Starting phenix.real_space_refine on Fri Aug 7 15:25:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wh4_37528/08_2026/8wh4_37528.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wh4_37528/08_2026/8wh4_37528.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wh4_37528/08_2026/8wh4_37528.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wh4_37528/08_2026/8wh4_37528.map" model { file = "/net/cci-nas-00/data/ceres_data/8wh4_37528/08_2026/8wh4_37528.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wh4_37528/08_2026/8wh4_37528.cif" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 96 5.16 5 C 14304 2.51 5 N 3780 2.21 5 O 4170 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22354 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3713 Classifications: {'peptide': 463} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 21, 'TRANS': 441} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 3713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3713 Classifications: {'peptide': 463} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 21, 'TRANS': 441} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 3713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3713 Classifications: {'peptide': 463} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 21, 'TRANS': 441} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 3713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3713 Classifications: {'peptide': 463} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 21, 'TRANS': 441} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 3713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3713 Classifications: {'peptide': 463} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 21, 'TRANS': 441} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "F" Number of atoms: 3713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3713 Classifications: {'peptide': 463} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 21, 'TRANS': 441} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "T" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 76 Classifications: {'DNA': 4} Link IDs: {'rna3p': 3} Time building chain proxies: 5.13, per 1000 atoms: 0.23 Number of scatterers: 22354 At special positions: 0 Unit cell: (124.32, 136.08, 114.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 96 16.00 P 4 15.00 O 4170 8.00 N 3780 7.00 C 14304 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: 2.04 Conformation dependent library (CDL) restraints added in 1.2 seconds 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5304 Finding SS restraints... Secondary structure from input PDB file: 151 helices and 40 sheets defined 46.3% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 324 through 336 Processing helix chain 'A' and resid 363 through 372 Processing helix chain 'A' and resid 376 through 381 removed outlier: 4.305A pdb=" N SER A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 384 No H-bonds generated for 'chain 'A' and resid 382 through 384' Processing helix chain 'A' and resid 385 through 400 Processing helix chain 'A' and resid 430 through 435 removed outlier: 3.882A pdb=" N LYS A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 469 Processing helix chain 'A' and resid 475 through 488 Processing helix chain 'A' and resid 508 through 521 Processing helix chain 'A' and resid 529 through 534 removed outlier: 3.568A pdb=" N ASP A 534 " --> pdb=" O THR A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 546 removed outlier: 3.987A pdb=" N ALA A 545 " --> pdb=" O ASN A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 579 Processing helix chain 'A' and resid 632 through 640 removed outlier: 5.252A pdb=" N GLU A 637 " --> pdb=" O SER A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 661 removed outlier: 4.612A pdb=" N GLY A 657 " --> pdb=" O GLU A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 679 Processing helix chain 'A' and resid 689 through 693 removed outlier: 3.763A pdb=" N GLU A 692 " --> pdb=" O THR A 689 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE A 693 " --> pdb=" O PRO A 690 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 689 through 693' Processing helix chain 'A' and resid 698 through 703 removed outlier: 3.709A pdb=" N GLY A 703 " --> pdb=" O TYR A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 715 No H-bonds generated for 'chain 'A' and resid 713 through 715' Processing helix chain 'A' and resid 716 through 722 removed outlier: 3.882A pdb=" N LEU A 720 " --> pdb=" O LEU A 716 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N LYS A 722 " --> pdb=" O THR A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 744 Processing helix chain 'A' and resid 752 through 763 Processing helix chain 'A' and resid 779 through 784 Processing helix chain 'B' and resid 324 through 336 Processing helix chain 'B' and resid 363 through 372 Processing helix chain 'B' and resid 376 through 381 removed outlier: 3.842A pdb=" N SER B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 384 No H-bonds generated for 'chain 'B' and resid 382 through 384' Processing helix chain 'B' and resid 385 through 400 Processing helix chain 'B' and resid 430 through 435 removed outlier: 3.803A pdb=" N LYS B 435 " --> pdb=" O ASP B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 469 Processing helix chain 'B' and resid 475 through 488 Processing helix chain 'B' and resid 489 through 491 No H-bonds generated for 'chain 'B' and resid 489 through 491' Processing helix chain 'B' and resid 508 through 521 Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 570 through 577 Processing helix chain 'B' and resid 616 through 619 Processing helix chain 'B' and resid 632 through 634 No H-bonds generated for 'chain 'B' and resid 632 through 634' Processing helix chain 'B' and resid 635 through 641 Processing helix chain 'B' and resid 654 through 661 Processing helix chain 'B' and resid 664 through 679 Processing helix chain 'B' and resid 689 through 695 removed outlier: 3.517A pdb=" N GLU B 692 " --> pdb=" O THR B 689 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE B 693 " --> pdb=" O PRO B 690 " (cutoff:3.500A) Proline residue: B 694 - end of helix No H-bonds generated for 'chain 'B' and resid 689 through 695' Processing helix chain 'B' and resid 696 through 704 removed outlier: 3.634A pdb=" N GLY B 703 " --> pdb=" O TYR B 699 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR B 704 " --> pdb=" O LEU B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 715 Proline residue: B 715 - end of helix Processing helix chain 'B' and resid 716 through 721 Processing helix chain 'B' and resid 722 through 724 No H-bonds generated for 'chain 'B' and resid 722 through 724' Processing helix chain 'B' and resid 735 through 744 Processing helix chain 'B' and resid 752 through 764 Processing helix chain 'B' and resid 779 through 784 Processing helix chain 'C' and resid 324 through 336 Processing helix chain 'C' and resid 363 through 372 Processing helix chain 'C' and resid 376 through 381 removed outlier: 4.180A pdb=" N SER C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 384 No H-bonds generated for 'chain 'C' and resid 382 through 384' Processing helix chain 'C' and resid 385 through 400 Processing helix chain 'C' and resid 430 through 435 removed outlier: 3.789A pdb=" N LYS C 435 " --> pdb=" O ASP C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 469 Processing helix chain 'C' and resid 472 through 474 No H-bonds generated for 'chain 'C' and resid 472 through 474' Processing helix chain 'C' and resid 475 through 488 Processing helix chain 'C' and resid 489 through 491 No H-bonds generated for 'chain 'C' and resid 489 through 491' Processing helix chain 'C' and resid 508 through 521 Processing helix chain 'C' and resid 529 through 534 removed outlier: 3.592A pdb=" N THR C 533 " --> pdb=" O GLN C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 546 Processing helix chain 'C' and resid 570 through 579 removed outlier: 3.522A pdb=" N THR C 578 " --> pdb=" O ILE C 574 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU C 579 " --> pdb=" O LYS C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 619 removed outlier: 3.686A pdb=" N ARG C 619 " --> pdb=" O ALA C 616 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 616 through 619' Processing helix chain 'C' and resid 632 through 634 No H-bonds generated for 'chain 'C' and resid 632 through 634' Processing helix chain 'C' and resid 635 through 641 Processing helix chain 'C' and resid 654 through 661 Processing helix chain 'C' and resid 664 through 679 Processing helix chain 'C' and resid 693 through 695 No H-bonds generated for 'chain 'C' and resid 693 through 695' Processing helix chain 'C' and resid 696 through 704 Processing helix chain 'C' and resid 716 through 721 removed outlier: 3.598A pdb=" N SER C 721 " --> pdb=" O MET C 717 " (cutoff:3.500A) Processing helix chain 'C' and resid 736 through 744 Processing helix chain 'C' and resid 752 through 764 Processing helix chain 'C' and resid 779 through 784 Processing helix chain 'D' and resid 324 through 336 Processing helix chain 'D' and resid 363 through 372 Processing helix chain 'D' and resid 376 through 381 removed outlier: 3.878A pdb=" N SER D 381 " --> pdb=" O LYS D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 384 No H-bonds generated for 'chain 'D' and resid 382 through 384' Processing helix chain 'D' and resid 385 through 400 Processing helix chain 'D' and resid 430 through 435 removed outlier: 3.998A pdb=" N LYS D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 451 Processing helix chain 'D' and resid 455 through 469 removed outlier: 3.847A pdb=" N GLU D 459 " --> pdb=" O SER D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 474 No H-bonds generated for 'chain 'D' and resid 472 through 474' Processing helix chain 'D' and resid 475 through 488 Processing helix chain 'D' and resid 508 through 521 Processing helix chain 'D' and resid 528 through 533 removed outlier: 3.729A pdb=" N ILE D 531 " --> pdb=" O GLY D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 547 removed outlier: 3.803A pdb=" N ALA D 545 " --> pdb=" O ASN D 541 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N MET D 547 " --> pdb=" O PHE D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 578 removed outlier: 3.571A pdb=" N ILE D 574 " --> pdb=" O ARG D 570 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR D 578 " --> pdb=" O ILE D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 616 through 619 Processing helix chain 'D' and resid 632 through 634 No H-bonds generated for 'chain 'D' and resid 632 through 634' Processing helix chain 'D' and resid 635 through 641 Processing helix chain 'D' and resid 653 through 661 removed outlier: 4.446A pdb=" N GLY D 657 " --> pdb=" O GLU D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 679 Processing helix chain 'D' and resid 689 through 693 removed outlier: 3.919A pdb=" N ILE D 693 " --> pdb=" O PRO D 690 " (cutoff:3.500A) Processing helix chain 'D' and resid 694 through 704 removed outlier: 4.361A pdb=" N PHE D 698 " --> pdb=" O PRO D 694 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N TYR D 699 " --> pdb=" O ASP D 695 " (cutoff:3.500A) Processing helix chain 'D' and resid 710 through 715 Proline residue: D 715 - end of helix Processing helix chain 'D' and resid 716 through 721 Processing helix chain 'D' and resid 722 through 724 No H-bonds generated for 'chain 'D' and resid 722 through 724' Processing helix chain 'D' and resid 736 through 744 Processing helix chain 'D' and resid 752 through 763 Processing helix chain 'E' and resid 324 through 336 Processing helix chain 'E' and resid 363 through 372 Processing helix chain 'E' and resid 376 through 381 removed outlier: 4.033A pdb=" N SER E 381 " --> pdb=" O LYS E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 382 through 384 No H-bonds generated for 'chain 'E' and resid 382 through 384' Processing helix chain 'E' and resid 385 through 400 Processing helix chain 'E' and resid 430 through 435 Processing helix chain 'E' and resid 447 through 451 removed outlier: 3.511A pdb=" N LYS E 450 " --> pdb=" O ASP E 447 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 469 Processing helix chain 'E' and resid 472 through 474 No H-bonds generated for 'chain 'E' and resid 472 through 474' Processing helix chain 'E' and resid 475 through 488 Processing helix chain 'E' and resid 508 through 521 Processing helix chain 'E' and resid 529 through 534 removed outlier: 3.548A pdb=" N ASP E 534 " --> pdb=" O THR E 530 " (cutoff:3.500A) Processing helix chain 'E' and resid 541 through 546 Processing helix chain 'E' and resid 570 through 578 Processing helix chain 'E' and resid 614 through 619 removed outlier: 4.320A pdb=" N MET E 618 " --> pdb=" O ASP E 614 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ARG E 619 " --> pdb=" O ASN E 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 614 through 619' Processing helix chain 'E' and resid 632 through 634 No H-bonds generated for 'chain 'E' and resid 632 through 634' Processing helix chain 'E' and resid 635 through 641 Processing helix chain 'E' and resid 654 through 661 Processing helix chain 'E' and resid 664 through 679 Processing helix chain 'E' and resid 689 through 694 removed outlier: 3.530A pdb=" N GLU E 692 " --> pdb=" O THR E 689 " (cutoff:3.500A) Proline residue: E 694 - end of helix Processing helix chain 'E' and resid 695 through 700 removed outlier: 4.172A pdb=" N TYR E 699 " --> pdb=" O ASP E 695 " (cutoff:3.500A) Processing helix chain 'E' and resid 710 through 714 Processing helix chain 'E' and resid 718 through 723 removed outlier: 3.520A pdb=" N LYS E 723 " --> pdb=" O LEU E 720 " (cutoff:3.500A) Processing helix chain 'E' and resid 735 through 747 removed outlier: 3.529A pdb=" N LYS E 745 " --> pdb=" O GLN E 741 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR E 746 " --> pdb=" O LYS E 742 " (cutoff:3.500A) Processing helix chain 'E' and resid 752 through 763 Processing helix chain 'E' and resid 778 through 784 removed outlier: 4.006A pdb=" N ILE E 782 " --> pdb=" O PHE E 778 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER E 783 " --> pdb=" O ILE E 779 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER E 784 " --> pdb=" O GLU E 780 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 778 through 784' Processing helix chain 'F' and resid 324 through 337 Processing helix chain 'F' and resid 363 through 372 Processing helix chain 'F' and resid 373 through 375 No H-bonds generated for 'chain 'F' and resid 373 through 375' Processing helix chain 'F' and resid 376 through 381 removed outlier: 4.150A pdb=" N SER F 381 " --> pdb=" O LYS F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 384 No H-bonds generated for 'chain 'F' and resid 382 through 384' Processing helix chain 'F' and resid 385 through 400 Processing helix chain 'F' and resid 430 through 435 Processing helix chain 'F' and resid 455 through 469 Processing helix chain 'F' and resid 475 through 488 Processing helix chain 'F' and resid 489 through 491 No H-bonds generated for 'chain 'F' and resid 489 through 491' Processing helix chain 'F' and resid 508 through 521 Processing helix chain 'F' and resid 529 through 534 removed outlier: 3.749A pdb=" N THR F 533 " --> pdb=" O GLN F 529 " (cutoff:3.500A) Processing helix chain 'F' and resid 541 through 546 removed outlier: 3.530A pdb=" N ASN F 546 " --> pdb=" O PRO F 542 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 578 removed outlier: 3.796A pdb=" N THR F 578 " --> pdb=" O ILE F 574 " (cutoff:3.500A) Processing helix chain 'F' and resid 614 through 619 Processing helix chain 'F' and resid 632 through 634 No H-bonds generated for 'chain 'F' and resid 632 through 634' Processing helix chain 'F' and resid 635 through 641 Processing helix chain 'F' and resid 654 through 661 Processing helix chain 'F' and resid 664 through 679 Processing helix chain 'F' and resid 689 through 695 removed outlier: 3.540A pdb=" N GLU F 692 " --> pdb=" O THR F 689 " (cutoff:3.500A) Proline residue: F 694 - end of helix Processing helix chain 'F' and resid 696 through 704 removed outlier: 3.596A pdb=" N GLY F 703 " --> pdb=" O TYR F 699 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR F 704 " --> pdb=" O LEU F 700 " (cutoff:3.500A) Processing helix chain 'F' and resid 710 through 715 Proline residue: F 715 - end of helix Processing helix chain 'F' and resid 716 through 721 Processing helix chain 'F' and resid 722 through 724 No H-bonds generated for 'chain 'F' and resid 722 through 724' Processing helix chain 'F' and resid 736 through 744 Processing helix chain 'F' and resid 752 through 763 Processing helix chain 'F' and resid 778 through 784 removed outlier: 3.607A pdb=" N SER F 784 " --> pdb=" O GLU F 780 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 339 through 341 Processing sheet with id=AA2, first strand: chain 'A' and resid 412 through 414 Processing sheet with id=AA3, first strand: chain 'A' and resid 524 through 527 removed outlier: 3.777A pdb=" N THR A 604 " --> pdb=" O PHE A 501 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LEU A 498 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N VAL A 624 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N PHE A 500 " --> pdb=" O VAL A 624 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 582 through 583 removed outlier: 4.569A pdb=" N VAL A 582 " --> pdb=" O ASN A 594 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ASN A 594 " --> pdb=" O VAL A 582 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 628 through 631 removed outlier: 5.871A pdb=" N HIS A 629 " --> pdb=" O LYS A 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 706 through 707 removed outlier: 4.048A pdb=" N VAL A 707 " --> pdb=" O ILE A 777 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ILE A 777 " --> pdb=" O VAL A 707 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 726 through 728 Processing sheet with id=AA8, first strand: chain 'B' and resid 339 through 341 Processing sheet with id=AA9, first strand: chain 'B' and resid 412 through 414 Processing sheet with id=AB1, first strand: chain 'B' and resid 524 through 526 removed outlier: 6.689A pdb=" N VAL B 553 " --> pdb=" O ILE B 601 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ASP B 603 " --> pdb=" O VAL B 553 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N CYS B 555 " --> pdb=" O ASP B 603 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LEU B 498 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N VAL B 624 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N PHE B 500 " --> pdb=" O VAL B 624 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N PHE B 626 " --> pdb=" O PHE B 500 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N PHE B 502 " --> pdb=" O PHE B 626 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 581 through 583 Processing sheet with id=AB3, first strand: chain 'B' and resid 628 through 631 Processing sheet with id=AB4, first strand: chain 'B' and resid 706 through 708 removed outlier: 3.708A pdb=" N ILE B 777 " --> pdb=" O VAL B 707 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 726 through 727 Processing sheet with id=AB6, first strand: chain 'B' and resid 765 through 766 Processing sheet with id=AB7, first strand: chain 'C' and resid 339 through 341 Processing sheet with id=AB8, first strand: chain 'C' and resid 412 through 414 Processing sheet with id=AB9, first strand: chain 'C' and resid 524 through 526 removed outlier: 6.584A pdb=" N VAL C 525 " --> pdb=" O PHE C 554 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N VAL C 553 " --> pdb=" O ILE C 601 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ASP C 603 " --> pdb=" O VAL C 553 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N THR C 499 " --> pdb=" O ILE C 602 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N LEU C 498 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N VAL C 624 " --> pdb=" O LEU C 498 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N PHE C 500 " --> pdb=" O VAL C 624 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N PHE C 626 " --> pdb=" O PHE C 500 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N PHE C 502 " --> pdb=" O PHE C 626 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 581 through 583 Processing sheet with id=AC2, first strand: chain 'C' and resid 629 through 631 Processing sheet with id=AC3, first strand: chain 'C' and resid 706 through 708 Processing sheet with id=AC4, first strand: chain 'C' and resid 726 through 728 Processing sheet with id=AC5, first strand: chain 'D' and resid 339 through 341 Processing sheet with id=AC6, first strand: chain 'D' and resid 412 through 415 removed outlier: 4.035A pdb=" N GLY D 418 " --> pdb=" O PHE D 415 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 524 through 527 removed outlier: 6.967A pdb=" N VAL D 553 " --> pdb=" O ILE D 601 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N ASP D 603 " --> pdb=" O VAL D 553 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N CYS D 555 " --> pdb=" O ASP D 603 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N THR D 604 " --> pdb=" O PHE D 501 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N LEU D 498 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N VAL D 624 " --> pdb=" O LEU D 498 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N PHE D 500 " --> pdb=" O VAL D 624 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N PHE D 626 " --> pdb=" O PHE D 500 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N PHE D 502 " --> pdb=" O PHE D 626 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 581 through 583 removed outlier: 3.639A pdb=" N VAL D 582 " --> pdb=" O ASN D 594 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN D 594 " --> pdb=" O VAL D 582 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'D' and resid 628 through 630 removed outlier: 6.697A pdb=" N HIS D 629 " --> pdb=" O LYS D 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'D' and resid 726 through 728 Processing sheet with id=AD2, first strand: chain 'E' and resid 339 through 341 Processing sheet with id=AD3, first strand: chain 'E' and resid 412 through 415 removed outlier: 3.557A pdb=" N GLY E 418 " --> pdb=" O PHE E 415 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 524 through 527 removed outlier: 6.309A pdb=" N VAL E 553 " --> pdb=" O ILE E 601 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N ASP E 603 " --> pdb=" O VAL E 553 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N CYS E 555 " --> pdb=" O ASP E 603 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU E 498 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N VAL E 624 " --> pdb=" O LEU E 498 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N PHE E 500 " --> pdb=" O VAL E 624 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N PHE E 626 " --> pdb=" O PHE E 500 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N PHE E 502 " --> pdb=" O PHE E 626 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 581 through 583 Processing sheet with id=AD6, first strand: chain 'E' and resid 630 through 631 Processing sheet with id=AD7, first strand: chain 'E' and resid 726 through 728 removed outlier: 3.682A pdb=" N ILE E 726 " --> pdb=" O THR E 733 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 339 through 341 Processing sheet with id=AD9, first strand: chain 'F' and resid 412 through 415 removed outlier: 3.920A pdb=" N GLY F 418 " --> pdb=" O PHE F 415 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 524 through 526 removed outlier: 6.982A pdb=" N VAL F 525 " --> pdb=" O PHE F 554 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N VAL F 553 " --> pdb=" O ILE F 601 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ASP F 603 " --> pdb=" O VAL F 553 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N CYS F 555 " --> pdb=" O ASP F 603 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N LEU F 498 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL F 624 " --> pdb=" O LEU F 498 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N PHE F 500 " --> pdb=" O VAL F 624 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N PHE F 626 " --> pdb=" O PHE F 500 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N PHE F 502 " --> pdb=" O PHE F 626 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 581 through 583 Processing sheet with id=AE3, first strand: chain 'F' and resid 628 through 631 removed outlier: 6.594A pdb=" N HIS F 629 " --> pdb=" O LYS F 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'F' and resid 726 through 728 removed outlier: 3.781A pdb=" N ILE F 726 " --> pdb=" O THR F 733 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU F 734 " --> pdb=" O LEU F 774 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU F 774 " --> pdb=" O LEU F 734 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N TYR F 773 " --> pdb=" O LYS F 765 " (cutoff:3.500A) 788 hydrogen bonds defined for protein. 2244 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: 4.22 Time building geometry restraints manager: 2.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.85 - 1.09: 2 1.09 - 1.34: 7183 1.34 - 1.59: 15507 1.59 - 1.84: 148 1.84 - 2.09: 1 Bond restraints: 22841 Sorted by residual: bond pdb=" CG PRO E 559 " pdb=" CD PRO E 559 " ideal model delta sigma weight residual 1.503 0.846 0.657 3.40e-02 8.65e+02 3.74e+02 bond pdb=" CG PRO A 456 " pdb=" CD PRO A 456 " ideal model delta sigma weight residual 1.503 0.986 0.517 3.40e-02 8.65e+02 2.32e+02 bond pdb=" CB PRO E 559 " pdb=" CG PRO E 559 " ideal model delta sigma weight residual 1.492 2.087 -0.595 5.00e-02 4.00e+02 1.41e+02 bond pdb=" CA PRO E 559 " pdb=" CB PRO E 559 " ideal model delta sigma weight residual 1.530 1.442 0.088 1.03e-02 9.43e+03 7.34e+01 bond pdb=" CG PRO E 456 " pdb=" CD PRO E 456 " ideal model delta sigma weight residual 1.503 1.221 0.282 3.40e-02 8.65e+02 6.87e+01 ... (remaining 22836 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.59: 30856 7.59 - 15.17: 24 15.17 - 22.76: 8 22.76 - 30.35: 1 30.35 - 37.94: 3 Bond angle restraints: 30892 Sorted by residual: angle pdb=" N PRO E 559 " pdb=" CD PRO E 559 " pdb=" CG PRO E 559 " ideal model delta sigma weight residual 103.20 66.34 36.86 1.50e+00 4.44e-01 6.04e+02 angle pdb=" N PRO E 559 " pdb=" CA PRO E 559 " pdb=" CB PRO E 559 " ideal model delta sigma weight residual 102.65 87.25 15.40 6.80e-01 2.16e+00 5.13e+02 angle pdb=" CA PRO E 559 " pdb=" CB PRO E 559 " pdb=" CG PRO E 559 " ideal model delta sigma weight residual 104.50 66.56 37.94 1.90e+00 2.77e-01 3.99e+02 angle pdb=" N PRO A 456 " pdb=" CD PRO A 456 " pdb=" CG PRO A 456 " ideal model delta sigma weight residual 103.20 77.55 25.65 1.50e+00 4.44e-01 2.92e+02 angle pdb=" CA PRO E 694 " pdb=" N PRO E 694 " pdb=" CD PRO E 694 " ideal model delta sigma weight residual 112.00 92.62 19.38 1.40e+00 5.10e-01 1.92e+02 ... (remaining 30887 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.76: 13059 32.76 - 65.52: 791 65.52 - 98.27: 33 98.27 - 131.03: 1 131.03 - 163.79: 1 Dihedral angle restraints: 13885 sinusoidal: 5707 harmonic: 8178 Sorted by residual: dihedral pdb=" CA ILE E 681 " pdb=" C ILE E 681 " pdb=" N PRO E 682 " pdb=" CA PRO E 682 " ideal model delta harmonic sigma weight residual -180.00 -150.29 -29.71 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA PRO E 559 " pdb=" C PRO E 559 " pdb=" N ASP E 560 " pdb=" CA ASP E 560 " ideal model delta harmonic sigma weight residual -180.00 -150.81 -29.19 0 5.00e+00 4.00e-02 3.41e+01 dihedral pdb=" CA PRO E 559 " pdb=" CB PRO E 559 " pdb=" CG PRO E 559 " pdb=" CD PRO E 559 " ideal model delta sinusoidal sigma weight residual -38.00 -139.76 101.76 1 2.00e+01 2.50e-03 2.89e+01 ... (remaining 13882 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2745 0.049 - 0.098: 580 0.098 - 0.147: 139 0.147 - 0.196: 6 0.196 - 0.245: 2 Chirality restraints: 3472 Sorted by residual: chirality pdb=" CA PRO E 559 " pdb=" N PRO E 559 " pdb=" C PRO E 559 " pdb=" CB PRO E 559 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA PRO A 456 " pdb=" N PRO A 456 " pdb=" C PRO A 456 " pdb=" CB PRO A 456 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA GLU C 483 " pdb=" N GLU C 483 " pdb=" C GLU C 483 " pdb=" CB GLU C 483 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.29e-01 ... (remaining 3469 not shown) Planarity restraints: 3940 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE E 693 " 0.125 5.00e-02 4.00e+02 1.69e-01 4.57e+01 pdb=" N PRO E 694 " -0.291 5.00e-02 4.00e+02 pdb=" CA PRO E 694 " 0.084 5.00e-02 4.00e+02 pdb=" CD PRO E 694 " 0.083 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 681 " -0.122 5.00e-02 4.00e+02 1.67e-01 4.47e+01 pdb=" N PRO C 682 " 0.288 5.00e-02 4.00e+02 pdb=" CA PRO C 682 " -0.084 5.00e-02 4.00e+02 pdb=" CD PRO C 682 " -0.082 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 455 " 0.097 5.00e-02 4.00e+02 1.31e-01 2.76e+01 pdb=" N PRO A 456 " -0.226 5.00e-02 4.00e+02 pdb=" CA PRO A 456 " 0.061 5.00e-02 4.00e+02 pdb=" CD PRO A 456 " 0.068 5.00e-02 4.00e+02 ... (remaining 3937 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 293 2.64 - 3.21: 20053 3.21 - 3.77: 34159 3.77 - 4.34: 47349 4.34 - 4.90: 76478 Nonbonded interactions: 178332 Sorted by model distance: nonbonded pdb=" OG SER A 710 " pdb=" O ALA E 639 " model vdw 2.077 3.040 nonbonded pdb=" OG SER E 455 " pdb=" OE1 GLU E 457 " model vdw 2.164 3.040 nonbonded pdb=" O GLU D 504 " pdb=" OG1 THR D 507 " model vdw 2.175 3.040 nonbonded pdb=" O GLU D 780 " pdb=" OG SER D 784 " model vdw 2.221 3.040 nonbonded pdb=" O ILE F 531 " pdb=" ND2 ASN F 573 " model vdw 2.223 3.120 ... (remaining 178327 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 21.460 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 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 : 0.008 0.657 22841 Z= 0.269 Angle : 0.833 37.935 30892 Z= 0.478 Chirality : 0.043 0.245 3472 Planarity : 0.007 0.169 3940 Dihedral : 18.554 163.790 8581 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.10 % Allowed : 30.84 % Favored : 66.06 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.16), residues: 2766 helix: 0.28 (0.16), residues: 1052 sheet: -0.46 (0.30), residues: 365 loop : -0.87 (0.16), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 585 TYR 0.020 0.001 TYR A 606 PHE 0.031 0.001 PHE F 502 TRP 0.010 0.001 TRP E 675 HIS 0.007 0.001 HIS E 548 Details of bonding type rmsd/Z covalent geometry : bond 0.00835 / 0.27 (22841) covalent geometry : angle 0.83330 / 0.48 (30892) hydrogen bonds : bond 0.17756 / 11.79 ( 788) hydrogen bonds : angle 6.17378 / 4.26 ( 2244) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 212 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 387 ARG cc_start: 0.7903 (mpp-170) cc_final: 0.7580 (mpp-170) REVERT: E 456 PRO cc_start: 0.6120 (OUTLIER) cc_final: 0.5733 (Cg_endo) REVERT: E 459 GLU cc_start: 0.6829 (mm-30) cc_final: 0.6479 (mm-30) REVERT: E 573 ASN cc_start: 0.3853 (m-40) cc_final: 0.3631 (m-40) REVERT: F 683 ILE cc_start: 0.8640 (pp) cc_final: 0.8359 (pt) REVERT: F 699 TYR cc_start: 0.6976 (OUTLIER) cc_final: 0.6658 (m-80) outliers start: 77 outliers final: 66 residues processed: 285 average time/residue: 0.1577 time to fit residues: 71.9840 Evaluate side-chains 268 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 200 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 436 TYR Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 501 PHE Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 645 TYR Chi-restraints excluded: chain A residue 757 GLU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 593 ASN Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 435 LYS Chi-restraints excluded: chain C residue 441 SER Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 556 SER Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 324 ASN Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 454 ASP Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 512 THR Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 693 ILE Chi-restraints excluded: chain D residue 765 LYS Chi-restraints excluded: chain E residue 324 ASN Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain E residue 337 ASN Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 390 LYS Chi-restraints excluded: chain E residue 419 VAL Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain E residue 456 PRO Chi-restraints excluded: chain E residue 488 SER Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 605 ASN Chi-restraints excluded: chain F residue 336 THR Chi-restraints excluded: chain F residue 356 LYS Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 486 LEU Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 525 VAL Chi-restraints excluded: chain F residue 531 ILE Chi-restraints excluded: chain F residue 578 THR Chi-restraints excluded: chain F residue 581 CYS Chi-restraints excluded: chain F residue 695 ASP Chi-restraints excluded: chain F residue 699 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 30.0000 chunk 111 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 GLN ** B 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 ASN D 417 ASN ** D 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 629 HIS D 641 ASN D 661 ASN E 463 ASN ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 713 HIS F 324 ASN F 475 ASN F 662 ASN F 763 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.243915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.200662 restraints weight = 25239.453| |-----------------------------------------------------------------------------| r_work (start): 0.4262 rms_B_bonded: 2.66 r_work: 0.3856 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3760 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.116 22841 Z= 0.429 Angle : 0.817 8.504 30892 Z= 0.425 Chirality : 0.055 0.244 3472 Planarity : 0.007 0.089 3940 Dihedral : 9.475 169.935 3164 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 7.81 % Allowed : 26.69 % Favored : 65.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.15), residues: 2766 helix: -0.20 (0.16), residues: 1030 sheet: -0.90 (0.27), residues: 383 loop : -1.19 (0.16), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 387 TYR 0.021 0.002 TYR A 482 PHE 0.023 0.002 PHE C 357 TRP 0.024 0.003 TRP C 350 HIS 0.009 0.002 HIS A 347 Details of bonding type rmsd/Z covalent geometry : bond 0.01093 / 0.43 (22841) covalent geometry : angle 0.81737 / 0.42 (30892) hydrogen bonds : bond 0.07356 / 4.84 ( 788) hydrogen bonds : angle 5.80161 / 4.00 ( 2244) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 212 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8447 (mt) REVERT: A 465 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8485 (mp) REVERT: B 457 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.5485 (tm-30) REVERT: B 481 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7882 (tt) REVERT: B 554 PHE cc_start: 0.9000 (OUTLIER) cc_final: 0.7648 (t80) REVERT: B 583 ILE cc_start: 0.7982 (OUTLIER) cc_final: 0.7535 (mp) REVERT: C 426 MET cc_start: 0.7905 (OUTLIER) cc_final: 0.7572 (ttm) REVERT: C 600 ILE cc_start: 0.8898 (OUTLIER) cc_final: 0.8664 (mm) REVERT: C 692 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7008 (mp0) REVERT: C 736 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7414 (tt) REVERT: D 611 ASP cc_start: 0.5711 (p0) cc_final: 0.5452 (p0) REVERT: D 679 TYR cc_start: 0.5825 (OUTLIER) cc_final: 0.5253 (m-80) REVERT: E 351 ILE cc_start: 0.8616 (OUTLIER) cc_final: 0.8124 (mt) REVERT: E 455 SER cc_start: 0.4948 (OUTLIER) cc_final: 0.4467 (p) REVERT: E 529 GLN cc_start: 0.5669 (mm-40) cc_final: 0.5433 (mm-40) REVERT: E 548 HIS cc_start: 0.6530 (OUTLIER) cc_final: 0.5270 (t-170) REVERT: E 610 PHE cc_start: 0.3844 (OUTLIER) cc_final: 0.3138 (m-80) REVERT: F 532 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7651 (mm) REVERT: F 656 ASP cc_start: 0.7112 (OUTLIER) cc_final: 0.6217 (t0) REVERT: F 660 GLN cc_start: 0.7850 (OUTLIER) cc_final: 0.6939 (mp10) REVERT: F 683 ILE cc_start: 0.8491 (pp) cc_final: 0.8272 (pt) outliers start: 194 outliers final: 108 residues processed: 372 average time/residue: 0.1442 time to fit residues: 84.7923 Evaluate side-chains 326 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 200 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 ASN Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 436 TYR Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 636 ARG Chi-restraints excluded: chain A residue 723 LYS Chi-restraints excluded: chain A residue 757 GLU Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 502 PHE Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 561 PHE Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 483 GLU Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 575 LYS Chi-restraints excluded: chain C residue 600 ILE Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 649 LYS Chi-restraints excluded: chain C residue 656 ASP Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain C residue 683 ILE Chi-restraints excluded: chain C residue 689 THR Chi-restraints excluded: chain C residue 692 GLU Chi-restraints excluded: chain C residue 699 TYR Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 324 ASN Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 411 ASP Chi-restraints excluded: chain D residue 417 ASN Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 512 THR Chi-restraints excluded: chain D residue 556 SER Chi-restraints excluded: chain D residue 575 LYS Chi-restraints excluded: chain D residue 578 THR Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 679 TYR Chi-restraints excluded: chain D residue 693 ILE Chi-restraints excluded: chain E residue 324 ASN Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain E residue 337 ASN Chi-restraints excluded: chain E residue 351 ILE Chi-restraints excluded: chain E residue 390 LYS Chi-restraints excluded: chain E residue 419 VAL Chi-restraints excluded: chain E residue 436 TYR Chi-restraints excluded: chain E residue 455 SER Chi-restraints excluded: chain E residue 463 ASN Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain E residue 546 ASN Chi-restraints excluded: chain E residue 548 HIS Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 605 ASN Chi-restraints excluded: chain E residue 610 PHE Chi-restraints excluded: chain E residue 624 VAL Chi-restraints excluded: chain E residue 628 THR Chi-restraints excluded: chain F residue 324 ASN Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 336 THR Chi-restraints excluded: chain F residue 354 SER Chi-restraints excluded: chain F residue 356 LYS Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 402 ASP Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain F residue 447 ASP Chi-restraints excluded: chain F residue 467 ASP Chi-restraints excluded: chain F residue 471 LEU Chi-restraints excluded: chain F residue 483 GLU Chi-restraints excluded: chain F residue 494 THR Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 525 VAL Chi-restraints excluded: chain F residue 531 ILE Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 547 MET Chi-restraints excluded: chain F residue 553 VAL Chi-restraints excluded: chain F residue 555 CYS Chi-restraints excluded: chain F residue 578 THR Chi-restraints excluded: chain F residue 581 CYS Chi-restraints excluded: chain F residue 656 ASP Chi-restraints excluded: chain F residue 660 GLN Chi-restraints excluded: chain F residue 671 LEU Chi-restraints excluded: chain F residue 680 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 135 optimal weight: 7.9990 chunk 246 optimal weight: 0.9980 chunk 225 optimal weight: 40.0000 chunk 221 optimal weight: 10.0000 chunk 94 optimal weight: 0.6980 chunk 127 optimal weight: 0.9990 chunk 122 optimal weight: 7.9990 chunk 144 optimal weight: 0.7980 chunk 140 optimal weight: 0.9990 chunk 63 optimal weight: 0.0770 chunk 232 optimal weight: 0.5980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 740 GLN D 475 ASN D 661 ASN ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 324 ASN F 337 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.249513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.207238 restraints weight = 25367.410| |-----------------------------------------------------------------------------| r_work (start): 0.4315 rms_B_bonded: 2.60 r_work: 0.3939 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 22841 Z= 0.119 Angle : 0.552 10.524 30892 Z= 0.293 Chirality : 0.042 0.223 3472 Planarity : 0.004 0.075 3940 Dihedral : 8.481 166.901 3120 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 5.11 % Allowed : 28.30 % Favored : 66.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.16), residues: 2766 helix: 0.34 (0.16), residues: 1057 sheet: -0.71 (0.30), residues: 338 loop : -0.97 (0.16), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 585 TYR 0.013 0.001 TYR A 645 PHE 0.018 0.001 PHE E 668 TRP 0.010 0.001 TRP D 350 HIS 0.010 0.001 HIS D 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (22841) covalent geometry : angle 0.55233 / 0.29 (30892) hydrogen bonds : bond 0.03838 / 2.56 ( 788) hydrogen bonds : angle 5.13171 / 3.54 ( 2244) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 228 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 529 GLN cc_start: 0.6749 (tt0) cc_final: 0.6549 (tt0) REVERT: B 583 ILE cc_start: 0.7780 (OUTLIER) cc_final: 0.7387 (mp) REVERT: C 361 GLU cc_start: 0.7042 (OUTLIER) cc_final: 0.6783 (pp20) REVERT: C 627 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.7949 (mtp180) REVERT: D 611 ASP cc_start: 0.5722 (p0) cc_final: 0.5506 (p0) REVERT: E 458 MET cc_start: 0.3639 (tmm) cc_final: 0.2859 (tmm) REVERT: E 517 LYS cc_start: 0.6893 (OUTLIER) cc_final: 0.6638 (tptp) REVERT: E 592 ILE cc_start: 0.3862 (OUTLIER) cc_final: 0.3557 (tt) REVERT: E 610 PHE cc_start: 0.3788 (OUTLIER) cc_final: 0.3206 (m-80) REVERT: E 684 MET cc_start: 0.3516 (tpp) cc_final: 0.3260 (tpp) REVERT: E 702 ILE cc_start: 0.5486 (OUTLIER) cc_final: 0.5192 (tp) REVERT: F 656 ASP cc_start: 0.7142 (OUTLIER) cc_final: 0.6769 (t0) REVERT: F 660 GLN cc_start: 0.7717 (OUTLIER) cc_final: 0.7503 (mp10) outliers start: 127 outliers final: 72 residues processed: 338 average time/residue: 0.1523 time to fit residues: 80.7747 Evaluate side-chains 290 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 209 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 561 PHE Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 645 TYR Chi-restraints excluded: chain A residue 723 LYS Chi-restraints excluded: chain A residue 757 GLU Chi-restraints excluded: chain B residue 435 LYS Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 483 GLU Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 575 LYS Chi-restraints excluded: chain C residue 581 CYS Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 627 ARG Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 699 TYR Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 324 ASN Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 512 THR Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 693 ILE Chi-restraints excluded: chain E residue 324 ASN Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain E residue 463 ASN Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 517 LYS Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain E residue 546 ASN Chi-restraints excluded: chain E residue 582 VAL Chi-restraints excluded: chain E residue 592 ILE Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 605 ASN Chi-restraints excluded: chain E residue 610 PHE Chi-restraints excluded: chain E residue 624 VAL Chi-restraints excluded: chain E residue 691 GLU Chi-restraints excluded: chain E residue 702 ILE Chi-restraints excluded: chain F residue 324 ASN Chi-restraints excluded: chain F residue 336 THR Chi-restraints excluded: chain F residue 337 ASN Chi-restraints excluded: chain F residue 356 LYS Chi-restraints excluded: chain F residue 402 ASP Chi-restraints excluded: chain F residue 447 ASP Chi-restraints excluded: chain F residue 471 LEU Chi-restraints excluded: chain F residue 483 GLU Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 525 VAL Chi-restraints excluded: chain F residue 547 MET Chi-restraints excluded: chain F residue 578 THR Chi-restraints excluded: chain F residue 581 CYS Chi-restraints excluded: chain F residue 656 ASP Chi-restraints excluded: chain F residue 659 ILE Chi-restraints excluded: chain F residue 660 GLN Chi-restraints excluded: chain F residue 680 HIS Chi-restraints excluded: chain F residue 695 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 205 optimal weight: 7.9990 chunk 95 optimal weight: 5.9990 chunk 215 optimal weight: 0.7980 chunk 128 optimal weight: 0.0980 chunk 195 optimal weight: 2.9990 chunk 182 optimal weight: 7.9990 chunk 106 optimal weight: 8.9990 chunk 137 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 158 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 324 ASN B 469 GLN C 324 ASN D 661 ASN ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 324 ASN ** F 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.248193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.205801 restraints weight = 25597.497| |-----------------------------------------------------------------------------| r_work (start): 0.4299 rms_B_bonded: 2.60 r_work: 0.3793 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 22841 Z= 0.165 Angle : 0.573 12.303 30892 Z= 0.300 Chirality : 0.044 0.232 3472 Planarity : 0.004 0.074 3940 Dihedral : 8.111 168.396 3100 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 5.27 % Allowed : 27.94 % Favored : 66.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.16), residues: 2766 helix: 0.43 (0.16), residues: 1044 sheet: -0.69 (0.30), residues: 335 loop : -0.95 (0.16), residues: 1387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 663 TYR 0.012 0.001 TYR D 482 PHE 0.016 0.001 PHE E 668 TRP 0.012 0.001 TRP D 350 HIS 0.008 0.001 HIS D 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.17 (22841) covalent geometry : angle 0.57250 / 0.30 (30892) hydrogen bonds : bond 0.04324 / 2.86 ( 788) hydrogen bonds : angle 5.06595 / 3.49 ( 2244) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 214 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 382 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7427 (tt0) REVERT: B 447 ASP cc_start: 0.7732 (OUTLIER) cc_final: 0.7519 (t0) REVERT: B 481 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7761 (tt) REVERT: B 554 PHE cc_start: 0.8997 (OUTLIER) cc_final: 0.7725 (t80) REVERT: B 583 ILE cc_start: 0.7780 (OUTLIER) cc_final: 0.7391 (mp) REVERT: C 361 GLU cc_start: 0.6989 (OUTLIER) cc_final: 0.6710 (pp20) REVERT: C 600 ILE cc_start: 0.8813 (OUTLIER) cc_final: 0.8599 (mm) REVERT: C 678 LYS cc_start: 0.8277 (tttm) cc_final: 0.8025 (tttm) REVERT: D 611 ASP cc_start: 0.5948 (p0) cc_final: 0.5649 (p0) REVERT: E 339 VAL cc_start: 0.8969 (OUTLIER) cc_final: 0.8371 (m) REVERT: E 455 SER cc_start: 0.5048 (OUTLIER) cc_final: 0.4271 (t) REVERT: E 561 PHE cc_start: 0.3078 (OUTLIER) cc_final: 0.1685 (m-10) REVERT: E 592 ILE cc_start: 0.4180 (OUTLIER) cc_final: 0.3867 (tt) REVERT: E 610 PHE cc_start: 0.4044 (OUTLIER) cc_final: 0.3465 (m-80) REVERT: E 650 LEU cc_start: 0.1728 (OUTLIER) cc_final: 0.1034 (tt) REVERT: E 702 ILE cc_start: 0.5581 (OUTLIER) cc_final: 0.5130 (tp) REVERT: F 554 PHE cc_start: 0.7474 (OUTLIER) cc_final: 0.6014 (m-80) REVERT: F 656 ASP cc_start: 0.7106 (OUTLIER) cc_final: 0.6729 (t0) REVERT: F 660 GLN cc_start: 0.7826 (OUTLIER) cc_final: 0.7511 (mp10) outliers start: 131 outliers final: 83 residues processed: 324 average time/residue: 0.1386 time to fit residues: 70.8844 Evaluate side-chains 307 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 207 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 436 TYR Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 561 PHE Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 645 TYR Chi-restraints excluded: chain A residue 723 LYS Chi-restraints excluded: chain A residue 757 GLU Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 435 LYS Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 581 CYS Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 733 THR Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 483 GLU Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 575 LYS Chi-restraints excluded: chain C residue 581 CYS Chi-restraints excluded: chain C residue 600 ILE Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 656 ASP Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 699 TYR Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 324 ASN Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 477 LYS Chi-restraints excluded: chain D residue 512 THR Chi-restraints excluded: chain D residue 607 LYS Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 693 ILE Chi-restraints excluded: chain E residue 324 ASN Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain E residue 337 ASN Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 390 LYS Chi-restraints excluded: chain E residue 455 SER Chi-restraints excluded: chain E residue 463 ASN Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain E residue 546 ASN Chi-restraints excluded: chain E residue 561 PHE Chi-restraints excluded: chain E residue 582 VAL Chi-restraints excluded: chain E residue 592 ILE Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 610 PHE Chi-restraints excluded: chain E residue 624 VAL Chi-restraints excluded: chain E residue 628 THR Chi-restraints excluded: chain E residue 650 LEU Chi-restraints excluded: chain E residue 702 ILE Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 336 THR Chi-restraints excluded: chain F residue 356 LYS Chi-restraints excluded: chain F residue 402 ASP Chi-restraints excluded: chain F residue 447 ASP Chi-restraints excluded: chain F residue 471 LEU Chi-restraints excluded: chain F residue 483 GLU Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 525 VAL Chi-restraints excluded: chain F residue 547 MET Chi-restraints excluded: chain F residue 554 PHE Chi-restraints excluded: chain F residue 578 THR Chi-restraints excluded: chain F residue 581 CYS Chi-restraints excluded: chain F residue 656 ASP Chi-restraints excluded: chain F residue 660 GLN Chi-restraints excluded: chain F residue 680 HIS Chi-restraints excluded: chain F residue 695 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 118 optimal weight: 8.9990 chunk 168 optimal weight: 9.9990 chunk 39 optimal weight: 40.0000 chunk 217 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 73 optimal weight: 8.9990 chunk 52 optimal weight: 0.0040 chunk 192 optimal weight: 0.0970 chunk 69 optimal weight: 10.0000 chunk 198 optimal weight: 8.9990 chunk 4 optimal weight: 0.6980 overall best weight: 1.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 740 GLN ** D 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 324 ASN ** F 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4662 r_free = 0.4662 target = 0.248929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.206999 restraints weight = 25219.892| |-----------------------------------------------------------------------------| r_work (start): 0.4312 rms_B_bonded: 2.56 r_work: 0.3814 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 22841 Z= 0.138 Angle : 0.543 10.806 30892 Z= 0.285 Chirality : 0.043 0.218 3472 Planarity : 0.004 0.071 3940 Dihedral : 7.926 168.292 3097 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 5.31 % Allowed : 27.78 % Favored : 66.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.16), residues: 2766 helix: 0.54 (0.16), residues: 1042 sheet: -0.73 (0.29), residues: 339 loop : -0.93 (0.16), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 663 TYR 0.012 0.001 TYR E 482 PHE 0.014 0.001 PHE E 668 TRP 0.011 0.001 TRP D 350 HIS 0.008 0.001 HIS D 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.14 (22841) covalent geometry : angle 0.54348 / 0.29 (30892) hydrogen bonds : bond 0.03871 / 2.56 ( 788) hydrogen bonds : angle 4.93149 / 3.41 ( 2244) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 222 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 351 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.7781 (mt) REVERT: B 382 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7401 (tt0) REVERT: B 481 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7758 (tt) REVERT: B 554 PHE cc_start: 0.8987 (OUTLIER) cc_final: 0.7686 (t80) REVERT: B 583 ILE cc_start: 0.7780 (OUTLIER) cc_final: 0.7411 (mp) REVERT: C 361 GLU cc_start: 0.6911 (OUTLIER) cc_final: 0.6709 (pp20) REVERT: C 458 MET cc_start: 0.7513 (tpp) cc_final: 0.7017 (tpp) REVERT: C 600 ILE cc_start: 0.8819 (OUTLIER) cc_final: 0.8609 (mm) REVERT: C 678 LYS cc_start: 0.8278 (tttm) cc_final: 0.8009 (tttm) REVERT: E 339 VAL cc_start: 0.8940 (OUTLIER) cc_final: 0.8651 (t) REVERT: E 455 SER cc_start: 0.5040 (OUTLIER) cc_final: 0.4323 (t) REVERT: E 458 MET cc_start: 0.3671 (tmm) cc_final: 0.2475 (tpt) REVERT: E 459 GLU cc_start: 0.6467 (mm-30) cc_final: 0.6014 (mm-30) REVERT: E 517 LYS cc_start: 0.6858 (OUTLIER) cc_final: 0.6646 (tptp) REVERT: E 561 PHE cc_start: 0.3087 (OUTLIER) cc_final: 0.1700 (m-10) REVERT: E 592 ILE cc_start: 0.4275 (OUTLIER) cc_final: 0.3972 (tt) REVERT: E 610 PHE cc_start: 0.4046 (OUTLIER) cc_final: 0.3520 (m-80) REVERT: E 650 LEU cc_start: 0.1663 (OUTLIER) cc_final: 0.0956 (tt) REVERT: E 702 ILE cc_start: 0.5543 (OUTLIER) cc_final: 0.5094 (tp) REVERT: F 484 LYS cc_start: 0.7724 (OUTLIER) cc_final: 0.7208 (tptt) REVERT: F 554 PHE cc_start: 0.7501 (OUTLIER) cc_final: 0.5958 (m-80) REVERT: F 656 ASP cc_start: 0.7136 (OUTLIER) cc_final: 0.6747 (t0) REVERT: F 660 GLN cc_start: 0.7825 (OUTLIER) cc_final: 0.7573 (mp10) REVERT: F 699 TYR cc_start: 0.7188 (OUTLIER) cc_final: 0.6791 (m-80) REVERT: F 707 VAL cc_start: 0.5904 (OUTLIER) cc_final: 0.5701 (p) outliers start: 132 outliers final: 80 residues processed: 332 average time/residue: 0.1422 time to fit residues: 74.3711 Evaluate side-chains 313 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 212 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 561 PHE Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 636 ARG Chi-restraints excluded: chain A residue 645 TYR Chi-restraints excluded: chain A residue 723 LYS Chi-restraints excluded: chain A residue 757 GLU Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 435 LYS Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 581 CYS Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 733 THR Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 483 GLU Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 575 LYS Chi-restraints excluded: chain C residue 581 CYS Chi-restraints excluded: chain C residue 600 ILE Chi-restraints excluded: chain C residue 656 ASP Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 699 TYR Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 324 ASN Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 512 THR Chi-restraints excluded: chain D residue 607 LYS Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 693 ILE Chi-restraints excluded: chain E residue 324 ASN Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain E residue 337 ASN Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 390 LYS Chi-restraints excluded: chain E residue 455 SER Chi-restraints excluded: chain E residue 463 ASN Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 517 LYS Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain E residue 546 ASN Chi-restraints excluded: chain E residue 561 PHE Chi-restraints excluded: chain E residue 582 VAL Chi-restraints excluded: chain E residue 592 ILE Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 605 ASN Chi-restraints excluded: chain E residue 610 PHE Chi-restraints excluded: chain E residue 624 VAL Chi-restraints excluded: chain E residue 650 LEU Chi-restraints excluded: chain E residue 691 GLU Chi-restraints excluded: chain E residue 702 ILE Chi-restraints excluded: chain F residue 324 ASN Chi-restraints excluded: chain F residue 356 LYS Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 447 ASP Chi-restraints excluded: chain F residue 471 LEU Chi-restraints excluded: chain F residue 483 GLU Chi-restraints excluded: chain F residue 484 LYS Chi-restraints excluded: chain F residue 487 SER Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 525 VAL Chi-restraints excluded: chain F residue 547 MET Chi-restraints excluded: chain F residue 554 PHE Chi-restraints excluded: chain F residue 578 THR Chi-restraints excluded: chain F residue 581 CYS Chi-restraints excluded: chain F residue 656 ASP Chi-restraints excluded: chain F residue 660 GLN Chi-restraints excluded: chain F residue 680 HIS Chi-restraints excluded: chain F residue 695 ASP Chi-restraints excluded: chain F residue 699 TYR Chi-restraints excluded: chain F residue 707 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 104 optimal weight: 0.0270 chunk 138 optimal weight: 2.9990 chunk 85 optimal weight: 0.3980 chunk 105 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 132 optimal weight: 20.0000 chunk 157 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 87 optimal weight: 20.0000 chunk 267 optimal weight: 10.0000 chunk 7 optimal weight: 0.8980 overall best weight: 1.2642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 324 ASN ** D 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 661 ASN ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 324 ASN ** F 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 546 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.249192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.205863 restraints weight = 25393.823| |-----------------------------------------------------------------------------| r_work (start): 0.4301 rms_B_bonded: 2.59 r_work: 0.3802 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22841 Z= 0.125 Angle : 0.535 9.892 30892 Z= 0.281 Chirality : 0.042 0.216 3472 Planarity : 0.004 0.070 3940 Dihedral : 7.756 168.377 3089 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 5.19 % Allowed : 27.82 % Favored : 66.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.16), residues: 2766 helix: 0.60 (0.16), residues: 1049 sheet: -0.69 (0.30), residues: 334 loop : -0.93 (0.16), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 514 TYR 0.011 0.001 TYR C 645 PHE 0.017 0.001 PHE E 668 TRP 0.011 0.001 TRP D 350 HIS 0.007 0.001 HIS D 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (22841) covalent geometry : angle 0.53480 / 0.28 (30892) hydrogen bonds : bond 0.03625 / 2.40 ( 788) hydrogen bonds : angle 4.84008 / 3.35 ( 2244) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 212 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 581 CYS cc_start: 0.6119 (m) cc_final: 0.5761 (m) REVERT: B 351 ILE cc_start: 0.8383 (OUTLIER) cc_final: 0.7746 (mt) REVERT: B 382 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7448 (tt0) REVERT: B 447 ASP cc_start: 0.7739 (OUTLIER) cc_final: 0.7506 (t0) REVERT: B 481 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7730 (tt) REVERT: B 554 PHE cc_start: 0.8957 (OUTLIER) cc_final: 0.7624 (t80) REVERT: B 583 ILE cc_start: 0.7771 (OUTLIER) cc_final: 0.7379 (mp) REVERT: C 678 LYS cc_start: 0.8233 (tttm) cc_final: 0.7999 (tttm) REVERT: C 736 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7371 (tt) REVERT: D 757 GLU cc_start: 0.5536 (OUTLIER) cc_final: 0.4813 (tp30) REVERT: E 339 VAL cc_start: 0.8919 (OUTLIER) cc_final: 0.8625 (t) REVERT: E 459 GLU cc_start: 0.6391 (mm-30) cc_final: 0.6169 (mm-30) REVERT: E 477 LYS cc_start: 0.7683 (tmmt) cc_final: 0.6949 (tttt) REVERT: E 517 LYS cc_start: 0.6876 (OUTLIER) cc_final: 0.6675 (tptp) REVERT: E 548 HIS cc_start: 0.6641 (OUTLIER) cc_final: 0.5466 (t-170) REVERT: E 561 PHE cc_start: 0.3159 (OUTLIER) cc_final: 0.1680 (m-10) REVERT: E 592 ILE cc_start: 0.4315 (OUTLIER) cc_final: 0.4018 (tt) REVERT: E 650 LEU cc_start: 0.1699 (OUTLIER) cc_final: 0.1016 (tt) REVERT: E 702 ILE cc_start: 0.5530 (OUTLIER) cc_final: 0.5079 (tp) REVERT: F 484 LYS cc_start: 0.7715 (OUTLIER) cc_final: 0.7198 (tptt) REVERT: F 554 PHE cc_start: 0.7467 (OUTLIER) cc_final: 0.5949 (m-80) REVERT: F 656 ASP cc_start: 0.7201 (OUTLIER) cc_final: 0.6758 (t0) REVERT: F 660 GLN cc_start: 0.7855 (OUTLIER) cc_final: 0.7612 (mp10) REVERT: F 699 TYR cc_start: 0.7189 (OUTLIER) cc_final: 0.6783 (m-80) outliers start: 129 outliers final: 86 residues processed: 320 average time/residue: 0.1388 time to fit residues: 70.5968 Evaluate side-chains 312 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 206 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 436 TYR Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 561 PHE Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 636 ARG Chi-restraints excluded: chain A residue 645 TYR Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 723 LYS Chi-restraints excluded: chain A residue 757 GLU Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 435 LYS Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 733 THR Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 435 LYS Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 483 GLU Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 575 LYS Chi-restraints excluded: chain C residue 581 CYS Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 656 ASP Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 699 TYR Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 324 ASN Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 512 THR Chi-restraints excluded: chain D residue 607 LYS Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 693 ILE Chi-restraints excluded: chain D residue 757 GLU Chi-restraints excluded: chain E residue 324 ASN Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain E residue 337 ASN Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 390 LYS Chi-restraints excluded: chain E residue 463 ASN Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 517 LYS Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain E residue 546 ASN Chi-restraints excluded: chain E residue 548 HIS Chi-restraints excluded: chain E residue 561 PHE Chi-restraints excluded: chain E residue 582 VAL Chi-restraints excluded: chain E residue 592 ILE Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 605 ASN Chi-restraints excluded: chain E residue 623 VAL Chi-restraints excluded: chain E residue 624 VAL Chi-restraints excluded: chain E residue 650 LEU Chi-restraints excluded: chain E residue 702 ILE Chi-restraints excluded: chain F residue 324 ASN Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 356 LYS Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 447 ASP Chi-restraints excluded: chain F residue 471 LEU Chi-restraints excluded: chain F residue 483 GLU Chi-restraints excluded: chain F residue 484 LYS Chi-restraints excluded: chain F residue 487 SER Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 525 VAL Chi-restraints excluded: chain F residue 547 MET Chi-restraints excluded: chain F residue 554 PHE Chi-restraints excluded: chain F residue 578 THR Chi-restraints excluded: chain F residue 581 CYS Chi-restraints excluded: chain F residue 656 ASP Chi-restraints excluded: chain F residue 659 ILE Chi-restraints excluded: chain F residue 660 GLN Chi-restraints excluded: chain F residue 680 HIS Chi-restraints excluded: chain F residue 695 ASP Chi-restraints excluded: chain F residue 699 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 31 optimal weight: 0.0020 chunk 226 optimal weight: 50.0000 chunk 159 optimal weight: 7.9990 chunk 58 optimal weight: 0.6980 chunk 179 optimal weight: 8.9990 chunk 38 optimal weight: 9.9990 chunk 68 optimal weight: 6.9990 chunk 120 optimal weight: 4.9990 chunk 242 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 221 optimal weight: 8.9990 overall best weight: 2.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 324 ASN C 324 ASN C 740 GLN D 417 ASN ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 324 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.247795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.205533 restraints weight = 25339.298| |-----------------------------------------------------------------------------| r_work (start): 0.4297 rms_B_bonded: 2.53 r_work: 0.3808 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 22841 Z= 0.194 Angle : 0.576 8.988 30892 Z= 0.300 Chirality : 0.044 0.221 3472 Planarity : 0.004 0.067 3940 Dihedral : 7.794 168.784 3087 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 5.39 % Allowed : 27.90 % Favored : 66.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.16), residues: 2766 helix: 0.51 (0.16), residues: 1044 sheet: -0.74 (0.28), residues: 363 loop : -0.95 (0.16), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 514 TYR 0.013 0.001 TYR D 482 PHE 0.015 0.001 PHE E 668 TRP 0.013 0.002 TRP D 350 HIS 0.006 0.001 HIS D 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.19 (22841) covalent geometry : angle 0.57585 / 0.30 (30892) hydrogen bonds : bond 0.04492 / 2.96 ( 788) hydrogen bonds : angle 4.92418 / 3.40 ( 2244) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 218 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 581 CYS cc_start: 0.5985 (m) cc_final: 0.5650 (m) REVERT: B 382 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7390 (tt0) REVERT: B 447 ASP cc_start: 0.7718 (OUTLIER) cc_final: 0.7500 (t0) REVERT: B 481 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7734 (tt) REVERT: B 554 PHE cc_start: 0.8978 (OUTLIER) cc_final: 0.7629 (t80) REVERT: B 583 ILE cc_start: 0.7801 (OUTLIER) cc_final: 0.7417 (mp) REVERT: C 426 MET cc_start: 0.7639 (OUTLIER) cc_final: 0.7403 (ttm) REVERT: C 600 ILE cc_start: 0.8810 (OUTLIER) cc_final: 0.8588 (mm) REVERT: C 678 LYS cc_start: 0.8358 (tttm) cc_final: 0.8118 (tttm) REVERT: C 736 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7366 (tt) REVERT: D 757 GLU cc_start: 0.5411 (OUTLIER) cc_final: 0.4654 (tp30) REVERT: E 339 VAL cc_start: 0.8961 (OUTLIER) cc_final: 0.8682 (t) REVERT: E 548 HIS cc_start: 0.6587 (OUTLIER) cc_final: 0.5507 (t-170) REVERT: E 561 PHE cc_start: 0.3181 (OUTLIER) cc_final: 0.1688 (m-80) REVERT: E 592 ILE cc_start: 0.4321 (OUTLIER) cc_final: 0.4013 (tt) REVERT: E 607 LYS cc_start: 0.5846 (tmtt) cc_final: 0.5551 (tttp) REVERT: E 650 LEU cc_start: 0.1805 (OUTLIER) cc_final: 0.1104 (tt) REVERT: E 702 ILE cc_start: 0.5535 (OUTLIER) cc_final: 0.5074 (tp) REVERT: F 554 PHE cc_start: 0.7486 (OUTLIER) cc_final: 0.5937 (m-80) REVERT: F 656 ASP cc_start: 0.7155 (OUTLIER) cc_final: 0.6745 (t0) REVERT: F 660 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.7552 (mp10) REVERT: F 699 TYR cc_start: 0.7180 (OUTLIER) cc_final: 0.6775 (m-80) outliers start: 134 outliers final: 90 residues processed: 329 average time/residue: 0.1437 time to fit residues: 75.0366 Evaluate side-chains 323 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 214 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 436 TYR Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 501 PHE Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 561 PHE Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 636 ARG Chi-restraints excluded: chain A residue 645 TYR Chi-restraints excluded: chain A residue 723 LYS Chi-restraints excluded: chain A residue 757 GLU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 435 LYS Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 733 THR Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 435 LYS Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 483 GLU Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 581 CYS Chi-restraints excluded: chain C residue 600 ILE Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 656 ASP Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 699 TYR Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 324 ASN Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 417 ASN Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 512 THR Chi-restraints excluded: chain D residue 607 LYS Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 693 ILE Chi-restraints excluded: chain D residue 757 GLU Chi-restraints excluded: chain E residue 324 ASN Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain E residue 337 ASN Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 390 LYS Chi-restraints excluded: chain E residue 463 ASN Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain E residue 546 ASN Chi-restraints excluded: chain E residue 548 HIS Chi-restraints excluded: chain E residue 561 PHE Chi-restraints excluded: chain E residue 582 VAL Chi-restraints excluded: chain E residue 592 ILE Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 605 ASN Chi-restraints excluded: chain E residue 624 VAL Chi-restraints excluded: chain E residue 650 LEU Chi-restraints excluded: chain E residue 691 GLU Chi-restraints excluded: chain E residue 702 ILE Chi-restraints excluded: chain F residue 324 ASN Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 356 LYS Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 402 ASP Chi-restraints excluded: chain F residue 447 ASP Chi-restraints excluded: chain F residue 471 LEU Chi-restraints excluded: chain F residue 483 GLU Chi-restraints excluded: chain F residue 487 SER Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 547 MET Chi-restraints excluded: chain F residue 554 PHE Chi-restraints excluded: chain F residue 578 THR Chi-restraints excluded: chain F residue 581 CYS Chi-restraints excluded: chain F residue 656 ASP Chi-restraints excluded: chain F residue 659 ILE Chi-restraints excluded: chain F residue 660 GLN Chi-restraints excluded: chain F residue 680 HIS Chi-restraints excluded: chain F residue 695 ASP Chi-restraints excluded: chain F residue 699 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 109 optimal weight: 10.0000 chunk 110 optimal weight: 1.9990 chunk 234 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 227 optimal weight: 30.0000 chunk 207 optimal weight: 20.0000 chunk 147 optimal weight: 0.0010 chunk 144 optimal weight: 0.4980 chunk 47 optimal weight: 0.6980 chunk 273 optimal weight: 20.0000 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 324 ASN D 661 ASN E 573 ASN ** E 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 324 ASN F 475 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.254217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.230025 restraints weight = 25150.717| |-----------------------------------------------------------------------------| r_work (start): 0.4482 rms_B_bonded: 1.30 r_work: 0.4116 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work (final): 0.4116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 22841 Z= 0.102 Angle : 0.519 9.108 30892 Z= 0.272 Chirality : 0.041 0.209 3472 Planarity : 0.004 0.063 3940 Dihedral : 7.565 168.569 3084 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.63 % Allowed : 28.42 % Favored : 66.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.16), residues: 2766 helix: 0.72 (0.17), residues: 1052 sheet: -0.63 (0.29), residues: 362 loop : -0.89 (0.16), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 514 TYR 0.014 0.001 TYR A 606 PHE 0.023 0.001 PHE E 501 TRP 0.010 0.001 TRP D 350 HIS 0.006 0.000 HIS D 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.10 (22841) covalent geometry : angle 0.51938 / 0.27 (30892) hydrogen bonds : bond 0.03193 / 2.12 ( 788) hydrogen bonds : angle 4.70437 / 3.25 ( 2244) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 217 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 581 CYS cc_start: 0.5118 (m) cc_final: 0.4845 (m) REVERT: B 481 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.7866 (tt) REVERT: B 554 PHE cc_start: 0.8947 (OUTLIER) cc_final: 0.7749 (t80) REVERT: B 583 ILE cc_start: 0.7722 (OUTLIER) cc_final: 0.7323 (mp) REVERT: C 507 THR cc_start: 0.7376 (OUTLIER) cc_final: 0.7129 (m) REVERT: D 757 GLU cc_start: 0.4841 (OUTLIER) cc_final: 0.3860 (tp30) REVERT: E 339 VAL cc_start: 0.8849 (OUTLIER) cc_final: 0.8529 (t) REVERT: E 477 LYS cc_start: 0.7182 (tmmt) cc_final: 0.6706 (tttt) REVERT: E 548 HIS cc_start: 0.6108 (OUTLIER) cc_final: 0.4955 (t-170) REVERT: E 561 PHE cc_start: 0.3037 (OUTLIER) cc_final: 0.1759 (m-80) REVERT: E 650 LEU cc_start: 0.1903 (OUTLIER) cc_final: 0.1084 (tt) REVERT: E 684 MET cc_start: 0.3428 (tpp) cc_final: 0.2686 (tpp) REVERT: E 702 ILE cc_start: 0.5303 (OUTLIER) cc_final: 0.4957 (tp) REVERT: F 475 ASN cc_start: 0.6657 (OUTLIER) cc_final: 0.6429 (t0) REVERT: F 547 MET cc_start: 0.7663 (OUTLIER) cc_final: 0.7335 (ttm) REVERT: F 554 PHE cc_start: 0.7333 (OUTLIER) cc_final: 0.5867 (m-80) REVERT: F 656 ASP cc_start: 0.6794 (OUTLIER) cc_final: 0.6436 (t0) REVERT: F 699 TYR cc_start: 0.6877 (OUTLIER) cc_final: 0.6671 (m-80) outliers start: 115 outliers final: 77 residues processed: 313 average time/residue: 0.1436 time to fit residues: 71.2544 Evaluate side-chains 304 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 212 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 501 PHE Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 561 PHE Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 636 ARG Chi-restraints excluded: chain A residue 645 TYR Chi-restraints excluded: chain A residue 723 LYS Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain B residue 435 LYS Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 733 THR Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 435 LYS Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 483 GLU Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 581 CYS Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 699 TYR Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 324 ASN Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 477 LYS Chi-restraints excluded: chain D residue 512 THR Chi-restraints excluded: chain D residue 607 LYS Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 693 ILE Chi-restraints excluded: chain D residue 757 GLU Chi-restraints excluded: chain E residue 324 ASN Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain E residue 337 ASN Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 390 LYS Chi-restraints excluded: chain E residue 463 ASN Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain E residue 546 ASN Chi-restraints excluded: chain E residue 548 HIS Chi-restraints excluded: chain E residue 561 PHE Chi-restraints excluded: chain E residue 582 VAL Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 624 VAL Chi-restraints excluded: chain E residue 650 LEU Chi-restraints excluded: chain E residue 691 GLU Chi-restraints excluded: chain E residue 702 ILE Chi-restraints excluded: chain F residue 324 ASN Chi-restraints excluded: chain F residue 356 LYS Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 447 ASP Chi-restraints excluded: chain F residue 471 LEU Chi-restraints excluded: chain F residue 475 ASN Chi-restraints excluded: chain F residue 483 GLU Chi-restraints excluded: chain F residue 487 SER Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 547 MET Chi-restraints excluded: chain F residue 554 PHE Chi-restraints excluded: chain F residue 578 THR Chi-restraints excluded: chain F residue 581 CYS Chi-restraints excluded: chain F residue 656 ASP Chi-restraints excluded: chain F residue 659 ILE Chi-restraints excluded: chain F residue 680 HIS Chi-restraints excluded: chain F residue 695 ASP Chi-restraints excluded: chain F residue 699 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 22 optimal weight: 7.9990 chunk 163 optimal weight: 8.9990 chunk 216 optimal weight: 10.0000 chunk 177 optimal weight: 50.0000 chunk 75 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 176 optimal weight: 8.9990 chunk 227 optimal weight: 40.0000 chunk 5 optimal weight: 0.9980 chunk 147 optimal weight: 0.7980 chunk 215 optimal weight: 1.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 324 ASN ** B 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 ASN C 740 GLN D 417 ASN D 662 ASN ** E 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 324 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.251136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.218469 restraints weight = 25221.002| |-----------------------------------------------------------------------------| r_work (start): 0.4373 rms_B_bonded: 1.61 r_work: 0.4023 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3857 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 22841 Z= 0.257 Angle : 0.638 11.378 30892 Z= 0.331 Chirality : 0.047 0.224 3472 Planarity : 0.005 0.068 3940 Dihedral : 7.707 169.343 3081 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 4.63 % Allowed : 28.30 % Favored : 67.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.16), residues: 2766 helix: 0.39 (0.16), residues: 1045 sheet: -0.80 (0.28), residues: 365 loop : -1.00 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 387 TYR 0.016 0.002 TYR A 606 PHE 0.053 0.002 PHE E 501 TRP 0.014 0.002 TRP C 350 HIS 0.006 0.001 HIS D 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00656 / 0.26 (22841) covalent geometry : angle 0.63847 / 0.33 (30892) hydrogen bonds : bond 0.05230 / 3.44 ( 788) hydrogen bonds : angle 4.98307 / 3.43 ( 2244) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 209 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 581 CYS cc_start: 0.5612 (m) cc_final: 0.5336 (m) REVERT: B 382 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.7740 (tt0) REVERT: B 481 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.7900 (tt) REVERT: B 554 PHE cc_start: 0.9034 (OUTLIER) cc_final: 0.7797 (t80) REVERT: B 583 ILE cc_start: 0.7902 (OUTLIER) cc_final: 0.7490 (mp) REVERT: C 361 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.6753 (pt0) REVERT: C 426 MET cc_start: 0.7807 (OUTLIER) cc_final: 0.7573 (ttm) REVERT: E 339 VAL cc_start: 0.8918 (OUTLIER) cc_final: 0.8677 (t) REVERT: E 548 HIS cc_start: 0.6416 (OUTLIER) cc_final: 0.5198 (t-170) REVERT: E 561 PHE cc_start: 0.3159 (OUTLIER) cc_final: 0.1734 (m-80) REVERT: E 650 LEU cc_start: 0.1615 (OUTLIER) cc_final: 0.0781 (tt) REVERT: E 702 ILE cc_start: 0.5504 (OUTLIER) cc_final: 0.5061 (tp) REVERT: F 554 PHE cc_start: 0.7517 (OUTLIER) cc_final: 0.5920 (m-80) REVERT: F 656 ASP cc_start: 0.7110 (OUTLIER) cc_final: 0.6899 (t0) outliers start: 115 outliers final: 85 residues processed: 304 average time/residue: 0.1477 time to fit residues: 71.4881 Evaluate side-chains 305 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 207 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 436 TYR Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 501 PHE Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 636 ARG Chi-restraints excluded: chain A residue 645 TYR Chi-restraints excluded: chain A residue 723 LYS Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 435 LYS Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 581 CYS Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 733 THR Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 435 LYS Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 483 GLU Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 581 CYS Chi-restraints excluded: chain C residue 656 ASP Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 699 TYR Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 324 ASN Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 512 THR Chi-restraints excluded: chain D residue 607 LYS Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 693 ILE Chi-restraints excluded: chain E residue 324 ASN Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain E residue 337 ASN Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 390 LYS Chi-restraints excluded: chain E residue 436 TYR Chi-restraints excluded: chain E residue 463 ASN Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain E residue 546 ASN Chi-restraints excluded: chain E residue 548 HIS Chi-restraints excluded: chain E residue 561 PHE Chi-restraints excluded: chain E residue 582 VAL Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 623 VAL Chi-restraints excluded: chain E residue 650 LEU Chi-restraints excluded: chain E residue 702 ILE Chi-restraints excluded: chain F residue 324 ASN Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 356 LYS Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 402 ASP Chi-restraints excluded: chain F residue 447 ASP Chi-restraints excluded: chain F residue 471 LEU Chi-restraints excluded: chain F residue 483 GLU Chi-restraints excluded: chain F residue 487 SER Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 547 MET Chi-restraints excluded: chain F residue 554 PHE Chi-restraints excluded: chain F residue 578 THR Chi-restraints excluded: chain F residue 581 CYS Chi-restraints excluded: chain F residue 656 ASP Chi-restraints excluded: chain F residue 680 HIS Chi-restraints excluded: chain F residue 695 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 16 optimal weight: 7.9990 chunk 108 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 133 optimal weight: 6.9990 chunk 221 optimal weight: 5.9990 chunk 128 optimal weight: 0.0020 chunk 224 optimal weight: 10.0000 chunk 24 optimal weight: 20.0000 chunk 114 optimal weight: 0.7980 chunk 201 optimal weight: 0.5980 chunk 70 optimal weight: 0.3980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 469 GLN ** B 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN ** E 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 324 ASN F 475 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4717 r_free = 0.4717 target = 0.254430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.223602 restraints weight = 25545.294| |-----------------------------------------------------------------------------| r_work (start): 0.4421 rms_B_bonded: 1.80 r_work: 0.4047 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work (final): 0.4047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 22841 Z= 0.105 Angle : 0.541 11.270 30892 Z= 0.282 Chirality : 0.041 0.206 3472 Planarity : 0.004 0.065 3940 Dihedral : 7.454 169.085 3081 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.46 % Allowed : 29.43 % Favored : 67.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.16), residues: 2766 helix: 0.67 (0.17), residues: 1053 sheet: -0.61 (0.29), residues: 358 loop : -0.87 (0.16), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 514 TYR 0.013 0.001 TYR A 699 PHE 0.039 0.001 PHE E 501 TRP 0.010 0.001 TRP D 350 HIS 0.005 0.001 HIS D 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.10 (22841) covalent geometry : angle 0.54086 / 0.28 (30892) hydrogen bonds : bond 0.03167 / 2.11 ( 788) hydrogen bonds : angle 4.67400 / 3.24 ( 2244) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 209 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 581 CYS cc_start: 0.5343 (m) cc_final: 0.5055 (m) REVERT: A 684 MET cc_start: 0.7933 (tmt) cc_final: 0.7456 (tmt) REVERT: B 481 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7838 (tt) REVERT: B 554 PHE cc_start: 0.8955 (OUTLIER) cc_final: 0.7787 (t80) REVERT: B 583 ILE cc_start: 0.7741 (OUTLIER) cc_final: 0.7368 (mp) REVERT: C 361 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6339 (pt0) REVERT: E 477 LYS cc_start: 0.7289 (tmmt) cc_final: 0.6773 (tttt) REVERT: E 548 HIS cc_start: 0.6270 (OUTLIER) cc_final: 0.5094 (t-170) REVERT: E 561 PHE cc_start: 0.3003 (OUTLIER) cc_final: 0.1702 (m-80) REVERT: E 650 LEU cc_start: 0.1756 (OUTLIER) cc_final: 0.0932 (tt) REVERT: E 702 ILE cc_start: 0.5416 (OUTLIER) cc_final: 0.4998 (tp) REVERT: F 475 ASN cc_start: 0.6738 (OUTLIER) cc_final: 0.6527 (t0) REVERT: F 547 MET cc_start: 0.7742 (OUTLIER) cc_final: 0.7440 (ttm) REVERT: F 554 PHE cc_start: 0.7380 (OUTLIER) cc_final: 0.5851 (m-80) outliers start: 86 outliers final: 66 residues processed: 280 average time/residue: 0.1561 time to fit residues: 69.2826 Evaluate side-chains 283 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 206 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 636 ARG Chi-restraints excluded: chain A residue 645 TYR Chi-restraints excluded: chain A residue 723 LYS Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain B residue 435 LYS Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 581 CYS Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 733 THR Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 435 LYS Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 483 GLU Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 699 TYR Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 324 ASN Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 512 THR Chi-restraints excluded: chain D residue 607 LYS Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 693 ILE Chi-restraints excluded: chain E residue 324 ASN Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain E residue 337 ASN Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 390 LYS Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain E residue 546 ASN Chi-restraints excluded: chain E residue 548 HIS Chi-restraints excluded: chain E residue 561 PHE Chi-restraints excluded: chain E residue 582 VAL Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 623 VAL Chi-restraints excluded: chain E residue 650 LEU Chi-restraints excluded: chain E residue 702 ILE Chi-restraints excluded: chain F residue 324 ASN Chi-restraints excluded: chain F residue 356 LYS Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 447 ASP Chi-restraints excluded: chain F residue 471 LEU Chi-restraints excluded: chain F residue 475 ASN Chi-restraints excluded: chain F residue 483 GLU Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 547 MET Chi-restraints excluded: chain F residue 554 PHE Chi-restraints excluded: chain F residue 578 THR Chi-restraints excluded: chain F residue 581 CYS Chi-restraints excluded: chain F residue 659 ILE Chi-restraints excluded: chain F residue 680 HIS Chi-restraints excluded: chain F residue 695 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 81 optimal weight: 8.9990 chunk 41 optimal weight: 30.0000 chunk 262 optimal weight: 20.0000 chunk 32 optimal weight: 6.9990 chunk 182 optimal weight: 20.0000 chunk 235 optimal weight: 0.8980 chunk 43 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 221 optimal weight: 20.0000 chunk 52 optimal weight: 0.9980 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 ASN ** C 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 661 ASN ** E 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 475 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.248993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.199863 restraints weight = 25499.661| |-----------------------------------------------------------------------------| r_work (start): 0.4246 rms_B_bonded: 2.90 r_work: 0.3511 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 22841 Z= 0.183 Angle : 0.712 58.793 30892 Z= 0.392 Chirality : 0.044 0.264 3472 Planarity : 0.004 0.091 3940 Dihedral : 7.453 169.062 3079 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.62 % Allowed : 29.27 % Favored : 67.11 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.16), residues: 2766 helix: 0.59 (0.16), residues: 1053 sheet: -0.60 (0.29), residues: 358 loop : -0.87 (0.16), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 514 TYR 0.014 0.001 TYR C 776 PHE 0.041 0.001 PHE E 501 TRP 0.011 0.001 TRP D 350 HIS 0.005 0.001 HIS D 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.18 (22841) covalent geometry : angle 0.71187 / 0.39 (30892) hydrogen bonds : bond 0.03666 / 2.43 ( 788) hydrogen bonds : angle 4.66704 / 3.23 ( 2244) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4895.59 seconds wall clock time: 84 minutes 48.40 seconds (5088.40 seconds total)