Chi-restraints excluded: chain I residue 432 VAL Chi-restraints excluded: chain I residue 472 THR Chi-restraints excluded: chain I residue 498 THR Chi-restraints excluded: chain I residue 503 HIS Chi-restraints excluded: chain I residue 540 VAL Chi-restraints excluded: chain I residue 622 VAL Chi-restraints excluded: chain I residue 665 MET Chi-restraints excluded: chain J residue 390 LEU Chi-restraints excluded: chain J residue 432 VAL Chi-restraints excluded: chain J residue 493 HIS Chi-restraints excluded: chain J residue 498 THR Chi-restraints excluded: chain J residue 503 HIS Chi-restraints excluded: chain J residue 540 VAL Chi-restraints excluded: chain J residue 622 VAL Chi-restraints excluded: chain J residue 665 MET Chi-restraints excluded: chain K residue 390 LEU Chi-restraints excluded: chain K residue 432 VAL Chi-restraints excluded: chain K residue 503 HIS Chi-restraints excluded: chain K residue 540 VAL Chi-restraints excluded: chain K residue 622 VAL Chi-restraints excluded: chain L residue 390 LEU Chi-restraints excluded: chain L residue 432 VAL Chi-restraints excluded: chain L residue 472 THR Chi-restraints excluded: chain L residue 498 THR Chi-restraints excluded: chain L residue 503 HIS Chi-restraints excluded: chain L residue 540 VAL Chi-restraints excluded: chain L residue 622 VAL Chi-restraints excluded: chain L residue 665 MET Chi-restraints excluded: chain M residue 390 LEU Chi-restraints excluded: chain M residue 432 VAL Chi-restraints excluded: chain M residue 503 HIS Chi-restraints excluded: chain M residue 540 VAL Chi-restraints excluded: chain M residue 622 VAL Chi-restraints excluded: chain M residue 665 MET Chi-restraints excluded: chain M residue 690 LEU Chi-restraints excluded: chain M residue 696 ILE Chi-restraints excluded: chain N residue 390 LEU Chi-restraints excluded: chain N residue 392 ASP Chi-restraints excluded: chain N residue 432 VAL Chi-restraints excluded: chain N residue 493 HIS Chi-restraints excluded: chain N residue 503 HIS Chi-restraints excluded: chain N residue 622 VAL Chi-restraints excluded: chain N residue 665 MET Chi-restraints excluded: chain O residue 432 VAL Chi-restraints excluded: chain O residue 493 HIS Chi-restraints excluded: chain O residue 540 VAL Chi-restraints excluded: chain O residue 622 VAL Chi-restraints excluded: chain P residue 390 LEU Chi-restraints excluded: chain P residue 432 VAL Chi-restraints excluded: chain P residue 480 GLU Chi-restraints excluded: chain P residue 493 HIS Chi-restraints excluded: chain P residue 503 HIS Chi-restraints excluded: chain P residue 540 VAL Chi-restraints excluded: chain P residue 559 ILE Chi-restraints excluded: chain P residue 622 VAL Chi-restraints excluded: chain Q residue 390 LEU Chi-restraints excluded: chain Q residue 432 VAL Chi-restraints excluded: chain Q residue 472 THR Chi-restraints excluded: chain Q residue 493 HIS Chi-restraints excluded: chain Q residue 498 THR Chi-restraints excluded: chain Q residue 503 HIS Chi-restraints excluded: chain Q residue 540 VAL Chi-restraints excluded: chain Q residue 559 ILE Chi-restraints excluded: chain Q residue 622 VAL Chi-restraints excluded: chain Q residue 696 ILE Chi-restraints excluded: chain R residue 432 VAL Chi-restraints excluded: chain R residue 503 HIS Chi-restraints excluded: chain R residue 622 VAL Chi-restraints excluded: chain R residue 665 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 199 optimal weight: 0.3980 chunk 532 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 347 optimal weight: 0.9990 chunk 146 optimal weight: 8.9990 chunk 592 optimal weight: 3.9990 chunk 491 optimal weight: 3.9990 chunk 274 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 195 optimal weight: 2.9990 chunk 310 optimal weight: 1.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 452 GLN E 465 HIS ** F 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 452 GLN G 500 HIS ** H 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 452 GLN J 465 HIS J 500 HIS ** K 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 465 HIS M 452 GLN M 465 HIS ** N 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 452 GLN Q 452 GLN R 452 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 51012 Z= 0.297 Angle : 0.723 11.082 68994 Z= 0.359 Chirality : 0.049 0.261 7758 Planarity : 0.003 0.080 8928 Dihedral : 6.432 51.043 6942 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.99 % Favored : 89.72 % Rotamer: Outliers : 3.25 % Allowed : 16.79 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % Twisted General : 0.60 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.32 (0.10), residues: 6156 helix: -1.31 (0.09), residues: 2790 sheet: -1.38 (0.23), residues: 486 loop : -3.34 (0.10), residues: 2880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 474 HIS 0.004 0.001 HIS E 465 PHE 0.011 0.001 PHE G 473 TYR 0.016 0.001 TYR Q 460 ARG 0.013 0.000 ARG P 447 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 5526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 549 time to evaluate : 4.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 503 HIS cc_start: 0.8374 (OUTLIER) cc_final: 0.7985 (t-90) REVERT: B 473 PHE cc_start: 0.7820 (m-80) cc_final: 0.7387 (m-80) REVERT: B 480 GLU cc_start: 0.8083 (tm-30) cc_final: 0.7872 (pt0) REVERT: B 503 HIS cc_start: 0.8376 (OUTLIER) cc_final: 0.7967 (t-90) REVERT: B 562 MET cc_start: 0.8720 (tpt) cc_final: 0.8343 (tpt) REVERT: B 689 GLU cc_start: 0.8337 (mt-10) cc_final: 0.8105 (mt-10) REVERT: C 473 PHE cc_start: 0.7740 (m-80) cc_final: 0.7111 (m-80) REVERT: C 480 GLU cc_start: 0.7878 (tm-30) cc_final: 0.7251 (tm-30) REVERT: D 503 HIS cc_start: 0.8349 (OUTLIER) cc_final: 0.7886 (t-90) REVERT: E 417 ASN cc_start: 0.8001 (m-40) cc_final: 0.7688 (m-40) REVERT: E 480 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7353 (tm-30) REVERT: E 503 HIS cc_start: 0.8260 (OUTLIER) cc_final: 0.7914 (t-90) REVERT: E 689 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7949 (mt-10) REVERT: F 473 PHE cc_start: 0.7753 (m-80) cc_final: 0.7189 (m-80) REVERT: F 480 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7209 (tm-30) REVERT: F 503 HIS cc_start: 0.8284 (OUTLIER) cc_final: 0.7909 (t-90) REVERT: G 473 PHE cc_start: 0.7790 (m-80) cc_final: 0.7268 (m-80) REVERT: G 507 GLU cc_start: 0.7219 (mt-10) cc_final: 0.6893 (mt-10) REVERT: G 689 GLU cc_start: 0.8351 (mt-10) cc_final: 0.8150 (mt-10) REVERT: H 473 PHE cc_start: 0.7742 (m-80) cc_final: 0.7445 (m-80) REVERT: H 480 GLU cc_start: 0.7862 (tm-30) cc_final: 0.7299 (tm-30) REVERT: H 503 HIS cc_start: 0.8356 (OUTLIER) cc_final: 0.7920 (t-90) REVERT: H 547 GLU cc_start: 0.7774 (tt0) cc_final: 0.7574 (tt0) REVERT: H 562 MET cc_start: 0.8559 (tpt) cc_final: 0.8249 (tpt) REVERT: H 639 GLU cc_start: 0.8121 (tp30) cc_final: 0.7885 (tp30) REVERT: I 473 PHE cc_start: 0.7775 (m-80) cc_final: 0.7344 (m-80) REVERT: I 480 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7359 (tm-30) REVERT: I 503 HIS cc_start: 0.8360 (OUTLIER) cc_final: 0.7878 (t-90) REVERT: J 473 PHE cc_start: 0.7590 (m-80) cc_final: 0.7252 (m-80) REVERT: J 480 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7609 (tm-30) REVERT: J 503 HIS cc_start: 0.8299 (OUTLIER) cc_final: 0.7797 (t-90) REVERT: J 689 GLU cc_start: 0.8355 (mt-10) cc_final: 0.8107 (mt-10) REVERT: K 393 GLU cc_start: 0.7544 (tp30) cc_final: 0.7213 (tp30) REVERT: K 473 PHE cc_start: 0.7736 (m-80) cc_final: 0.7439 (m-80) REVERT: K 480 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7305 (tm-30) REVERT: K 503 HIS cc_start: 0.8351 (OUTLIER) cc_final: 0.7927 (t-90) REVERT: K 639 GLU cc_start: 0.8114 (tp30) cc_final: 0.7888 (tp30) REVERT: L 473 PHE cc_start: 0.7757 (m-80) cc_final: 0.7324 (m-80) REVERT: L 480 GLU cc_start: 0.7854 (tm-30) cc_final: 0.7329 (tm-30) REVERT: L 503 HIS cc_start: 0.8331 (OUTLIER) cc_final: 0.7860 (t-90) REVERT: M 503 HIS cc_start: 0.8375 (OUTLIER) cc_final: 0.7987 (t-90) REVERT: M 689 GLU cc_start: 0.8285 (mt-10) cc_final: 0.8075 (mt-10) REVERT: N 473 PHE cc_start: 0.7824 (m-80) cc_final: 0.7387 (m-80) REVERT: N 480 GLU cc_start: 0.8079 (tm-30) cc_final: 0.7870 (pt0) REVERT: N 503 HIS cc_start: 0.8376 (OUTLIER) cc_final: 0.7968 (t-90) REVERT: N 562 MET cc_start: 0.8697 (tpt) cc_final: 0.8358 (tpt) REVERT: N 689 GLU cc_start: 0.8327 (mt-10) cc_final: 0.8107 (mt-10) REVERT: O 473 PHE cc_start: 0.7756 (m-80) cc_final: 0.7134 (m-80) REVERT: O 480 GLU cc_start: 0.7896 (tm-30) cc_final: 0.7279 (tm-30) REVERT: P 473 PHE cc_start: 0.7819 (m-80) cc_final: 0.7586 (m-80) REVERT: P 480 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7288 (pt0) REVERT: P 503 HIS cc_start: 0.8294 (OUTLIER) cc_final: 0.7916 (t-90) REVERT: Q 417 ASN cc_start: 0.7991 (m-40) cc_final: 0.7677 (m-40) REVERT: Q 447 ARG cc_start: 0.8150 (mtp85) cc_final: 0.7886 (mtp85) REVERT: Q 473 PHE cc_start: 0.7850 (m-80) cc_final: 0.7234 (m-80) REVERT: Q 480 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7340 (tm-30) REVERT: Q 503 HIS cc_start: 0.8255 (OUTLIER) cc_final: 0.7904 (t-90) REVERT: R 473 PHE cc_start: 0.7655 (m-80) cc_final: 0.7119 (m-80) REVERT: R 480 GLU cc_start: 0.7876 (tm-30) cc_final: 0.7614 (pt0) REVERT: R 503 HIS cc_start: 0.8281 (OUTLIER) cc_final: 0.7922 (t-90) outliers start: 179 outliers final: 120 residues processed: 697 average time/residue: 0.4243 time to fit residues: 522.2694 Evaluate side-chains 642 residues out of total 5526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 506 time to evaluate : 4.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 493 HIS Chi-restraints excluded: chain B residue 503 HIS Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 665 MET Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 694 ILE Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 493 HIS Chi-restraints excluded: chain D residue 503 HIS Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 559 ILE Chi-restraints excluded: chain D residue 622 VAL Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain E residue 493 HIS Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 503 HIS Chi-restraints excluded: chain E residue 540 VAL Chi-restraints excluded: chain E residue 559 ILE Chi-restraints excluded: chain E residue 622 VAL Chi-restraints excluded: chain E residue 696 ILE Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 420 MET Chi-restraints excluded: chain F residue 432 VAL Chi-restraints excluded: chain F residue 472 THR Chi-restraints excluded: chain F residue 503 HIS Chi-restraints excluded: chain F residue 540 VAL Chi-restraints excluded: chain F residue 622 VAL Chi-restraints excluded: chain F residue 665 MET Chi-restraints excluded: chain F residue 690 LEU Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 432 VAL Chi-restraints excluded: chain G residue 472 THR Chi-restraints excluded: chain G residue 480 GLU Chi-restraints excluded: chain G residue 493 HIS Chi-restraints excluded: chain G residue 498 THR Chi-restraints excluded: chain G residue 540 VAL Chi-restraints excluded: chain G residue 622 VAL Chi-restraints excluded: chain G residue 665 MET Chi-restraints excluded: chain H residue 390 LEU Chi-restraints excluded: chain H residue 432 VAL Chi-restraints excluded: chain H residue 493 HIS Chi-restraints excluded: chain H residue 498 THR Chi-restraints excluded: chain H residue 503 HIS Chi-restraints excluded: chain H residue 540 VAL Chi-restraints excluded: chain H residue 622 VAL Chi-restraints excluded: chain I residue 390 LEU Chi-restraints excluded: chain I residue 432 VAL Chi-restraints excluded: chain I residue 498 THR Chi-restraints excluded: chain I residue 503 HIS Chi-restraints excluded: chain I residue 540 VAL Chi-restraints excluded: chain I residue 622 VAL Chi-restraints excluded: chain I residue 665 MET Chi-restraints excluded: chain J residue 390 LEU Chi-restraints excluded: chain J residue 432 VAL Chi-restraints excluded: chain J residue 439 LEU Chi-restraints excluded: chain J residue 493 HIS Chi-restraints excluded: chain J residue 498 THR Chi-restraints excluded: chain J residue 503 HIS Chi-restraints excluded: chain J residue 540 VAL Chi-restraints excluded: chain J residue 622 VAL Chi-restraints excluded: chain J residue 665 MET Chi-restraints excluded: chain K residue 390 LEU Chi-restraints excluded: chain K residue 432 VAL Chi-restraints excluded: chain K residue 503 HIS Chi-restraints excluded: chain K residue 540 VAL Chi-restraints excluded: chain K residue 622 VAL Chi-restraints excluded: chain L residue 390 LEU Chi-restraints excluded: chain L residue 432 VAL Chi-restraints excluded: chain L residue 498 THR Chi-restraints excluded: chain L residue 503 HIS Chi-restraints excluded: chain L residue 540 VAL Chi-restraints excluded: chain L residue 622 VAL Chi-restraints excluded: chain L residue 665 MET Chi-restraints excluded: chain M residue 390 LEU Chi-restraints excluded: chain M residue 432 VAL Chi-restraints excluded: chain M residue 503 HIS Chi-restraints excluded: chain M residue 540 VAL Chi-restraints excluded: chain M residue 622 VAL Chi-restraints excluded: chain M residue 665 MET Chi-restraints excluded: chain M residue 690 LEU Chi-restraints excluded: chain M residue 696 ILE Chi-restraints excluded: chain N residue 390 LEU Chi-restraints excluded: chain N residue 432 VAL Chi-restraints excluded: chain N residue 493 HIS Chi-restraints excluded: chain N residue 503 HIS Chi-restraints excluded: chain N residue 622 VAL Chi-restraints excluded: chain N residue 665 MET Chi-restraints excluded: chain O residue 390 LEU Chi-restraints excluded: chain O residue 392 ASP Chi-restraints excluded: chain O residue 432 VAL Chi-restraints excluded: chain O residue 493 HIS Chi-restraints excluded: chain O residue 540 VAL Chi-restraints excluded: chain O residue 622 VAL Chi-restraints excluded: chain P residue 390 LEU Chi-restraints excluded: chain P residue 420 MET Chi-restraints excluded: chain P residue 432 VAL Chi-restraints excluded: chain P residue 472 THR Chi-restraints excluded: chain P residue 480 GLU Chi-restraints excluded: chain P residue 493 HIS Chi-restraints excluded: chain P residue 503 HIS Chi-restraints excluded: chain P residue 540 VAL Chi-restraints excluded: chain P residue 559 ILE Chi-restraints excluded: chain P residue 622 VAL Chi-restraints excluded: chain Q residue 390 LEU Chi-restraints excluded: chain Q residue 432 VAL Chi-restraints excluded: chain Q residue 472 THR Chi-restraints excluded: chain Q residue 493 HIS Chi-restraints excluded: chain Q residue 498 THR Chi-restraints excluded: chain Q residue 503 HIS Chi-restraints excluded: chain Q residue 540 VAL Chi-restraints excluded: chain Q residue 559 ILE Chi-restraints excluded: chain Q residue 622 VAL Chi-restraints excluded: chain Q residue 696 ILE Chi-restraints excluded: chain R residue 390 LEU Chi-restraints excluded: chain R residue 420 MET Chi-restraints excluded: chain R residue 432 VAL Chi-restraints excluded: chain R residue 503 HIS Chi-restraints excluded: chain R residue 622 VAL Chi-restraints excluded: chain R residue 665 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 570 optimal weight: 0.9980 chunk 66 optimal weight: 7.9990 chunk 337 optimal weight: 6.9990 chunk 432 optimal weight: 0.0970 chunk 335 optimal weight: 3.9990 chunk 498 optimal weight: 0.8980 chunk 330 optimal weight: 4.9990 chunk 589 optimal weight: 3.9990 chunk 369 optimal weight: 6.9990 chunk 359 optimal weight: 0.8980 chunk 272 optimal weight: 10.0000 overall best weight: 1.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 GLN ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 452 GLN ** E 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 452 GLN I 452 GLN I 465 HIS J 417 ASN K 452 GLN L 452 GLN ** M 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 452 GLN ** O 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 51012 Z= 0.230 Angle : 0.696 11.701 68994 Z= 0.345 Chirality : 0.047 0.270 7758 Planarity : 0.003 0.045 8928 Dihedral : 6.228 49.838 6942 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.36 % Favored : 89.36 % Rotamer: Outliers : 3.40 % Allowed : 17.07 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.60 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.10), residues: 6156 helix: -1.06 (0.09), residues: 2844 sheet: -1.21 (0.23), residues: 486 loop : -3.29 (0.11), residues: 2826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 474 HIS 0.004 0.001 HIS G 503 PHE 0.013 0.001 PHE D 473 TYR 0.011 0.001 TYR E 460 ARG 0.008 0.000 ARG Q 447 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 760 residues out of total 5526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 573 time to evaluate : 4.405 Fit side-chains REVERT: A 503 HIS cc_start: 0.8274 (OUTLIER) cc_final: 0.8023 (t-90) REVERT: A 689 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7745 (mt-10) REVERT: B 473 PHE cc_start: 0.7826 (m-80) cc_final: 0.7388 (m-80) REVERT: B 480 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7845 (pt0) REVERT: B 503 HIS cc_start: 0.8358 (OUTLIER) cc_final: 0.8038 (t-90) REVERT: B 562 MET cc_start: 0.8676 (tpt) cc_final: 0.8322 (tpt) REVERT: B 689 GLU cc_start: 0.8342 (mt-10) cc_final: 0.8124 (mt-10) REVERT: C 473 PHE cc_start: 0.7615 (m-80) cc_final: 0.7102 (m-80) REVERT: C 480 GLU cc_start: 0.7876 (tm-30) cc_final: 0.7250 (tm-30) REVERT: C 689 GLU cc_start: 0.8369 (mt-10) cc_final: 0.8075 (mt-10) REVERT: D 503 HIS cc_start: 0.8326 (OUTLIER) cc_final: 0.7977 (t-90) REVERT: D 562 MET cc_start: 0.8467 (tpt) cc_final: 0.8077 (tpt) REVERT: E 417 ASN cc_start: 0.7968 (m-40) cc_final: 0.7704 (m-40) REVERT: E 480 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7579 (tm-30) REVERT: E 503 HIS cc_start: 0.8260 (OUTLIER) cc_final: 0.7999 (t-90) REVERT: E 689 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7964 (mt-10) REVERT: F 480 GLU cc_start: 0.7992 (tm-30) cc_final: 0.7695 (pt0) REVERT: F 503 HIS cc_start: 0.8228 (OUTLIER) cc_final: 0.7997 (t-90) REVERT: G 473 PHE cc_start: 0.7833 (m-80) cc_final: 0.7435 (m-80) REVERT: G 507 GLU cc_start: 0.7161 (mt-10) cc_final: 0.6859 (mt-10) REVERT: G 689 GLU cc_start: 0.8351 (mt-10) cc_final: 0.8145 (mt-10) REVERT: H 480 GLU cc_start: 0.7836 (tm-30) cc_final: 0.7280 (tm-30) REVERT: H 503 HIS cc_start: 0.8321 (OUTLIER) cc_final: 0.8009 (t-90) REVERT: H 639 GLU cc_start: 0.8138 (tp30) cc_final: 0.7934 (tp30) REVERT: H 689 GLU cc_start: 0.8462 (mt-10) cc_final: 0.8260 (mt-10) REVERT: I 473 PHE cc_start: 0.7857 (m-80) cc_final: 0.7512 (m-80) REVERT: I 503 HIS cc_start: 0.8305 (OUTLIER) cc_final: 0.7947 (t-90) REVERT: J 382 GLN cc_start: 0.6795 (pm20) cc_final: 0.6363 (pp30) REVERT: J 473 PHE cc_start: 0.7621 (m-80) cc_final: 0.7321 (m-80) REVERT: J 503 HIS cc_start: 0.8245 (OUTLIER) cc_final: 0.7843 (t-90) REVERT: J 689 GLU cc_start: 0.8331 (mt-10) cc_final: 0.8123 (mt-10) REVERT: K 480 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7283 (tm-30) REVERT: K 503 HIS cc_start: 0.8311 (OUTLIER) cc_final: 0.8045 (t-90) REVERT: K 562 MET cc_start: 0.8573 (tpt) cc_final: 0.8249 (tpt) REVERT: K 689 GLU cc_start: 0.8444 (mt-10) cc_final: 0.7872 (mt-10) REVERT: L 473 PHE cc_start: 0.7856 (m-80) cc_final: 0.7525 (m-80) REVERT: L 480 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7429 (tm-30) REVERT: L 503 HIS cc_start: 0.8280 (OUTLIER) cc_final: 0.7925 (t-90) REVERT: M 503 HIS cc_start: 0.8279 (OUTLIER) cc_final: 0.8020 (t-90) REVERT: M 689 GLU cc_start: 0.8295 (mt-10) cc_final: 0.8040 (mt-10) REVERT: N 473 PHE cc_start: 0.7828 (m-80) cc_final: 0.7423 (m-80) REVERT: N 480 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7837 (pt0) REVERT: N 503 HIS cc_start: 0.8367 (OUTLIER) cc_final: 0.8063 (t-90) REVERT: N 689 GLU cc_start: 0.8338 (mt-10) cc_final: 0.8125 (mt-10) REVERT: O 473 PHE cc_start: 0.7640 (m-80) cc_final: 0.7108 (m-80) REVERT: O 480 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7275 (tm-30) REVERT: P 480 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7301 (pt0) REVERT: P 503 HIS cc_start: 0.8264 (OUTLIER) cc_final: 0.7987 (t-90) REVERT: Q 417 ASN cc_start: 0.7963 (m-40) cc_final: 0.7693 (m-40) REVERT: Q 473 PHE cc_start: 0.7822 (m-80) cc_final: 0.7147 (m-80) REVERT: Q 480 GLU cc_start: 0.7885 (tm-30) cc_final: 0.7568 (tm-30) REVERT: Q 503 HIS cc_start: 0.8256 (OUTLIER) cc_final: 0.7978 (t-90) REVERT: R 473 PHE cc_start: 0.7701 (m-80) cc_final: 0.7159 (m-80) REVERT: R 480 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7738 (pt0) REVERT: R 503 HIS cc_start: 0.8244 (OUTLIER) cc_final: 0.8002 (t-90) outliers start: 187 outliers final: 128 residues processed: 713 average time/residue: 0.4194 time to fit residues: 530.7476 Evaluate side-chains 653 residues out of total 5526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 509 time to evaluate : 4.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 493 HIS Chi-restraints excluded: chain B residue 503 HIS Chi-restraints excluded: chain B residue 610 PHE Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 420 MET Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 493 HIS Chi-restraints excluded: chain D residue 503 HIS Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 559 ILE Chi-restraints excluded: chain D residue 622 VAL Chi-restraints excluded: chain D residue 694 ILE Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain E residue 493 HIS Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 503 HIS Chi-restraints excluded: chain E residue 540 VAL Chi-restraints excluded: chain E residue 559 ILE Chi-restraints excluded: chain E residue 622 VAL Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 420 MET Chi-restraints excluded: chain F residue 432 VAL Chi-restraints excluded: chain F residue 472 THR Chi-restraints excluded: chain F residue 503 HIS Chi-restraints excluded: chain F residue 540 VAL Chi-restraints excluded: chain F residue 622 VAL Chi-restraints excluded: chain F residue 665 MET Chi-restraints excluded: chain F residue 690 LEU Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 432 VAL Chi-restraints excluded: chain G residue 480 GLU Chi-restraints excluded: chain G residue 493 HIS Chi-restraints excluded: chain G residue 498 THR Chi-restraints excluded: chain G residue 540 VAL Chi-restraints excluded: chain G residue 622 VAL Chi-restraints excluded: chain G residue 665 MET Chi-restraints excluded: chain H residue 390 LEU Chi-restraints excluded: chain H residue 432 VAL Chi-restraints excluded: chain H residue 493 HIS Chi-restraints excluded: chain H residue 498 THR Chi-restraints excluded: chain H residue 503 HIS Chi-restraints excluded: chain H residue 540 VAL Chi-restraints excluded: chain H residue 622 VAL Chi-restraints excluded: chain I residue 390 LEU Chi-restraints excluded: chain I residue 432 VAL Chi-restraints excluded: chain I residue 472 THR Chi-restraints excluded: chain I residue 498 THR Chi-restraints excluded: chain I residue 503 HIS Chi-restraints excluded: chain I residue 540 VAL Chi-restraints excluded: chain I residue 622 VAL Chi-restraints excluded: chain I residue 665 MET Chi-restraints excluded: chain J residue 390 LEU Chi-restraints excluded: chain J residue 420 MET Chi-restraints excluded: chain J residue 432 VAL Chi-restraints excluded: chain J residue 472 THR Chi-restraints excluded: chain J residue 493 HIS Chi-restraints excluded: chain J residue 498 THR Chi-restraints excluded: chain J residue 503 HIS Chi-restraints excluded: chain J residue 540 VAL Chi-restraints excluded: chain J residue 622 VAL Chi-restraints excluded: chain J residue 665 MET Chi-restraints excluded: chain K residue 390 LEU Chi-restraints excluded: chain K residue 432 VAL Chi-restraints excluded: chain K residue 503 HIS Chi-restraints excluded: chain K residue 540 VAL Chi-restraints excluded: chain K residue 622 VAL Chi-restraints excluded: chain L residue 390 LEU Chi-restraints excluded: chain L residue 432 VAL Chi-restraints excluded: chain L residue 472 THR Chi-restraints excluded: chain L residue 498 THR Chi-restraints excluded: chain L residue 503 HIS Chi-restraints excluded: chain L residue 540 VAL Chi-restraints excluded: chain L residue 622 VAL Chi-restraints excluded: chain L residue 665 MET Chi-restraints excluded: chain M residue 390 LEU Chi-restraints excluded: chain M residue 432 VAL Chi-restraints excluded: chain M residue 472 THR Chi-restraints excluded: chain M residue 503 HIS Chi-restraints excluded: chain M residue 540 VAL Chi-restraints excluded: chain M residue 622 VAL Chi-restraints excluded: chain M residue 665 MET Chi-restraints excluded: chain M residue 690 LEU Chi-restraints excluded: chain M residue 696 ILE Chi-restraints excluded: chain N residue 390 LEU Chi-restraints excluded: chain N residue 420 MET Chi-restraints excluded: chain N residue 432 VAL Chi-restraints excluded: chain N residue 493 HIS Chi-restraints excluded: chain N residue 503 HIS Chi-restraints excluded: chain N residue 622 VAL Chi-restraints excluded: chain N residue 665 MET Chi-restraints excluded: chain O residue 390 LEU Chi-restraints excluded: chain O residue 392 ASP Chi-restraints excluded: chain O residue 432 VAL Chi-restraints excluded: chain O residue 493 HIS Chi-restraints excluded: chain O residue 540 VAL Chi-restraints excluded: chain O residue 622 VAL Chi-restraints excluded: chain O residue 694 ILE Chi-restraints excluded: chain P residue 392 ASP Chi-restraints excluded: chain P residue 420 MET Chi-restraints excluded: chain P residue 432 VAL Chi-restraints excluded: chain P residue 480 GLU Chi-restraints excluded: chain P residue 493 HIS Chi-restraints excluded: chain P residue 503 HIS Chi-restraints excluded: chain P residue 540 VAL Chi-restraints excluded: chain P residue 559 ILE Chi-restraints excluded: chain P residue 622 VAL Chi-restraints excluded: chain P residue 694 ILE Chi-restraints excluded: chain Q residue 390 LEU Chi-restraints excluded: chain Q residue 432 VAL Chi-restraints excluded: chain Q residue 472 THR Chi-restraints excluded: chain Q residue 493 HIS Chi-restraints excluded: chain Q residue 498 THR Chi-restraints excluded: chain Q residue 503 HIS Chi-restraints excluded: chain Q residue 540 VAL Chi-restraints excluded: chain Q residue 559 ILE Chi-restraints excluded: chain Q residue 622 VAL Chi-restraints excluded: chain R residue 390 LEU Chi-restraints excluded: chain R residue 420 MET Chi-restraints excluded: chain R residue 432 VAL Chi-restraints excluded: chain R residue 472 THR Chi-restraints excluded: chain R residue 503 HIS Chi-restraints excluded: chain R residue 540 VAL Chi-restraints excluded: chain R residue 622 VAL Chi-restraints excluded: chain R residue 665 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 364 optimal weight: 2.9990 chunk 235 optimal weight: 5.9990 chunk 352 optimal weight: 9.9990 chunk 177 optimal weight: 0.7980 chunk 115 optimal weight: 0.8980 chunk 114 optimal weight: 9.9990 chunk 375 optimal weight: 4.9990 chunk 401 optimal weight: 1.9990 chunk 291 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 463 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 452 GLN ** D 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 452 GLN F 452 GLN ** H 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 417 ASN ** K 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 452 GLN P 452 GLN Q 452 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 51012 Z= 0.232 Angle : 0.703 12.279 68994 Z= 0.348 Chirality : 0.047 0.258 7758 Planarity : 0.003 0.068 8928 Dihedral : 6.126 49.318 6942 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.06 % Favored : 89.86 % Rotamer: Outliers : 3.38 % Allowed : 18.25 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.39 % Twisted General : 0.60 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.10), residues: 6156 helix: -0.74 (0.09), residues: 2808 sheet: -1.09 (0.23), residues: 486 loop : -3.25 (0.11), residues: 2862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 474 HIS 0.004 0.001 HIS G 503 PHE 0.025 0.001 PHE K 473 TYR 0.009 0.001 TYR L 630 ARG 0.010 0.000 ARG G 447 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 735 residues out of total 5526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 549 time to evaluate : 4.398 Fit side-chains REVERT: A 417 ASN cc_start: 0.7809 (m-40) cc_final: 0.7546 (m-40) REVERT: A 503 HIS cc_start: 0.8280 (OUTLIER) cc_final: 0.8070 (t-90) REVERT: A 689 GLU cc_start: 0.8304 (mt-10) cc_final: 0.7749 (mt-10) REVERT: B 473 PHE cc_start: 0.7818 (m-80) cc_final: 0.7414 (m-80) REVERT: B 480 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7867 (pt0) REVERT: B 503 HIS cc_start: 0.8350 (OUTLIER) cc_final: 0.8089 (t-90) REVERT: B 559 ILE cc_start: 0.9265 (mm) cc_final: 0.8917 (mt) REVERT: B 562 MET cc_start: 0.8678 (tpt) cc_final: 0.8345 (tpt) REVERT: B 689 GLU cc_start: 0.8331 (mt-10) cc_final: 0.8117 (mt-10) REVERT: C 473 PHE cc_start: 0.7655 (m-80) cc_final: 0.7164 (m-80) REVERT: C 480 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7262 (tm-30) REVERT: C 689 GLU cc_start: 0.8371 (mt-10) cc_final: 0.8083 (mt-10) REVERT: D 503 HIS cc_start: 0.8311 (OUTLIER) cc_final: 0.7939 (t-90) REVERT: D 556 ASP cc_start: 0.7807 (m-30) cc_final: 0.7557 (t70) REVERT: E 382 GLN cc_start: 0.6776 (pm20) cc_final: 0.6358 (pp30) REVERT: E 417 ASN cc_start: 0.8022 (m-40) cc_final: 0.7767 (m-40) REVERT: E 503 HIS cc_start: 0.8219 (OUTLIER) cc_final: 0.8003 (t-90) REVERT: E 689 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7734 (mt-10) REVERT: F 382 GLN cc_start: 0.6666 (pm20) cc_final: 0.6135 (pm20) REVERT: F 480 GLU cc_start: 0.7963 (tm-30) cc_final: 0.7697 (pt0) REVERT: F 503 HIS cc_start: 0.8194 (OUTLIER) cc_final: 0.7987 (t-90) REVERT: G 473 PHE cc_start: 0.7793 (m-80) cc_final: 0.7476 (m-80) REVERT: G 507 GLU cc_start: 0.7173 (mt-10) cc_final: 0.6908 (mt-10) REVERT: G 689 GLU cc_start: 0.8334 (mt-10) cc_final: 0.8091 (mt-10) REVERT: H 480 GLU cc_start: 0.7839 (tm-30) cc_final: 0.7295 (tm-30) REVERT: H 503 HIS cc_start: 0.8299 (OUTLIER) cc_final: 0.8033 (t-90) REVERT: H 562 MET cc_start: 0.8536 (tpt) cc_final: 0.8236 (tpt) REVERT: H 689 GLU cc_start: 0.8426 (mt-10) cc_final: 0.7857 (mt-10) REVERT: I 473 PHE cc_start: 0.7870 (m-80) cc_final: 0.7596 (m-80) REVERT: I 503 HIS cc_start: 0.8272 (OUTLIER) cc_final: 0.7975 (t-90) REVERT: J 473 PHE cc_start: 0.7602 (m-80) cc_final: 0.7313 (m-80) REVERT: J 503 HIS cc_start: 0.8292 (OUTLIER) cc_final: 0.7951 (t-90) REVERT: K 480 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7298 (tm-30) REVERT: K 503 HIS cc_start: 0.8296 (OUTLIER) cc_final: 0.8049 (t-90) REVERT: K 689 GLU cc_start: 0.8428 (mt-10) cc_final: 0.7865 (mt-10) REVERT: L 473 PHE cc_start: 0.7870 (m-80) cc_final: 0.7599 (m-80) REVERT: L 503 HIS cc_start: 0.8246 (OUTLIER) cc_final: 0.7948 (t-90) REVERT: M 417 ASN cc_start: 0.7765 (m-40) cc_final: 0.7503 (m-40) REVERT: M 503 HIS cc_start: 0.8267 (OUTLIER) cc_final: 0.8054 (t-90) REVERT: M 689 GLU cc_start: 0.8297 (mt-10) cc_final: 0.8032 (mt-10) REVERT: N 473 PHE cc_start: 0.7812 (m-80) cc_final: 0.7410 (m-80) REVERT: N 480 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7859 (pt0) REVERT: N 503 HIS cc_start: 0.8346 (OUTLIER) cc_final: 0.8067 (t-90) REVERT: N 689 GLU cc_start: 0.8325 (mt-10) cc_final: 0.8113 (mt-10) REVERT: O 473 PHE cc_start: 0.7684 (m-80) cc_final: 0.7178 (m-80) REVERT: O 480 GLU cc_start: 0.7877 (tm-30) cc_final: 0.7290 (tm-30) REVERT: P 480 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.8036 (pt0) REVERT: P 503 HIS cc_start: 0.8322 (OUTLIER) cc_final: 0.8059 (t-90) REVERT: Q 382 GLN cc_start: 0.6780 (pm20) cc_final: 0.6372 (pp30) REVERT: Q 417 ASN cc_start: 0.8013 (m-40) cc_final: 0.7735 (m-40) REVERT: Q 473 PHE cc_start: 0.7900 (m-80) cc_final: 0.7340 (m-80) REVERT: Q 480 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7558 (tm-30) REVERT: Q 503 HIS cc_start: 0.8226 (OUTLIER) cc_final: 0.8007 (t-90) REVERT: R 473 PHE cc_start: 0.7741 (m-80) cc_final: 0.7157 (m-80) REVERT: R 480 GLU cc_start: 0.8011 (tm-30) cc_final: 0.7735 (pt0) REVERT: R 503 HIS cc_start: 0.8243 (OUTLIER) cc_final: 0.8037 (t-90) outliers start: 186 outliers final: 134 residues processed: 687 average time/residue: 0.4199 time to fit residues: 511.6205 Evaluate side-chains 660 residues out of total 5526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 510 time to evaluate : 4.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 493 HIS Chi-restraints excluded: chain B residue 503 HIS Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 610 PHE Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 665 MET Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 694 ILE Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 420 MET Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 493 HIS Chi-restraints excluded: chain D residue 503 HIS Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 559 ILE Chi-restraints excluded: chain D residue 622 VAL Chi-restraints excluded: chain D residue 694 ILE Chi-restraints excluded: chain E residue 392 ASP Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain E residue 493 HIS Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 503 HIS Chi-restraints excluded: chain E residue 540 VAL Chi-restraints excluded: chain E residue 559 ILE Chi-restraints excluded: chain E residue 622 VAL Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 420 MET Chi-restraints excluded: chain F residue 432 VAL Chi-restraints excluded: chain F residue 472 THR Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 503 HIS Chi-restraints excluded: chain F residue 540 VAL Chi-restraints excluded: chain F residue 622 VAL Chi-restraints excluded: chain F residue 665 MET Chi-restraints excluded: chain F residue 690 LEU Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 432 VAL Chi-restraints excluded: chain G residue 480 GLU Chi-restraints excluded: chain G residue 493 HIS Chi-restraints excluded: chain G residue 498 THR Chi-restraints excluded: chain G residue 540 VAL Chi-restraints excluded: chain G residue 622 VAL Chi-restraints excluded: chain G residue 665 MET Chi-restraints excluded: chain H residue 390 LEU Chi-restraints excluded: chain H residue 432 VAL Chi-restraints excluded: chain H residue 493 HIS Chi-restraints excluded: chain H residue 498 THR Chi-restraints excluded: chain H residue 503 HIS Chi-restraints excluded: chain H residue 540 VAL Chi-restraints excluded: chain H residue 622 VAL Chi-restraints excluded: chain I residue 390 LEU Chi-restraints excluded: chain I residue 432 VAL Chi-restraints excluded: chain I residue 498 THR Chi-restraints excluded: chain I residue 503 HIS Chi-restraints excluded: chain I residue 540 VAL Chi-restraints excluded: chain I residue 622 VAL Chi-restraints excluded: chain I residue 665 MET Chi-restraints excluded: chain J residue 392 ASP Chi-restraints excluded: chain J residue 417 ASN Chi-restraints excluded: chain J residue 420 MET Chi-restraints excluded: chain J residue 432 VAL Chi-restraints excluded: chain J residue 472 THR Chi-restraints excluded: chain J residue 493 HIS Chi-restraints excluded: chain J residue 498 THR Chi-restraints excluded: chain J residue 503 HIS Chi-restraints excluded: chain J residue 540 VAL Chi-restraints excluded: chain J residue 622 VAL Chi-restraints excluded: chain J residue 665 MET Chi-restraints excluded: chain K residue 390 LEU Chi-restraints excluded: chain K residue 432 VAL Chi-restraints excluded: chain K residue 498 THR Chi-restraints excluded: chain K residue 503 HIS Chi-restraints excluded: chain K residue 540 VAL Chi-restraints excluded: chain K residue 622 VAL Chi-restraints excluded: chain L residue 390 LEU Chi-restraints excluded: chain L residue 432 VAL Chi-restraints excluded: chain L residue 498 THR Chi-restraints excluded: chain L residue 503 HIS Chi-restraints excluded: chain L residue 540 VAL Chi-restraints excluded: chain L residue 622 VAL Chi-restraints excluded: chain L residue 665 MET Chi-restraints excluded: chain M residue 432 VAL Chi-restraints excluded: chain M residue 472 THR Chi-restraints excluded: chain M residue 498 THR Chi-restraints excluded: chain M residue 503 HIS Chi-restraints excluded: chain M residue 540 VAL Chi-restraints excluded: chain M residue 622 VAL Chi-restraints excluded: chain M residue 665 MET Chi-restraints excluded: chain M residue 690 LEU Chi-restraints excluded: chain M residue 696 ILE Chi-restraints excluded: chain N residue 390 LEU Chi-restraints excluded: chain N residue 420 MET Chi-restraints excluded: chain N residue 432 VAL Chi-restraints excluded: chain N residue 493 HIS Chi-restraints excluded: chain N residue 503 HIS Chi-restraints excluded: chain N residue 610 PHE Chi-restraints excluded: chain N residue 622 VAL Chi-restraints excluded: chain N residue 665 MET Chi-restraints excluded: chain O residue 390 LEU Chi-restraints excluded: chain O residue 392 ASP Chi-restraints excluded: chain O residue 432 VAL Chi-restraints excluded: chain O residue 493 HIS Chi-restraints excluded: chain O residue 498 THR Chi-restraints excluded: chain O residue 540 VAL Chi-restraints excluded: chain O residue 622 VAL Chi-restraints excluded: chain O residue 694 ILE Chi-restraints excluded: chain P residue 392 ASP Chi-restraints excluded: chain P residue 420 MET Chi-restraints excluded: chain P residue 432 VAL Chi-restraints excluded: chain P residue 480 GLU Chi-restraints excluded: chain P residue 493 HIS Chi-restraints excluded: chain P residue 498 THR Chi-restraints excluded: chain P residue 503 HIS Chi-restraints excluded: chain P residue 540 VAL Chi-restraints excluded: chain P residue 559 ILE Chi-restraints excluded: chain P residue 622 VAL Chi-restraints excluded: chain P residue 694 ILE Chi-restraints excluded: chain Q residue 392 ASP Chi-restraints excluded: chain Q residue 432 VAL Chi-restraints excluded: chain Q residue 472 THR Chi-restraints excluded: chain Q residue 493 HIS Chi-restraints excluded: chain Q residue 498 THR Chi-restraints excluded: chain Q residue 503 HIS Chi-restraints excluded: chain Q residue 540 VAL Chi-restraints excluded: chain Q residue 559 ILE Chi-restraints excluded: chain Q residue 622 VAL Chi-restraints excluded: chain R residue 390 LEU Chi-restraints excluded: chain R residue 432 VAL Chi-restraints excluded: chain R residue 472 THR Chi-restraints excluded: chain R residue 503 HIS Chi-restraints excluded: chain R residue 540 VAL Chi-restraints excluded: chain R residue 622 VAL Chi-restraints excluded: chain R residue 665 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 536 optimal weight: 0.0370 chunk 565 optimal weight: 0.1980 chunk 515 optimal weight: 0.0020 chunk 549 optimal weight: 0.0040 chunk 564 optimal weight: 0.6980 chunk 330 optimal weight: 0.4980 chunk 239 optimal weight: 4.9990 chunk 431 optimal weight: 1.9990 chunk 168 optimal weight: 0.9990 chunk 496 optimal weight: 0.8980 chunk 519 optimal weight: 9.9990 overall best weight: 0.1478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 452 GLN ** F 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 452 GLN H 452 GLN ** I 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 417 ASN J 452 GLN K 452 GLN ** L 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 452 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.4212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 51012 Z= 0.168 Angle : 0.692 12.791 68994 Z= 0.343 Chirality : 0.045 0.232 7758 Planarity : 0.003 0.077 8928 Dihedral : 5.732 47.012 6942 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 2.41 % Allowed : 19.61 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.10), residues: 6156 helix: -0.29 (0.10), residues: 2790 sheet: -1.31 (0.23), residues: 522 loop : -3.05 (0.11), residues: 2844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 474 HIS 0.004 0.000 HIS G 503 PHE 0.016 0.001 PHE K 473 TYR 0.009 0.001 TYR L 630 ARG 0.014 0.000 ARG G 447 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 783 residues out of total 5526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 650 time to evaluate : 4.346 Fit side-chains REVERT: A 473 PHE cc_start: 0.7901 (m-80) cc_final: 0.7555 (m-80) REVERT: A 689 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7822 (mt-10) REVERT: B 466 LEU cc_start: 0.5818 (OUTLIER) cc_final: 0.5569 (pp) REVERT: B 473 PHE cc_start: 0.7666 (m-80) cc_final: 0.7327 (m-80) REVERT: B 480 GLU cc_start: 0.8037 (tm-30) cc_final: 0.7816 (pt0) REVERT: B 503 HIS cc_start: 0.8228 (OUTLIER) cc_final: 0.8021 (t-90) REVERT: B 507 GLU cc_start: 0.7136 (mt-10) cc_final: 0.6888 (mt-10) REVERT: B 559 ILE cc_start: 0.9203 (mm) cc_final: 0.8884 (mt) REVERT: B 562 MET cc_start: 0.8604 (tpt) cc_final: 0.8272 (tpt) REVERT: B 616 GLU cc_start: 0.7667 (tp30) cc_final: 0.7363 (tp30) REVERT: B 689 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7895 (mt-10) REVERT: C 473 PHE cc_start: 0.7541 (m-80) cc_final: 0.7190 (m-80) REVERT: C 480 GLU cc_start: 0.7838 (tm-30) cc_final: 0.7250 (tm-30) REVERT: C 689 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7874 (mt-10) REVERT: D 466 LEU cc_start: 0.5608 (OUTLIER) cc_final: 0.5280 (pp) REVERT: D 556 ASP cc_start: 0.7804 (m-30) cc_final: 0.7548 (t70) REVERT: D 562 MET cc_start: 0.8368 (tpt) cc_final: 0.8011 (tpt) REVERT: E 382 GLN cc_start: 0.6630 (pm20) cc_final: 0.6306 (pp30) REVERT: E 417 ASN cc_start: 0.7961 (m-40) cc_final: 0.7677 (m-40) REVERT: E 689 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7995 (mt-10) REVERT: F 473 PHE cc_start: 0.7637 (m-80) cc_final: 0.7129 (m-80) REVERT: F 480 GLU cc_start: 0.8001 (tm-30) cc_final: 0.7755 (pt0) REVERT: F 493 HIS cc_start: 0.7280 (OUTLIER) cc_final: 0.6984 (m170) REVERT: F 507 GLU cc_start: 0.7160 (mt-10) cc_final: 0.6941 (mt-10) REVERT: G 507 GLU cc_start: 0.7110 (mt-10) cc_final: 0.6903 (mt-10) REVERT: G 689 GLU cc_start: 0.8290 (mt-10) cc_final: 0.8036 (mt-10) REVERT: H 473 PHE cc_start: 0.7616 (m-80) cc_final: 0.7223 (m-80) REVERT: H 480 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7312 (tm-30) REVERT: H 503 HIS cc_start: 0.8191 (OUTLIER) cc_final: 0.7633 (t-90) REVERT: H 507 GLU cc_start: 0.7278 (mt-10) cc_final: 0.6789 (mt-10) REVERT: H 562 MET cc_start: 0.8377 (tpt) cc_final: 0.8120 (tpt) REVERT: H 689 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8065 (mt-10) REVERT: I 473 PHE cc_start: 0.7772 (m-80) cc_final: 0.7457 (m-80) REVERT: I 545 MET cc_start: 0.8221 (ttp) cc_final: 0.7989 (ttm) REVERT: J 466 LEU cc_start: 0.5465 (OUTLIER) cc_final: 0.5152 (pp) REVERT: J 473 PHE cc_start: 0.7553 (m-80) cc_final: 0.7187 (m-80) REVERT: J 503 HIS cc_start: 0.8157 (OUTLIER) cc_final: 0.7632 (t-90) REVERT: J 507 GLU cc_start: 0.7137 (mt-10) cc_final: 0.6554 (mt-10) REVERT: K 473 PHE cc_start: 0.7624 (m-80) cc_final: 0.7231 (m-80) REVERT: K 480 GLU cc_start: 0.7813 (tm-30) cc_final: 0.7314 (tm-30) REVERT: K 562 MET cc_start: 0.8359 (tpt) cc_final: 0.8132 (tpt) REVERT: K 689 GLU cc_start: 0.8371 (mt-10) cc_final: 0.7799 (mt-10) REVERT: L 473 PHE cc_start: 0.7774 (m-80) cc_final: 0.7462 (m-80) REVERT: M 473 PHE cc_start: 0.7875 (m-80) cc_final: 0.7544 (m-80) REVERT: M 689 GLU cc_start: 0.8317 (mt-10) cc_final: 0.7947 (mt-10) REVERT: N 466 LEU cc_start: 0.5811 (OUTLIER) cc_final: 0.5576 (pp) REVERT: N 473 PHE cc_start: 0.7664 (m-80) cc_final: 0.7330 (m-80) REVERT: N 480 GLU cc_start: 0.8027 (tm-30) cc_final: 0.7811 (pt0) REVERT: N 507 GLU cc_start: 0.7160 (mt-10) cc_final: 0.6932 (mt-10) REVERT: N 561 ASN cc_start: 0.8965 (t0) cc_final: 0.8727 (t0) REVERT: N 562 MET cc_start: 0.8648 (tpt) cc_final: 0.8393 (tpt) REVERT: N 689 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7920 (mt-10) REVERT: O 473 PHE cc_start: 0.7566 (m-80) cc_final: 0.7194 (m-80) REVERT: O 480 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7263 (tm-30) REVERT: P 473 PHE cc_start: 0.7599 (m-80) cc_final: 0.7336 (m-80) REVERT: P 480 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7933 (pt0) REVERT: P 562 MET cc_start: 0.8448 (tpt) cc_final: 0.8097 (tpt) REVERT: Q 382 GLN cc_start: 0.6623 (pm20) cc_final: 0.6304 (pp30) REVERT: Q 417 ASN cc_start: 0.7958 (m-40) cc_final: 0.7712 (m-40) REVERT: Q 473 PHE cc_start: 0.7816 (m-80) cc_final: 0.7296 (m-80) REVERT: Q 480 GLU cc_start: 0.7844 (tm-30) cc_final: 0.7569 (tm-30) REVERT: R 473 PHE cc_start: 0.7584 (m-80) cc_final: 0.7078 (m-80) REVERT: R 480 GLU cc_start: 0.8052 (tm-30) cc_final: 0.7803 (pt0) REVERT: R 507 GLU cc_start: 0.7163 (mt-10) cc_final: 0.6915 (mt-10) outliers start: 133 outliers final: 87 residues processed: 742 average time/residue: 0.4206 time to fit residues: 554.5089 Evaluate side-chains 644 residues out of total 5526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 548 time to evaluate : 4.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 493 HIS Chi-restraints excluded: chain B residue 503 HIS Chi-restraints excluded: chain B residue 610 PHE Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 493 HIS Chi-restraints excluded: chain D residue 622 VAL Chi-restraints excluded: chain D residue 694 ILE Chi-restraints excluded: chain E residue 392 ASP Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain E residue 493 HIS Chi-restraints excluded: chain E residue 540 VAL Chi-restraints excluded: chain E residue 622 VAL Chi-restraints excluded: chain F residue 432 VAL Chi-restraints excluded: chain F residue 472 THR Chi-restraints excluded: chain F residue 493 HIS Chi-restraints excluded: chain F residue 540 VAL Chi-restraints excluded: chain F residue 622 VAL Chi-restraints excluded: chain G residue 432 VAL Chi-restraints excluded: chain G residue 493 HIS Chi-restraints excluded: chain G residue 540 VAL Chi-restraints excluded: chain G residue 622 VAL Chi-restraints excluded: chain G residue 665 MET Chi-restraints excluded: chain H residue 432 VAL Chi-restraints excluded: chain H residue 493 HIS Chi-restraints excluded: chain H residue 503 HIS Chi-restraints excluded: chain H residue 540 VAL Chi-restraints excluded: chain H residue 622 VAL Chi-restraints excluded: chain H residue 665 MET Chi-restraints excluded: chain I residue 432 VAL Chi-restraints excluded: chain I residue 540 VAL Chi-restraints excluded: chain I residue 622 VAL Chi-restraints excluded: chain I residue 665 MET Chi-restraints excluded: chain J residue 417 ASN Chi-restraints excluded: chain J residue 432 VAL Chi-restraints excluded: chain J residue 466 LEU Chi-restraints excluded: chain J residue 472 THR Chi-restraints excluded: chain J residue 493 HIS Chi-restraints excluded: chain J residue 503 HIS Chi-restraints excluded: chain J residue 540 VAL Chi-restraints excluded: chain J residue 622 VAL Chi-restraints excluded: chain J residue 665 MET Chi-restraints excluded: chain K residue 432 VAL Chi-restraints excluded: chain K residue 540 VAL Chi-restraints excluded: chain K residue 622 VAL Chi-restraints excluded: chain K residue 665 MET Chi-restraints excluded: chain L residue 420 MET Chi-restraints excluded: chain L residue 432 VAL Chi-restraints excluded: chain L residue 540 VAL Chi-restraints excluded: chain L residue 622 VAL Chi-restraints excluded: chain L residue 665 MET Chi-restraints excluded: chain M residue 432 VAL Chi-restraints excluded: chain M residue 472 THR Chi-restraints excluded: chain M residue 622 VAL Chi-restraints excluded: chain M residue 665 MET Chi-restraints excluded: chain M residue 696 ILE Chi-restraints excluded: chain N residue 420 MET Chi-restraints excluded: chain N residue 432 VAL Chi-restraints excluded: chain N residue 466 LEU Chi-restraints excluded: chain N residue 493 HIS Chi-restraints excluded: chain N residue 610 PHE Chi-restraints excluded: chain N residue 622 VAL Chi-restraints excluded: chain O residue 432 VAL Chi-restraints excluded: chain O residue 493 HIS Chi-restraints excluded: chain O residue 540 VAL Chi-restraints excluded: chain O residue 622 VAL Chi-restraints excluded: chain P residue 420 MET Chi-restraints excluded: chain P residue 432 VAL Chi-restraints excluded: chain P residue 480 GLU Chi-restraints excluded: chain P residue 493 HIS Chi-restraints excluded: chain P residue 540 VAL Chi-restraints excluded: chain P residue 622 VAL Chi-restraints excluded: chain P residue 694 ILE Chi-restraints excluded: chain Q residue 392 ASP Chi-restraints excluded: chain Q residue 432 VAL Chi-restraints excluded: chain Q residue 472 THR Chi-restraints excluded: chain Q residue 493 HIS Chi-restraints excluded: chain Q residue 540 VAL Chi-restraints excluded: chain Q residue 622 VAL Chi-restraints excluded: chain R residue 420 MET Chi-restraints excluded: chain R residue 432 VAL Chi-restraints excluded: chain R residue 472 THR Chi-restraints excluded: chain R residue 622 VAL Chi-restraints excluded: chain R residue 665 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 547 optimal weight: 0.7980 chunk 360 optimal weight: 1.9990 chunk 581 optimal weight: 0.9990 chunk 354 optimal weight: 4.9990 chunk 275 optimal weight: 0.9990 chunk 404 optimal weight: 4.9990 chunk 609 optimal weight: 0.9980 chunk 561 optimal weight: 2.9990 chunk 485 optimal weight: 9.9990 chunk 50 optimal weight: 0.0970 chunk 375 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 452 GLN ** F 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 417 ASN ** I 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 417 ASN ** L 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 452 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.4247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 51012 Z= 0.196 Angle : 0.741 14.922 68994 Z= 0.358 Chirality : 0.046 0.220 7758 Planarity : 0.003 0.081 8928 Dihedral : 5.396 45.077 6918 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer: Outliers : 2.21 % Allowed : 20.59 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.10), residues: 6156 helix: -0.14 (0.10), residues: 2808 sheet: -1.27 (0.23), residues: 522 loop : -3.07 (0.11), residues: 2826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 474 HIS 0.004 0.001 HIS G 503 PHE 0.019 0.001 PHE G 473 TYR 0.009 0.001 TYR R 687 ARG 0.010 0.000 ARG J 415 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 5526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 565 time to evaluate : 4.394 Fit side-chains REVERT: A 382 GLN cc_start: 0.6673 (pm20) cc_final: 0.6265 (pp30) REVERT: A 473 PHE cc_start: 0.7922 (m-80) cc_final: 0.7721 (m-80) REVERT: A 689 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7829 (mt-10) REVERT: B 466 LEU cc_start: 0.5748 (OUTLIER) cc_final: 0.5490 (pp) REVERT: B 473 PHE cc_start: 0.7604 (m-80) cc_final: 0.7370 (m-80) REVERT: B 480 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7789 (pt0) REVERT: B 482 ARG cc_start: 0.8474 (mtp180) cc_final: 0.8268 (ptt180) REVERT: B 503 HIS cc_start: 0.8200 (OUTLIER) cc_final: 0.7990 (t-90) REVERT: B 507 GLU cc_start: 0.7165 (mt-10) cc_final: 0.6956 (mt-10) REVERT: B 689 GLU cc_start: 0.8248 (mt-10) cc_final: 0.8047 (mt-10) REVERT: C 473 PHE cc_start: 0.7632 (m-80) cc_final: 0.7110 (m-80) REVERT: C 480 GLU cc_start: 0.7836 (tm-30) cc_final: 0.7257 (tm-30) REVERT: C 689 GLU cc_start: 0.8312 (mt-10) cc_final: 0.8045 (mt-10) REVERT: D 466 LEU cc_start: 0.5725 (OUTLIER) cc_final: 0.5425 (pp) REVERT: E 417 ASN cc_start: 0.8025 (m-40) cc_final: 0.7744 (m-40) REVERT: E 689 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7741 (mt-10) REVERT: F 473 PHE cc_start: 0.7688 (m-80) cc_final: 0.7189 (m-80) REVERT: F 480 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7733 (pt0) REVERT: F 493 HIS cc_start: 0.7247 (OUTLIER) cc_final: 0.6985 (m170) REVERT: G 473 PHE cc_start: 0.7929 (m-80) cc_final: 0.7692 (m-80) REVERT: G 507 GLU cc_start: 0.7119 (mt-10) cc_final: 0.6839 (mt-10) REVERT: G 689 GLU cc_start: 0.8273 (mt-10) cc_final: 0.8028 (mt-10) REVERT: H 473 PHE cc_start: 0.7564 (m-80) cc_final: 0.7221 (m-80) REVERT: H 480 GLU cc_start: 0.7820 (tm-30) cc_final: 0.7312 (tm-30) REVERT: H 503 HIS cc_start: 0.8227 (OUTLIER) cc_final: 0.7570 (t-90) REVERT: H 507 GLU cc_start: 0.7303 (mt-10) cc_final: 0.6788 (mt-10) REVERT: I 473 PHE cc_start: 0.7856 (m-80) cc_final: 0.7467 (m-80) REVERT: I 480 GLU cc_start: 0.7907 (tm-30) cc_final: 0.7415 (tm-30) REVERT: J 466 LEU cc_start: 0.5576 (OUTLIER) cc_final: 0.5328 (pp) REVERT: J 473 PHE cc_start: 0.7613 (m-80) cc_final: 0.7338 (m-80) REVERT: J 503 HIS cc_start: 0.8128 (OUTLIER) cc_final: 0.7583 (t-90) REVERT: J 507 GLU cc_start: 0.7159 (mt-10) cc_final: 0.6640 (mt-10) REVERT: K 473 PHE cc_start: 0.7575 (m-80) cc_final: 0.7232 (m-80) REVERT: K 480 GLU cc_start: 0.7813 (tm-30) cc_final: 0.7298 (tm-30) REVERT: K 689 GLU cc_start: 0.8372 (mt-10) cc_final: 0.8039 (mt-10) REVERT: L 473 PHE cc_start: 0.7867 (m-80) cc_final: 0.7480 (m-80) REVERT: M 382 GLN cc_start: 0.6682 (pm20) cc_final: 0.6283 (pp30) REVERT: M 473 PHE cc_start: 0.7882 (m-80) cc_final: 0.7563 (m-80) REVERT: M 689 GLU cc_start: 0.8296 (mt-10) cc_final: 0.8045 (mt-10) REVERT: N 466 LEU cc_start: 0.5747 (OUTLIER) cc_final: 0.5522 (pp) REVERT: N 473 PHE cc_start: 0.7591 (m-80) cc_final: 0.7340 (m-80) REVERT: N 480 GLU cc_start: 0.8021 (tm-30) cc_final: 0.7783 (pt0) REVERT: N 482 ARG cc_start: 0.8480 (mtp180) cc_final: 0.8278 (ptt180) REVERT: N 562 MET cc_start: 0.8736 (tpt) cc_final: 0.8398 (tpt) REVERT: N 689 GLU cc_start: 0.8254 (mt-10) cc_final: 0.8048 (mt-10) REVERT: O 473 PHE cc_start: 0.7659 (m-80) cc_final: 0.7116 (m-80) REVERT: O 480 GLU cc_start: 0.7843 (tm-30) cc_final: 0.7265 (tm-30) REVERT: P 473 PHE cc_start: 0.7677 (m-80) cc_final: 0.7385 (m-80) REVERT: P 480 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7954 (pt0) REVERT: Q 417 ASN cc_start: 0.8006 (m-40) cc_final: 0.7762 (m-40) REVERT: Q 473 PHE cc_start: 0.7889 (m-80) cc_final: 0.7336 (m-80) REVERT: Q 480 GLU cc_start: 0.7813 (tm-30) cc_final: 0.7598 (tm-30) REVERT: R 473 PHE cc_start: 0.7606 (m-80) cc_final: 0.7095 (m-80) REVERT: R 480 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7817 (pt0) REVERT: R 493 HIS cc_start: 0.7272 (OUTLIER) cc_final: 0.6976 (m170) outliers start: 122 outliers final: 85 residues processed: 648 average time/residue: 0.4221 time to fit residues: 487.0489 Evaluate side-chains 626 residues out of total 5526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 531 time to evaluate : 4.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 493 HIS Chi-restraints excluded: chain B residue 503 HIS Chi-restraints excluded: chain B residue 610 PHE Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 493 HIS Chi-restraints excluded: chain D residue 622 VAL Chi-restraints excluded: chain D residue 694 ILE Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain E residue 493 HIS Chi-restraints excluded: chain E residue 540 VAL Chi-restraints excluded: chain E residue 622 VAL Chi-restraints excluded: chain F residue 432 VAL Chi-restraints excluded: chain F residue 472 THR Chi-restraints excluded: chain F residue 493 HIS Chi-restraints excluded: chain F residue 540 VAL Chi-restraints excluded: chain F residue 622 VAL Chi-restraints excluded: chain G residue 417 ASN Chi-restraints excluded: chain G residue 432 VAL Chi-restraints excluded: chain G residue 493 HIS Chi-restraints excluded: chain G residue 540 VAL Chi-restraints excluded: chain G residue 622 VAL Chi-restraints excluded: chain G residue 665 MET Chi-restraints excluded: chain H residue 432 VAL Chi-restraints excluded: chain H residue 493 HIS Chi-restraints excluded: chain H residue 503 HIS Chi-restraints excluded: chain H residue 540 VAL Chi-restraints excluded: chain H residue 610 PHE Chi-restraints excluded: chain H residue 622 VAL Chi-restraints excluded: chain H residue 665 MET Chi-restraints excluded: chain I residue 432 VAL Chi-restraints excluded: chain I residue 540 VAL Chi-restraints excluded: chain I residue 622 VAL Chi-restraints excluded: chain I residue 665 MET Chi-restraints excluded: chain J residue 417 ASN Chi-restraints excluded: chain J residue 432 VAL Chi-restraints excluded: chain J residue 466 LEU Chi-restraints excluded: chain J residue 472 THR Chi-restraints excluded: chain J residue 493 HIS Chi-restraints excluded: chain J residue 503 HIS Chi-restraints excluded: chain J residue 540 VAL Chi-restraints excluded: chain J residue 622 VAL Chi-restraints excluded: chain J residue 665 MET Chi-restraints excluded: chain K residue 432 VAL Chi-restraints excluded: chain K residue 540 VAL Chi-restraints excluded: chain K residue 622 VAL Chi-restraints excluded: chain K residue 665 MET Chi-restraints excluded: chain L residue 432 VAL Chi-restraints excluded: chain L residue 540 VAL Chi-restraints excluded: chain L residue 622 VAL Chi-restraints excluded: chain L residue 665 MET Chi-restraints excluded: chain M residue 432 VAL Chi-restraints excluded: chain M residue 622 VAL Chi-restraints excluded: chain M residue 690 LEU Chi-restraints excluded: chain M residue 696 ILE Chi-restraints excluded: chain N residue 420 MET Chi-restraints excluded: chain N residue 432 VAL Chi-restraints excluded: chain N residue 466 LEU Chi-restraints excluded: chain N residue 493 HIS Chi-restraints excluded: chain N residue 610 PHE Chi-restraints excluded: chain N residue 622 VAL Chi-restraints excluded: chain O residue 432 VAL Chi-restraints excluded: chain O residue 493 HIS Chi-restraints excluded: chain O residue 540 VAL Chi-restraints excluded: chain O residue 622 VAL Chi-restraints excluded: chain P residue 420 MET Chi-restraints excluded: chain P residue 432 VAL Chi-restraints excluded: chain P residue 480 GLU Chi-restraints excluded: chain P residue 493 HIS Chi-restraints excluded: chain P residue 540 VAL Chi-restraints excluded: chain P residue 622 VAL Chi-restraints excluded: chain Q residue 432 VAL Chi-restraints excluded: chain Q residue 472 THR Chi-restraints excluded: chain Q residue 493 HIS Chi-restraints excluded: chain Q residue 540 VAL Chi-restraints excluded: chain Q residue 622 VAL Chi-restraints excluded: chain R residue 420 MET Chi-restraints excluded: chain R residue 432 VAL Chi-restraints excluded: chain R residue 472 THR Chi-restraints excluded: chain R residue 493 HIS Chi-restraints excluded: chain R residue 540 VAL Chi-restraints excluded: chain R residue 622 VAL Chi-restraints excluded: chain R residue 665 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 297 optimal weight: 0.9990 chunk 385 optimal weight: 10.0000 chunk 517 optimal weight: 3.9990 chunk 148 optimal weight: 9.9990 chunk 447 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 134 optimal weight: 0.0670 chunk 486 optimal weight: 0.4980 chunk 203 optimal weight: 1.9990 chunk 499 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 overall best weight: 1.1124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 417 ASN ** J 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.134998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.104693 restraints weight = 82099.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.107472 restraints weight = 51328.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.109325 restraints weight = 37320.517| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 51012 Z= 0.221 Angle : 0.745 14.965 68994 Z= 0.364 Chirality : 0.046 0.220 7758 Planarity : 0.003 0.065 8928 Dihedral : 5.315 45.886 6918 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.89 % Favored : 90.11 % Rotamer: Outliers : 2.18 % Allowed : 21.02 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.11), residues: 6156 helix: -0.13 (0.10), residues: 2826 sheet: -1.71 (0.22), residues: 576 loop : -2.98 (0.11), residues: 2754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 474 HIS 0.006 0.001 HIS M 503 PHE 0.025 0.001 PHE J 416 TYR 0.008 0.001 TYR L 630 ARG 0.008 0.000 ARG E 447 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9868.88 seconds wall clock time: 171 minutes 49.77 seconds (10309.77 seconds total)