Starting phenix.real_space_refine on Sun Aug 24 19:42:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wh4_37528/08_2025/8wh4_37528.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wh4_37528/08_2025/8wh4_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_2025/8wh4_37528.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wh4_37528/08_2025/8wh4_37528.map" model { file = "/net/cci-nas-00/data/ceres_data/8wh4_37528/08_2025/8wh4_37528.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wh4_37528/08_2025/8wh4_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 5.85, per 1000 atoms: 0.26 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: 1.94 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.17 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: 4.58 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: 2747 0.049 - 0.098: 579 0.098 - 0.147: 139 0.147 - 0.196: 5 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: 2.380 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: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 23.020 Find NCS groups from input model: 0.390 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.010 Internal consistency checks: 0.000 Total: 27.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 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= 0.263 Angle : 0.832 37.935 30892 Z= 0.475 Chirality : 0.042 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 aren 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 covalent geometry : bond 0.00833 (22841) covalent geometry : angle 0.83209 (30892) hydrogen bonds : bond 0.17756 ( 788) hydrogen bonds : angle 6.17378 ( 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 : 0.964 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: 0.5734 (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: 0.1605 time to fit residues: 72.3090 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 : 0.894 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** A 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 GLN C 478 ASN C 573 ASN D 417 ASN ** D 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 629 HIS ** D 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 661 ASN E 463 ASN ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 324 ASN F 475 ASN F 662 ASN F 763 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.243289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.193900 restraints weight = 25365.235| |-----------------------------------------------------------------------------| r_work (start): 0.4198 rms_B_bonded: 2.95 r_work: 0.3442 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.115 22841 Z= 0.422 Angle : 0.791 8.409 30892 Z= 0.411 Chirality : 0.054 0.212 3472 Planarity : 0.006 0.100 3940 Dihedral : 9.467 166.268 3164 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 7.65 % Allowed : 26.77 % Favored : 65.58 % 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 aren not related in a simple way. whole: -1.18 (0.16), residues: 2766 helix: -0.19 (0.16), residues: 1038 sheet: -0.82 (0.28), residues: 371 loop : -1.19 (0.16), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 387 TYR 0.023 0.002 TYR E 679 PHE 0.022 0.002 PHE C 357 TRP 0.022 0.003 TRP D 350 HIS 0.009 0.002 HIS A 680 Details of bonding type rmsd covalent geometry : bond 0.01071 (22841) covalent geometry : angle 0.79080 (30892) hydrogen bonds : bond 0.07312 ( 788) hydrogen bonds : angle 5.74166 ( 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 403 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 213 time to evaluate : 0.935 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: 0.8881 (OUTLIER) cc_final: 0.8500 (mt) REVERT: B 457 GLU cc_start: 0.6869 (OUTLIER) cc_final: 0.5563 (tm-30) REVERT: B 481 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7538 (tt) REVERT: B 554 PHE cc_start: 0.8909 (OUTLIER) cc_final: 0.7425 (t80) REVERT: B 556 SER cc_start: 0.7748 (m) cc_final: 0.7510 (m) REVERT: B 583 ILE cc_start: 0.7856 (OUTLIER) cc_final: 0.7450 (mp) REVERT: C 426 MET cc_start: 0.7905 (OUTLIER) cc_final: 0.7555 (ttm) REVERT: C 600 ILE cc_start: 0.8905 (OUTLIER) cc_final: 0.8660 (mm) REVERT: C 692 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7191 (mp0) REVERT: C 736 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7471 (tt) REVERT: D 679 TYR cc_start: 0.5697 (OUTLIER) cc_final: 0.5207 (m-80) REVERT: E 529 GLN cc_start: 0.5353 (OUTLIER) cc_final: 0.4934 (mm-40) REVERT: E 548 HIS cc_start: 0.6920 (OUTLIER) cc_final: 0.5732 (t-170) REVERT: E 561 PHE cc_start: 0.3125 (OUTLIER) cc_final: 0.1554 (m-10) REVERT: E 610 PHE cc_start: 0.4430 (OUTLIER) cc_final: 0.3743 (m-80) REVERT: E 694 PRO cc_start: 0.5716 (Cg_exo) cc_final: 0.5441 (Cg_exo) REVERT: F 475 ASN cc_start: 0.6240 (OUTLIER) cc_final: 0.5896 (t0) REVERT: F 595 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.6880 (mmp-170) REVERT: F 656 ASP cc_start: 0.7076 (OUTLIER) cc_final: 0.5970 (t0) REVERT: F 660 GLN cc_start: 0.7780 (OUTLIER) cc_final: 0.6834 (mp10) REVERT: F 683 ILE cc_start: 0.8764 (pp) cc_final: 0.8506 (pt) outliers start: 190 outliers final: 103 residues processed: 370 average time/residue: 0.1614 time to fit residues: 93.6112 Evaluate side-chains 325 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 204 time to evaluate : 0.931 ------------------------------------------------------------------------------- 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 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 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 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 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 573 ASN 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 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 547 MET Chi-restraints excluded: chain D residue 556 SER 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 390 LYS Chi-restraints excluded: chain E residue 419 VAL 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 529 GLN Chi-restraints excluded: chain E residue 548 HIS Chi-restraints excluded: chain E residue 561 PHE 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 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 475 ASN 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 531 ILE Chi-restraints excluded: chain F residue 553 VAL Chi-restraints excluded: chain F residue 578 THR Chi-restraints excluded: chain F residue 581 CYS Chi-restraints excluded: chain F residue 595 ARG 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 Chi-restraints excluded: chain F residue 710 SER Chi-restraints excluded: chain F residue 736 LEU 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: 0.8980 chunk 225 optimal weight: 9.9990 chunk 221 optimal weight: 5.9990 chunk 94 optimal weight: 0.6980 chunk 127 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 144 optimal weight: 0.6980 chunk 140 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 232 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 324 ASN C 740 GLN D 475 ASN D 641 ASN D 661 ASN ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 713 HIS ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.249807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.198211 restraints weight = 25375.412| |-----------------------------------------------------------------------------| r_work (start): 0.4224 rms_B_bonded: 3.01 r_work: 0.3490 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22841 Z= 0.114 Angle : 0.538 9.640 30892 Z= 0.285 Chirality : 0.042 0.197 3472 Planarity : 0.004 0.079 3940 Dihedral : 8.379 164.459 3119 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 5.03 % Allowed : 28.38 % 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 aren not related in a simple way. whole: -0.66 (0.16), residues: 2766 helix: 0.38 (0.16), residues: 1051 sheet: -0.68 (0.30), residues: 332 loop : -0.97 (0.16), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 762 TYR 0.014 0.001 TYR A 645 PHE 0.018 0.001 PHE E 668 TRP 0.009 0.001 TRP D 350 HIS 0.012 0.001 HIS A 713 Details of bonding type rmsd covalent geometry : bond 0.00269 (22841) covalent geometry : angle 0.53819 (30892) hydrogen bonds : bond 0.03503 ( 788) hydrogen bonds : angle 5.00900 ( 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 351 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 226 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 583 ILE cc_start: 0.7741 (OUTLIER) cc_final: 0.7388 (mp) REVERT: C 361 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6888 (pp20) REVERT: C 458 MET cc_start: 0.7480 (tpp) cc_final: 0.6938 (tpp) REVERT: C 649 LYS cc_start: 0.5523 (OUTLIER) cc_final: 0.5277 (tmtt) REVERT: C 678 LYS cc_start: 0.8375 (tttp) cc_final: 0.8102 (tttm) REVERT: D 611 ASP cc_start: 0.6322 (p0) cc_final: 0.6076 (p0) REVERT: E 458 MET cc_start: 0.4430 (tmm) cc_final: 0.3230 (tmm) REVERT: E 462 MET cc_start: 0.5854 (OUTLIER) cc_final: 0.5638 (pmt) REVERT: E 592 ILE cc_start: 0.4357 (OUTLIER) cc_final: 0.4090 (tt) REVERT: E 650 LEU cc_start: 0.1909 (OUTLIER) cc_final: 0.1439 (tt) REVERT: E 684 MET cc_start: 0.2950 (tpp) cc_final: 0.2615 (tpp) REVERT: F 547 MET cc_start: 0.8006 (OUTLIER) cc_final: 0.7767 (ttm) REVERT: F 554 PHE cc_start: 0.7467 (OUTLIER) cc_final: 0.5829 (m-80) REVERT: F 656 ASP cc_start: 0.7113 (OUTLIER) cc_final: 0.6542 (t0) REVERT: F 660 GLN cc_start: 0.7832 (OUTLIER) cc_final: 0.7486 (mp10) REVERT: F 683 ILE cc_start: 0.8673 (pp) cc_final: 0.8471 (pt) outliers start: 125 outliers final: 68 residues processed: 332 average time/residue: 0.1622 time to fit residues: 84.5541 Evaluate side-chains 282 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 204 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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 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 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 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 649 LYS 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 431 ASP Chi-restraints excluded: chain D residue 512 THR Chi-restraints excluded: chain D residue 547 MET 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 349 VAL Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 462 MET 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 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 F residue 324 ASN Chi-restraints excluded: chain F residue 336 THR Chi-restraints excluded: chain F residue 356 LYS 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 547 MET Chi-restraints excluded: chain F residue 554 PHE 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 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 750 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 205 optimal weight: 10.0000 chunk 95 optimal weight: 0.6980 chunk 215 optimal weight: 0.2980 chunk 128 optimal weight: 5.9990 chunk 195 optimal weight: 1.9990 chunk 182 optimal weight: 0.4980 chunk 106 optimal weight: 8.9990 chunk 137 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 158 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.249546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.201127 restraints weight = 25679.567| |-----------------------------------------------------------------------------| r_work (start): 0.4259 rms_B_bonded: 2.90 r_work: 0.3521 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22841 Z= 0.113 Angle : 0.525 10.945 30892 Z= 0.275 Chirality : 0.042 0.246 3472 Planarity : 0.004 0.074 3940 Dihedral : 7.761 165.169 3096 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 4.71 % Allowed : 28.42 % Favored : 66.87 % 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 aren not related in a simple way. whole: -0.43 (0.16), residues: 2766 helix: 0.64 (0.16), residues: 1049 sheet: -0.67 (0.31), residues: 307 loop : -0.87 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 663 TYR 0.016 0.001 TYR A 699 PHE 0.015 0.001 PHE E 668 TRP 0.009 0.001 TRP D 350 HIS 0.009 0.001 HIS D 680 Details of bonding type rmsd covalent geometry : bond 0.00268 (22841) covalent geometry : angle 0.52479 (30892) hydrogen bonds : bond 0.03338 ( 788) hydrogen bonds : angle 4.76204 ( 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 337 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 220 time to evaluate : 0.924 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 324 ASN cc_start: 0.8097 (OUTLIER) cc_final: 0.7861 (t0) REVERT: A 618 MET cc_start: 0.7519 (ptp) cc_final: 0.7263 (ptp) REVERT: B 382 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.7996 (tt0) REVERT: B 447 ASP cc_start: 0.8067 (OUTLIER) cc_final: 0.7631 (t0) REVERT: B 481 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7428 (tt) REVERT: B 554 PHE cc_start: 0.8904 (OUTLIER) cc_final: 0.7528 (t80) REVERT: B 583 ILE cc_start: 0.7726 (OUTLIER) cc_final: 0.7370 (mp) REVERT: C 361 GLU cc_start: 0.7026 (OUTLIER) cc_final: 0.6602 (pt0) REVERT: C 458 MET cc_start: 0.7549 (tpp) cc_final: 0.7017 (tpp) REVERT: C 570 ARG cc_start: 0.8010 (mtm180) cc_final: 0.7808 (mtm180) REVERT: C 627 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.8116 (ptm160) REVERT: C 649 LYS cc_start: 0.5655 (OUTLIER) cc_final: 0.5425 (tmtt) REVERT: D 475 ASN cc_start: 0.7232 (t0) cc_final: 0.6851 (t0) REVERT: D 757 GLU cc_start: 0.5940 (OUTLIER) cc_final: 0.5521 (tp30) REVERT: E 458 MET cc_start: 0.4989 (tmm) cc_final: 0.4167 (tmm) REVERT: E 459 GLU cc_start: 0.7114 (mm-30) cc_final: 0.6777 (mm-30) REVERT: E 477 LYS cc_start: 0.7829 (tmmt) cc_final: 0.7057 (tttt) REVERT: E 592 ILE cc_start: 0.4321 (OUTLIER) cc_final: 0.4111 (tt) REVERT: E 650 LEU cc_start: 0.1774 (OUTLIER) cc_final: 0.1278 (tt) REVERT: E 702 ILE cc_start: 0.5735 (OUTLIER) cc_final: 0.5209 (tp) REVERT: F 547 MET cc_start: 0.8026 (OUTLIER) cc_final: 0.7790 (ttm) REVERT: F 554 PHE cc_start: 0.7490 (OUTLIER) cc_final: 0.5814 (m-80) REVERT: F 656 ASP cc_start: 0.7141 (OUTLIER) cc_final: 0.6641 (t0) REVERT: F 699 TYR cc_start: 0.7100 (OUTLIER) cc_final: 0.6594 (m-80) outliers start: 117 outliers final: 64 residues processed: 320 average time/residue: 0.1683 time to fit residues: 83.0773 Evaluate side-chains 287 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 206 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 ASN 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 561 PHE 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 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 733 THR Chi-restraints excluded: chain C residue 324 ASN 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 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 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 649 LYS Chi-restraints excluded: chain C residue 656 ASP Chi-restraints excluded: chain C residue 681 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 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 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 339 VAL Chi-restraints excluded: chain E residue 349 VAL 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 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 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 547 MET Chi-restraints excluded: chain F residue 554 PHE 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 680 HIS Chi-restraints excluded: chain F residue 695 ASP Chi-restraints excluded: chain F residue 699 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 118 optimal weight: 4.9990 chunk 168 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 217 optimal weight: 8.9990 chunk 2 optimal weight: 0.6980 chunk 73 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 192 optimal weight: 4.9990 chunk 69 optimal weight: 10.0000 chunk 198 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** F 546 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.247382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.202709 restraints weight = 25162.442| |-----------------------------------------------------------------------------| r_work (start): 0.4267 rms_B_bonded: 2.60 r_work: 0.3859 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 22841 Z= 0.202 Angle : 0.583 9.667 30892 Z= 0.303 Chirality : 0.044 0.199 3472 Planarity : 0.005 0.071 3940 Dihedral : 7.825 165.783 3086 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 5.11 % Allowed : 28.02 % Favored : 66.87 % 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 aren not related in a simple way. whole: -0.59 (0.16), residues: 2766 helix: 0.51 (0.17), residues: 1035 sheet: -0.72 (0.28), residues: 363 loop : -0.96 (0.16), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 387 TYR 0.020 0.001 TYR C 664 PHE 0.014 0.001 PHE E 668 TRP 0.013 0.002 TRP D 350 HIS 0.008 0.001 HIS D 680 Details of bonding type rmsd covalent geometry : bond 0.00511 (22841) covalent geometry : angle 0.58347 (30892) hydrogen bonds : bond 0.04681 ( 788) hydrogen bonds : angle 4.96948 ( 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 344 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 217 time to evaluate : 0.918 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: 0.5889 (m) cc_final: 0.5580 (m) REVERT: B 382 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7413 (tt0) REVERT: B 481 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7804 (tt) REVERT: B 554 PHE cc_start: 0.8968 (OUTLIER) cc_final: 0.7714 (t80) REVERT: B 583 ILE cc_start: 0.7806 (OUTLIER) cc_final: 0.7422 (mp) REVERT: C 361 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.7000 (pp20) REVERT: C 600 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8581 (mm) REVERT: E 339 VAL cc_start: 0.8929 (OUTLIER) cc_final: 0.8680 (t) REVERT: E 477 LYS cc_start: 0.7558 (tmmt) cc_final: 0.6867 (tttt) REVERT: E 548 HIS cc_start: 0.6527 (OUTLIER) cc_final: 0.5270 (t-170) REVERT: E 561 PHE cc_start: 0.3210 (OUTLIER) cc_final: 0.1780 (m-80) REVERT: E 592 ILE cc_start: 0.4111 (OUTLIER) cc_final: 0.3806 (tt) REVERT: E 607 LYS cc_start: 0.6031 (tmtt) cc_final: 0.5752 (tttp) REVERT: E 702 ILE cc_start: 0.5462 (OUTLIER) cc_final: 0.5063 (tp) REVERT: F 554 PHE cc_start: 0.7528 (OUTLIER) cc_final: 0.5977 (m-80) REVERT: F 656 ASP cc_start: 0.7182 (OUTLIER) cc_final: 0.6875 (t0) outliers start: 127 outliers final: 76 residues processed: 323 average time/residue: 0.1644 time to fit residues: 82.4349 Evaluate side-chains 299 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 210 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 A residue 757 GLU 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 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 361 GLU 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 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 627 ARG 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 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 512 THR Chi-restraints excluded: chain D residue 547 MET 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 339 VAL Chi-restraints excluded: chain E residue 349 VAL 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 624 VAL 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 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 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 Chi-restraints excluded: chain F residue 700 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 104 optimal weight: 3.9990 chunk 138 optimal weight: 0.9990 chunk 85 optimal weight: 0.0010 chunk 105 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 157 optimal weight: 8.9990 chunk 65 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 267 optimal weight: 10.0000 chunk 7 optimal weight: 0.5980 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 ASN C 324 ASN D 478 ASN D 775 GLN ** 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 = 0.4720 r_free = 0.4720 target = 0.254381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.229803 restraints weight = 25392.610| |-----------------------------------------------------------------------------| r_work (start): 0.4481 rms_B_bonded: 1.32 r_work: 0.4091 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3697 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1756 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= 0.104 Angle : 0.513 9.122 30892 Z= 0.269 Chirality : 0.041 0.182 3472 Planarity : 0.004 0.065 3940 Dihedral : 7.535 165.744 3086 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.31 % Allowed : 28.62 % Favored : 67.07 % 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 aren not related in a simple way. whole: -0.36 (0.16), residues: 2766 helix: 0.75 (0.17), residues: 1050 sheet: -0.62 (0.29), residues: 357 loop : -0.87 (0.16), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 514 TYR 0.018 0.001 TYR A 699 PHE 0.015 0.001 PHE E 668 TRP 0.009 0.001 TRP D 350 HIS 0.006 0.001 HIS D 680 Details of bonding type rmsd covalent geometry : bond 0.00247 (22841) covalent geometry : angle 0.51326 (30892) hydrogen bonds : bond 0.03058 ( 788) hydrogen bonds : angle 4.63494 ( 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 328 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 221 time to evaluate : 0.940 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 324 ASN cc_start: 0.8022 (OUTLIER) cc_final: 0.7391 (m-40) REVERT: A 581 CYS cc_start: 0.5925 (m) cc_final: 0.5624 (m) REVERT: A 618 MET cc_start: 0.7668 (ptp) cc_final: 0.7431 (ptp) REVERT: B 382 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8044 (tt0) REVERT: B 554 PHE cc_start: 0.8983 (OUTLIER) cc_final: 0.7711 (t80) REVERT: B 583 ILE cc_start: 0.7719 (OUTLIER) cc_final: 0.7372 (mp) REVERT: C 627 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.7942 (mtp180) REVERT: C 736 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7418 (tt) REVERT: E 458 MET cc_start: 0.3925 (tmm) cc_final: 0.2766 (tpt) REVERT: E 459 GLU cc_start: 0.6684 (mm-30) cc_final: 0.6184 (mm-30) REVERT: E 477 LYS cc_start: 0.7685 (tmmt) cc_final: 0.7000 (tttt) REVERT: E 561 PHE cc_start: 0.3022 (OUTLIER) cc_final: 0.1529 (m-80) REVERT: E 592 ILE cc_start: 0.4389 (OUTLIER) cc_final: 0.4081 (tt) REVERT: E 650 LEU cc_start: 0.1739 (OUTLIER) cc_final: 0.1061 (tt) REVERT: E 702 ILE cc_start: 0.5546 (OUTLIER) cc_final: 0.5018 (tp) REVERT: F 547 MET cc_start: 0.8196 (OUTLIER) cc_final: 0.7949 (ttm) REVERT: F 554 PHE cc_start: 0.7561 (OUTLIER) cc_final: 0.5945 (m-80) REVERT: F 656 ASP cc_start: 0.7379 (OUTLIER) cc_final: 0.7027 (t0) REVERT: F 699 TYR cc_start: 0.7198 (OUTLIER) cc_final: 0.6823 (m-80) outliers start: 107 outliers final: 66 residues processed: 307 average time/residue: 0.1731 time to fit residues: 81.8199 Evaluate side-chains 289 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 209 time to evaluate : 0.994 ------------------------------------------------------------------------------- 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 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 A residue 780 GLU 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 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 558 LEU 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 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 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 656 ASP Chi-restraints excluded: chain C residue 659 ILE 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 336 THR Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 512 THR Chi-restraints excluded: chain D residue 547 MET 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 349 VAL 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 31 optimal weight: 9.9990 chunk 226 optimal weight: 30.0000 chunk 159 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 179 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 68 optimal weight: 0.9990 chunk 120 optimal weight: 0.8980 chunk 242 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 chunk 221 optimal weight: 20.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 ASN B 324 ASN C 324 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.247215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.197120 restraints weight = 25225.582| |-----------------------------------------------------------------------------| r_work (start): 0.4237 rms_B_bonded: 2.89 r_work: 0.3505 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1840 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= 0.147 Angle : 0.546 11.761 30892 Z= 0.284 Chirality : 0.042 0.175 3472 Planarity : 0.004 0.071 3940 Dihedral : 7.464 166.130 3081 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 4.55 % Allowed : 28.46 % Favored : 66.99 % Cbeta Deviations : 0.00 % 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 aren not related in a simple way. whole: -0.42 (0.16), residues: 2766 helix: 0.67 (0.17), residues: 1051 sheet: -0.61 (0.29), residues: 362 loop : -0.90 (0.16), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 387 TYR 0.012 0.001 TYR C 664 PHE 0.019 0.001 PHE E 501 TRP 0.011 0.001 TRP D 350 HIS 0.006 0.001 HIS D 680 Details of bonding type rmsd covalent geometry : bond 0.00368 (22841) covalent geometry : angle 0.54558 (30892) hydrogen bonds : bond 0.03886 ( 788) hydrogen bonds : angle 4.70611 ( 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 323 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 210 time to evaluate : 0.881 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 324 ASN cc_start: 0.8050 (OUTLIER) cc_final: 0.7640 (t0) REVERT: A 581 CYS cc_start: 0.6466 (m) cc_final: 0.6235 (m) REVERT: A 618 MET cc_start: 0.7511 (ptp) cc_final: 0.7277 (ptp) REVERT: B 351 ILE cc_start: 0.8528 (OUTLIER) cc_final: 0.7903 (mt) REVERT: B 382 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.7982 (tt0) REVERT: B 481 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7437 (tt) REVERT: B 554 PHE cc_start: 0.8879 (OUTLIER) cc_final: 0.7502 (t80) REVERT: B 583 ILE cc_start: 0.7783 (OUTLIER) cc_final: 0.7414 (mp) REVERT: C 736 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7426 (tt) REVERT: D 475 ASN cc_start: 0.7246 (t0) cc_final: 0.6749 (t0) REVERT: E 339 VAL cc_start: 0.9059 (OUTLIER) cc_final: 0.8734 (t) REVERT: E 477 LYS cc_start: 0.7771 (tmmt) cc_final: 0.7014 (tttt) REVERT: E 561 PHE cc_start: 0.3077 (OUTLIER) cc_final: 0.1618 (m-10) REVERT: E 592 ILE cc_start: 0.4746 (OUTLIER) cc_final: 0.4517 (tt) REVERT: E 650 LEU cc_start: 0.1878 (OUTLIER) cc_final: 0.1342 (tt) REVERT: E 702 ILE cc_start: 0.5799 (OUTLIER) cc_final: 0.5162 (tp) REVERT: F 554 PHE cc_start: 0.7486 (OUTLIER) cc_final: 0.5761 (m-80) REVERT: F 656 ASP cc_start: 0.7290 (OUTLIER) cc_final: 0.6911 (t0) REVERT: F 699 TYR cc_start: 0.7157 (OUTLIER) cc_final: 0.6651 (m-80) outliers start: 113 outliers final: 82 residues processed: 302 average time/residue: 0.1671 time to fit residues: 78.3262 Evaluate side-chains 300 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 203 time to evaluate : 1.291 ------------------------------------------------------------------------------- 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 423 VAL Chi-restraints excluded: chain A residue 436 TYR 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 535 VAL 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 780 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 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 558 LEU Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 702 ILE 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 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 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 656 ASP Chi-restraints excluded: chain C residue 659 ILE 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 339 VAL Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 512 THR Chi-restraints excluded: chain D residue 547 MET 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 339 VAL 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 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 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 354 SER 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 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 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: 9.9990 chunk 110 optimal weight: 0.9990 chunk 234 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 77 optimal weight: 9.9990 chunk 227 optimal weight: 30.0000 chunk 207 optimal weight: 0.0470 chunk 147 optimal weight: 0.0770 chunk 144 optimal weight: 0.2980 chunk 47 optimal weight: 0.8980 chunk 273 optimal weight: 8.9990 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 ASN B 469 GLN ** B 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 ASN C 641 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4723 r_free = 0.4723 target = 0.255035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.224344 restraints weight = 25245.084| |-----------------------------------------------------------------------------| r_work (start): 0.4430 rms_B_bonded: 1.80 r_work: 0.4072 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work (final): 0.4072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.1966 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= 0.097 Angle : 0.508 8.614 30892 Z= 0.266 Chirality : 0.041 0.169 3472 Planarity : 0.004 0.067 3940 Dihedral : 7.263 166.161 3079 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.58 % Allowed : 29.43 % Favored : 66.99 % Cbeta Deviations : 0.00 % 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 aren not related in a simple way. whole: -0.22 (0.16), residues: 2766 helix: 0.87 (0.17), residues: 1053 sheet: -0.54 (0.29), residues: 358 loop : -0.80 (0.16), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 514 TYR 0.012 0.001 TYR A 699 PHE 0.040 0.001 PHE E 501 TRP 0.008 0.001 TRP D 350 HIS 0.005 0.000 HIS D 680 Details of bonding type rmsd covalent geometry : bond 0.00227 (22841) covalent geometry : angle 0.50754 (30892) hydrogen bonds : bond 0.02836 ( 788) hydrogen bonds : angle 4.50782 ( 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 309 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 220 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 ASN cc_start: 0.7638 (OUTLIER) cc_final: 0.7419 (t0) REVERT: B 382 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7352 (tt0) REVERT: B 481 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.7833 (tt) REVERT: B 526 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7863 (mt-10) REVERT: B 554 PHE cc_start: 0.8978 (OUTLIER) cc_final: 0.7807 (t80) REVERT: B 583 ILE cc_start: 0.7694 (OUTLIER) cc_final: 0.7325 (mp) REVERT: C 618 MET cc_start: 0.7881 (tpt) cc_final: 0.7443 (tpt) REVERT: C 627 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7781 (mtp180) REVERT: D 475 ASN cc_start: 0.7076 (t0) cc_final: 0.6853 (t0) REVERT: E 477 LYS cc_start: 0.7228 (tmmt) cc_final: 0.6793 (tttt) REVERT: E 561 PHE cc_start: 0.3015 (OUTLIER) cc_final: 0.1894 (m-10) REVERT: E 650 LEU cc_start: 0.1723 (OUTLIER) cc_final: 0.0853 (tt) REVERT: E 702 ILE cc_start: 0.5403 (OUTLIER) cc_final: 0.5032 (tp) REVERT: F 547 MET cc_start: 0.7802 (OUTLIER) cc_final: 0.7592 (ttm) REVERT: F 554 PHE cc_start: 0.7376 (OUTLIER) cc_final: 0.5784 (m-80) REVERT: F 656 ASP cc_start: 0.6958 (OUTLIER) cc_final: 0.6651 (t0) outliers start: 89 outliers final: 63 residues processed: 293 average time/residue: 0.1637 time to fit residues: 75.4250 Evaluate side-chains 285 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 210 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 ASN 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 531 ILE Chi-restraints excluded: chain A residue 561 PHE Chi-restraints excluded: chain A residue 645 TYR Chi-restraints excluded: chain A residue 723 LYS Chi-restraints excluded: chain A residue 780 GLU 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 481 LEU Chi-restraints excluded: chain B residue 488 SER 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 726 ILE Chi-restraints excluded: chain B residue 733 THR Chi-restraints excluded: chain C residue 324 ASN 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 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 613 ILE Chi-restraints excluded: chain C residue 627 ARG Chi-restraints excluded: chain C residue 656 ASP Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain C residue 681 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 339 VAL Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 607 LYS 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 339 VAL Chi-restraints excluded: chain E residue 349 VAL 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 599 THR 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 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 651 LEU 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 736 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 22 optimal weight: 8.9990 chunk 163 optimal weight: 7.9990 chunk 216 optimal weight: 7.9990 chunk 177 optimal weight: 50.0000 chunk 75 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 176 optimal weight: 4.9990 chunk 227 optimal weight: 40.0000 chunk 5 optimal weight: 0.9980 chunk 147 optimal weight: 0.7980 chunk 215 optimal weight: 3.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 ASN B 324 ASN C 324 ASN C 740 GLN D 629 HIS ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 324 ASN F 546 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4700 r_free = 0.4700 target = 0.252069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.219602 restraints weight = 25244.158| |-----------------------------------------------------------------------------| r_work (start): 0.4386 rms_B_bonded: 1.78 r_work: 0.4035 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 22841 Z= 0.193 Angle : 0.584 9.572 30892 Z= 0.302 Chirality : 0.044 0.173 3472 Planarity : 0.004 0.068 3940 Dihedral : 7.468 166.730 3076 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.99 % Allowed : 28.86 % Favored : 67.15 % Cbeta Deviations : 0.00 % 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 aren not related in a simple way. whole: -0.42 (0.16), residues: 2766 helix: 0.66 (0.17), residues: 1037 sheet: -0.70 (0.28), residues: 366 loop : -0.85 (0.16), residues: 1363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 387 TYR 0.024 0.001 TYR D 645 PHE 0.044 0.001 PHE E 501 TRP 0.012 0.002 TRP C 350 HIS 0.008 0.001 HIS D 629 Details of bonding type rmsd covalent geometry : bond 0.00487 (22841) covalent geometry : angle 0.58444 (30892) hydrogen bonds : bond 0.04525 ( 788) hydrogen bonds : angle 4.76973 ( 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 315 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 216 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 351 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.7970 (mt) REVERT: B 481 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.7892 (tt) REVERT: B 554 PHE cc_start: 0.8932 (OUTLIER) cc_final: 0.7761 (t80) REVERT: B 583 ILE cc_start: 0.7778 (OUTLIER) cc_final: 0.7373 (mp) REVERT: C 361 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6463 (pt0) REVERT: C 426 MET cc_start: 0.7486 (OUTLIER) cc_final: 0.7239 (ttm) REVERT: E 339 VAL cc_start: 0.8880 (OUTLIER) cc_final: 0.8625 (t) REVERT: E 477 LYS cc_start: 0.7274 (tmmt) cc_final: 0.6791 (tttt) REVERT: E 561 PHE cc_start: 0.3020 (OUTLIER) cc_final: 0.1931 (m-80) REVERT: E 650 LEU cc_start: 0.1774 (OUTLIER) cc_final: 0.0866 (tt) REVERT: E 702 ILE cc_start: 0.5577 (OUTLIER) cc_final: 0.5146 (tp) REVERT: F 554 PHE cc_start: 0.7417 (OUTLIER) cc_final: 0.5918 (m-80) REVERT: F 656 ASP cc_start: 0.6947 (OUTLIER) cc_final: 0.6732 (t0) outliers start: 99 outliers final: 70 residues processed: 297 average time/residue: 0.1681 time to fit residues: 77.1213 Evaluate side-chains 295 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 213 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 LEU 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 531 ILE Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 561 PHE 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 780 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 435 LYS Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 488 SER 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 361 GLU Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 426 MET 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 581 CYS Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 627 ARG Chi-restraints excluded: chain C residue 656 ASP Chi-restraints excluded: chain C residue 659 ILE 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 336 THR Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain D residue 607 LYS 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 339 VAL Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 501 PHE 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 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 354 SER Chi-restraints excluded: chain F residue 356 LYS Chi-restraints excluded: chain F residue 424 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 651 LEU 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 736 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 16 optimal weight: 6.9990 chunk 108 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 133 optimal weight: 0.0870 chunk 221 optimal weight: 6.9990 chunk 128 optimal weight: 3.9990 chunk 224 optimal weight: 0.0470 chunk 24 optimal weight: 7.9990 chunk 114 optimal weight: 0.7980 chunk 201 optimal weight: 4.9990 chunk 70 optimal weight: 9.9990 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 529 GLN C 324 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4726 r_free = 0.4726 target = 0.255287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.224045 restraints weight = 25521.590| |-----------------------------------------------------------------------------| r_work (start): 0.4425 rms_B_bonded: 1.81 r_work: 0.4134 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.4057 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.4057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.2176 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= 0.099 Angle : 0.518 9.230 30892 Z= 0.269 Chirality : 0.041 0.170 3472 Planarity : 0.004 0.063 3940 Dihedral : 7.202 167.311 3076 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.86 % Allowed : 29.67 % Favored : 67.47 % Cbeta Deviations : 0.00 % 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 aren not related in a simple way. whole: -0.18 (0.16), residues: 2766 helix: 0.88 (0.17), residues: 1048 sheet: -0.54 (0.29), residues: 359 loop : -0.74 (0.16), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 514 TYR 0.012 0.001 TYR D 645 PHE 0.033 0.001 PHE E 501 TRP 0.011 0.001 TRP F 675 HIS 0.006 0.000 HIS D 680 Details of bonding type rmsd covalent geometry : bond 0.00233 (22841) covalent geometry : angle 0.51755 (30892) hydrogen bonds : bond 0.02839 ( 788) hydrogen bonds : angle 4.44959 ( 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 288 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 217 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 481 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.7856 (tt) REVERT: B 554 PHE cc_start: 0.8995 (OUTLIER) cc_final: 0.7883 (t80) REVERT: B 583 ILE cc_start: 0.7739 (OUTLIER) cc_final: 0.7391 (mp) REVERT: C 361 GLU cc_start: 0.6794 (OUTLIER) cc_final: 0.6036 (pt0) REVERT: C 618 MET cc_start: 0.7803 (tpt) cc_final: 0.7564 (tpt) REVERT: E 477 LYS cc_start: 0.7213 (tmmt) cc_final: 0.6778 (tttt) REVERT: E 561 PHE cc_start: 0.2953 (OUTLIER) cc_final: 0.1908 (m-10) REVERT: E 650 LEU cc_start: 0.1798 (OUTLIER) cc_final: 0.0865 (tt) REVERT: E 702 ILE cc_start: 0.5408 (OUTLIER) cc_final: 0.5070 (tp) REVERT: F 547 MET cc_start: 0.7916 (OUTLIER) cc_final: 0.7648 (ttm) REVERT: F 554 PHE cc_start: 0.7388 (OUTLIER) cc_final: 0.5836 (m-80) outliers start: 71 outliers final: 54 residues processed: 274 average time/residue: 0.1642 time to fit residues: 70.3847 Evaluate side-chains 273 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 210 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 LEU 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 531 ILE Chi-restraints excluded: chain A residue 561 PHE 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 481 LEU Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 554 PHE 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 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 361 GLU 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 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 627 ARG Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain C residue 681 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 339 VAL Chi-restraints excluded: chain D residue 607 LYS 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 339 VAL Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 501 PHE 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 599 THR 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 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 547 MET Chi-restraints excluded: chain F residue 554 PHE Chi-restraints excluded: chain F residue 651 LEU 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: 6.9990 chunk 41 optimal weight: 6.9990 chunk 262 optimal weight: 20.0000 chunk 32 optimal weight: 6.9990 chunk 182 optimal weight: 30.0000 chunk 235 optimal weight: 1.9990 chunk 43 optimal weight: 20.0000 chunk 47 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 221 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 ASN C 740 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.251904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.218295 restraints weight = 25314.581| |-----------------------------------------------------------------------------| r_work (start): 0.4372 rms_B_bonded: 1.72 r_work: 0.4025 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work (final): 0.4025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 22841 Z= 0.208 Angle : 0.603 11.882 30892 Z= 0.310 Chirality : 0.045 0.186 3472 Planarity : 0.004 0.064 3940 Dihedral : 7.434 167.367 3074 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.38 % Allowed : 29.07 % Favored : 67.55 % Cbeta Deviations : 0.00 % 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 aren not related in a simple way. whole: -0.45 (0.16), residues: 2766 helix: 0.59 (0.17), residues: 1044 sheet: -0.63 (0.29), residues: 363 loop : -0.85 (0.16), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 387 TYR 0.015 0.001 TYR D 645 PHE 0.035 0.002 PHE E 501 TRP 0.012 0.002 TRP C 350 HIS 0.005 0.001 HIS D 347 Details of bonding type rmsd covalent geometry : bond 0.00530 (22841) covalent geometry : angle 0.60345 (30892) hydrogen bonds : bond 0.04741 ( 788) hydrogen bonds : angle 4.81853 ( 2244) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5587.03 seconds wall clock time: 97 minutes 3.90 seconds (5823.90 seconds total)