Starting phenix.real_space_refine on Thu Jun 19 12:36:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wh4_37528/06_2025/8wh4_37528.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wh4_37528/06_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_37528/06_2025/8wh4_37528.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wh4_37528/06_2025/8wh4_37528.map" model { file = "/net/cci-nas-00/data/ceres_data/8wh4_37528/06_2025/8wh4_37528.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wh4_37528/06_2025/8wh4_37528.cif" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 2} 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: {'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 2} 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: {'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 2} 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: {'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 2} 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: {'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 2} 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: {'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 2} 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: 13.64, per 1000 atoms: 0.61 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: 5.81 Conformation dependent library (CDL) restraints added in 3.0 seconds 5532 Ramachandran restraints generated. 2766 Oldfield, 0 Emsley, 2766 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5304 Finding SS restraints... Secondary structure from input PDB file: 151 helices and 40 sheets defined 46.3% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.84 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: 7.73 Time building geometry restraints manager: 6.26 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: 2.160 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: 0.020 Extract box with map and model: 0.980 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 50.610 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.100 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.060 ------------------------------------------------------------------------------- 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 : 9.99 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.010 0.001 TRP E 675 HIS 0.007 0.001 HIS E 548 PHE 0.031 0.001 PHE F 502 TYR 0.020 0.001 TYR A 606 ARG 0.005 0.000 ARG C 585 Details of bonding type rmsd hydrogen bonds : bond 0.17756 ( 788) hydrogen bonds : angle 6.17378 ( 2244) covalent geometry : bond 0.00833 (22841) covalent geometry : angle 0.83209 (30892) *********************** 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 : 2.377 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: 0.3260 time to fit residues: 146.4310 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 : 2.705 ------------------------------------------------------------------------------- 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 233 optimal weight: 5.9990 chunk 209 optimal weight: 20.0000 chunk 116 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 216 optimal weight: 30.0000 chunk 83 optimal weight: 0.0970 chunk 131 optimal weight: 0.9990 chunk 161 optimal weight: 9.9990 chunk 250 optimal weight: 1.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 469 GLN C 573 ASN D 475 ASN ** D 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 641 ASN D 661 ASN ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 713 HIS F 324 ASN F 475 ASN F 763 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.252568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.215867 restraints weight = 25173.908| |-----------------------------------------------------------------------------| r_work (start): 0.4352 rms_B_bonded: 1.91 r_work: 0.4113 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.4074 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.0811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.145 22841 Z= 0.180 Angle : 0.587 8.131 30892 Z= 0.308 Chirality : 0.044 0.172 3472 Planarity : 0.005 0.099 3940 Dihedral : 8.689 164.408 3164 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 5.80 % Allowed : 26.61 % Favored : 67.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.16), residues: 2766 helix: 0.45 (0.16), residues: 1030 sheet: -0.55 (0.29), residues: 370 loop : -0.90 (0.16), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 350 HIS 0.009 0.001 HIS A 680 PHE 0.017 0.001 PHE E 561 TYR 0.020 0.001 TYR A 606 ARG 0.005 0.000 ARG D 762 Details of bonding type rmsd hydrogen bonds : bond 0.04822 ( 788) hydrogen bonds : angle 5.24165 ( 2244) covalent geometry : bond 0.00460 (22841) covalent geometry : angle 0.58672 (30892) *********************** 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 363 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 219 time to evaluate : 2.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 457 GLU cc_start: 0.6348 (OUTLIER) cc_final: 0.5276 (tm-30) REVERT: B 481 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.7937 (tt) REVERT: B 554 PHE cc_start: 0.8950 (OUTLIER) cc_final: 0.7743 (t80) REVERT: B 583 ILE cc_start: 0.7796 (OUTLIER) cc_final: 0.7378 (mp) REVERT: E 458 MET cc_start: 0.4091 (tmm) cc_final: 0.2971 (tmm) REVERT: E 462 MET cc_start: 0.5303 (OUTLIER) cc_final: 0.4939 (pmt) REVERT: E 477 LYS cc_start: 0.6972 (tmmt) cc_final: 0.6480 (tttt) REVERT: E 592 ILE cc_start: 0.3401 (OUTLIER) cc_final: 0.3095 (tt) REVERT: F 467 ASP cc_start: 0.8106 (OUTLIER) cc_final: 0.7893 (t0) REVERT: F 656 ASP cc_start: 0.6676 (OUTLIER) cc_final: 0.6429 (t0) outliers start: 144 outliers final: 70 residues processed: 340 average time/residue: 0.3310 time to fit residues: 177.2064 Evaluate side-chains 284 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 206 time to evaluate : 2.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 561 PHE Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 723 LYS Chi-restraints excluded: chain A residue 757 GLU Chi-restraints excluded: chain B residue 457 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 499 THR 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 561 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 C residue 363 LEU Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 483 GLU Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 656 ASP 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 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 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 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 693 ILE Chi-restraints excluded: chain E residue 324 ASN Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain E residue 462 MET Chi-restraints excluded: chain E residue 463 ASN Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain E residue 546 ASN 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 691 GLU Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 336 THR Chi-restraints excluded: chain F residue 356 LYS Chi-restraints excluded: chain F residue 447 ASP Chi-restraints excluded: chain F residue 467 ASP Chi-restraints excluded: chain F residue 471 LEU Chi-restraints excluded: chain F residue 483 GLU Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 525 VAL Chi-restraints excluded: chain F residue 547 MET Chi-restraints excluded: chain F residue 578 THR Chi-restraints excluded: chain F residue 581 CYS Chi-restraints excluded: chain F residue 656 ASP Chi-restraints excluded: chain F residue 680 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 12 optimal weight: 4.9990 chunk 269 optimal weight: 8.9990 chunk 241 optimal weight: 2.9990 chunk 267 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 168 optimal weight: 20.0000 chunk 242 optimal weight: 0.1980 chunk 182 optimal weight: 20.0000 chunk 56 optimal weight: 7.9990 chunk 231 optimal weight: 0.6980 chunk 60 optimal weight: 8.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 478 ASN D 469 GLN ** D 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 324 ASN F 662 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.247556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.200637 restraints weight = 25233.855| |-----------------------------------------------------------------------------| r_work (start): 0.4255 rms_B_bonded: 2.92 r_work: 0.3494 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 22841 Z= 0.184 Angle : 0.578 9.330 30892 Z= 0.302 Chirality : 0.044 0.204 3472 Planarity : 0.005 0.064 3940 Dihedral : 8.022 164.863 3101 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 5.84 % Allowed : 26.53 % Favored : 67.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.16), residues: 2766 helix: 0.48 (0.17), residues: 1035 sheet: -0.54 (0.30), residues: 333 loop : -0.92 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 350 HIS 0.010 0.001 HIS D 680 PHE 0.015 0.001 PHE E 668 TYR 0.013 0.001 TYR A 645 ARG 0.005 0.000 ARG E 663 Details of bonding type rmsd hydrogen bonds : bond 0.04632 ( 788) hydrogen bonds : angle 5.08142 ( 2244) covalent geometry : bond 0.00463 (22841) covalent geometry : angle 0.57839 (30892) *********************** 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 365 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 220 time to evaluate : 2.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 457 GLU cc_start: 0.6791 (OUTLIER) cc_final: 0.5710 (tm-30) REVERT: B 481 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7482 (tt) REVERT: B 554 PHE cc_start: 0.8916 (OUTLIER) cc_final: 0.7543 (t80) REVERT: B 583 ILE cc_start: 0.7776 (OUTLIER) cc_final: 0.7398 (mp) REVERT: C 361 GLU cc_start: 0.6927 (OUTLIER) cc_final: 0.6518 (pt0) REVERT: C 736 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7473 (tt) REVERT: E 455 SER cc_start: 0.5793 (OUTLIER) cc_final: 0.5058 (p) REVERT: E 458 MET cc_start: 0.4702 (tmm) cc_final: 0.3874 (tmm) REVERT: E 459 GLU cc_start: 0.6990 (mm-30) cc_final: 0.6690 (mm-30) REVERT: E 462 MET cc_start: 0.5848 (OUTLIER) cc_final: 0.5390 (pmt) REVERT: E 477 LYS cc_start: 0.7914 (tmmt) cc_final: 0.7086 (tttt) REVERT: E 529 GLN cc_start: 0.5350 (OUTLIER) cc_final: 0.5039 (mm-40) REVERT: E 548 HIS cc_start: 0.6895 (OUTLIER) cc_final: 0.5796 (t-170) REVERT: E 592 ILE cc_start: 0.4436 (OUTLIER) cc_final: 0.4147 (tt) REVERT: F 656 ASP cc_start: 0.7218 (OUTLIER) cc_final: 0.6735 (t0) outliers start: 145 outliers final: 88 residues processed: 344 average time/residue: 0.3369 time to fit residues: 183.2881 Evaluate side-chains 307 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 207 time to evaluate : 2.675 ------------------------------------------------------------------------------- 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 488 SER 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 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 457 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 499 THR Chi-restraints excluded: chain B residue 502 PHE 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 561 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 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 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 486 LEU Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 575 LYS Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 656 ASP Chi-restraints excluded: chain C residue 681 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 423 VAL Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 469 GLN Chi-restraints excluded: chain D residue 477 LYS Chi-restraints excluded: chain D residue 512 THR Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain D residue 578 THR Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 693 ILE Chi-restraints excluded: chain E residue 324 ASN Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain E residue 337 ASN Chi-restraints excluded: chain E residue 455 SER Chi-restraints excluded: chain E residue 462 MET 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 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 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 402 ASP Chi-restraints excluded: chain F residue 419 VAL 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 494 THR Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 525 VAL Chi-restraints excluded: chain F residue 547 MET Chi-restraints excluded: chain F residue 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 710 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 122 optimal weight: 4.9990 chunk 131 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 45 optimal weight: 7.9990 chunk 235 optimal weight: 1.9990 chunk 87 optimal weight: 10.0000 chunk 251 optimal weight: 7.9990 chunk 113 optimal weight: 3.9990 chunk 17 optimal weight: 8.9990 chunk 226 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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 573 ASN ** D 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 661 ASN ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.251131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.225213 restraints weight = 25306.416| |-----------------------------------------------------------------------------| r_work (start): 0.4441 rms_B_bonded: 1.34 r_work: 0.4032 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3700 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 22841 Z= 0.230 Angle : 0.612 7.395 30892 Z= 0.319 Chirality : 0.045 0.200 3472 Planarity : 0.005 0.060 3940 Dihedral : 8.106 165.746 3098 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 6.12 % Allowed : 26.73 % Favored : 67.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.16), residues: 2766 helix: 0.36 (0.17), residues: 1037 sheet: -0.81 (0.30), residues: 325 loop : -0.97 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 350 HIS 0.008 0.001 HIS D 680 PHE 0.015 0.002 PHE C 444 TYR 0.017 0.001 TYR A 699 ARG 0.004 0.000 ARG E 387 Details of bonding type rmsd hydrogen bonds : bond 0.05079 ( 788) hydrogen bonds : angle 5.11915 ( 2244) covalent geometry : bond 0.00582 (22841) covalent geometry : angle 0.61161 (30892) *********************** 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 374 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 222 time to evaluate : 2.394 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 324 ASN cc_start: 0.8273 (OUTLIER) cc_final: 0.8037 (t0) REVERT: A 581 CYS cc_start: 0.6015 (m) cc_final: 0.5659 (m) REVERT: B 481 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7831 (tt) REVERT: B 554 PHE cc_start: 0.9036 (OUTLIER) cc_final: 0.7762 (t80) REVERT: B 583 ILE cc_start: 0.7848 (OUTLIER) cc_final: 0.7436 (mp) REVERT: C 361 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6765 (pt0) REVERT: C 426 MET cc_start: 0.7802 (OUTLIER) cc_final: 0.7550 (ttm) REVERT: C 736 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7414 (tt) REVERT: E 459 GLU cc_start: 0.6753 (mm-30) cc_final: 0.6526 (mm-30) REVERT: E 462 MET cc_start: 0.5899 (OUTLIER) cc_final: 0.5421 (pmt) REVERT: E 548 HIS cc_start: 0.6699 (OUTLIER) cc_final: 0.5504 (t-170) REVERT: E 561 PHE cc_start: 0.3134 (OUTLIER) cc_final: 0.1666 (m-80) REVERT: E 610 PHE cc_start: 0.4029 (OUTLIER) cc_final: 0.3494 (m-80) REVERT: E 650 LEU cc_start: 0.1806 (OUTLIER) cc_final: 0.1075 (tt) REVERT: F 554 PHE cc_start: 0.7509 (OUTLIER) cc_final: 0.5984 (m-80) REVERT: F 656 ASP cc_start: 0.7325 (OUTLIER) cc_final: 0.7017 (t0) REVERT: F 699 TYR cc_start: 0.7252 (OUTLIER) cc_final: 0.6892 (m-80) REVERT: F 707 VAL cc_start: 0.5958 (OUTLIER) cc_final: 0.5742 (p) outliers start: 152 outliers final: 98 residues processed: 350 average time/residue: 0.3257 time to fit residues: 178.3335 Evaluate side-chains 331 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 217 time to evaluate : 2.412 ------------------------------------------------------------------------------- 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 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 488 SER 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 577 LEU Chi-restraints excluded: chain A residue 636 ARG Chi-restraints excluded: chain A residue 645 TYR Chi-restraints excluded: chain A residue 723 LYS Chi-restraints excluded: chain A residue 757 GLU Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain B residue 426 MET 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 554 PHE 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 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 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 486 LEU Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 573 ASN Chi-restraints excluded: chain C residue 575 LYS Chi-restraints excluded: chain C residue 581 CYS Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 656 ASP Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 689 THR Chi-restraints excluded: chain C residue 699 TYR Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 324 ASN Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 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 578 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 723 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 349 VAL Chi-restraints excluded: chain E residue 419 VAL Chi-restraints excluded: chain E residue 436 TYR Chi-restraints excluded: chain E residue 462 MET Chi-restraints excluded: chain E residue 463 ASN Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain E residue 546 ASN Chi-restraints excluded: chain E residue 548 HIS Chi-restraints excluded: chain E residue 561 PHE Chi-restraints excluded: chain E residue 582 VAL Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 605 ASN Chi-restraints excluded: chain E residue 610 PHE Chi-restraints excluded: chain E residue 624 VAL Chi-restraints excluded: chain E residue 650 LEU Chi-restraints excluded: chain E residue 691 GLU Chi-restraints excluded: chain 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 402 ASP Chi-restraints excluded: chain F residue 419 VAL 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 494 THR Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 525 VAL Chi-restraints excluded: chain F residue 547 MET Chi-restraints excluded: chain F residue 553 VAL 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 699 TYR Chi-restraints excluded: chain F residue 707 VAL Chi-restraints excluded: chain F residue 710 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 273 optimal weight: 5.9990 chunk 227 optimal weight: 30.0000 chunk 250 optimal weight: 5.9990 chunk 88 optimal weight: 8.9990 chunk 207 optimal weight: 20.0000 chunk 3 optimal weight: 0.4980 chunk 137 optimal weight: 2.9990 chunk 177 optimal weight: 40.0000 chunk 185 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 190 optimal weight: 0.8980 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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** C 740 GLN ** D 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 661 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 546 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.253301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.228499 restraints weight = 25201.821| |-----------------------------------------------------------------------------| r_work (start): 0.4470 rms_B_bonded: 1.32 r_work: 0.4065 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3687 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22841 Z= 0.126 Angle : 0.533 11.632 30892 Z= 0.280 Chirality : 0.042 0.263 3472 Planarity : 0.004 0.054 3940 Dihedral : 7.792 165.451 3097 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 4.95 % Allowed : 28.02 % Favored : 67.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.16), residues: 2766 helix: 0.56 (0.17), residues: 1046 sheet: -0.65 (0.29), residues: 359 loop : -0.93 (0.16), residues: 1361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 350 HIS 0.007 0.001 HIS D 680 PHE 0.015 0.001 PHE E 668 TYR 0.018 0.001 TYR A 699 ARG 0.003 0.000 ARG E 387 Details of bonding type rmsd hydrogen bonds : bond 0.03546 ( 788) hydrogen bonds : angle 4.81721 ( 2244) covalent geometry : bond 0.00310 (22841) covalent geometry : angle 0.53334 (30892) *********************** 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 348 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 225 time to evaluate : 2.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 581 CYS cc_start: 0.6111 (m) cc_final: 0.5775 (m) REVERT: A 684 MET cc_start: 0.8092 (tmt) cc_final: 0.7534 (tmt) REVERT: B 554 PHE cc_start: 0.9012 (OUTLIER) cc_final: 0.7703 (t80) REVERT: B 583 ILE cc_start: 0.7789 (OUTLIER) cc_final: 0.7394 (mp) REVERT: C 426 MET cc_start: 0.8035 (OUTLIER) cc_final: 0.7808 (ttm) REVERT: C 575 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8474 (mmmt) REVERT: D 475 ASN cc_start: 0.7262 (t0) cc_final: 0.6992 (t0) REVERT: D 757 GLU cc_start: 0.5430 (OUTLIER) cc_final: 0.4730 (tp30) REVERT: E 339 VAL cc_start: 0.8968 (OUTLIER) cc_final: 0.8668 (t) REVERT: E 462 MET cc_start: 0.5970 (OUTLIER) cc_final: 0.5623 (pmt) REVERT: E 561 PHE cc_start: 0.3066 (OUTLIER) cc_final: 0.1579 (m-80) REVERT: E 592 ILE cc_start: 0.4291 (OUTLIER) cc_final: 0.3903 (tt) REVERT: E 650 LEU cc_start: 0.1737 (OUTLIER) cc_final: 0.1013 (tt) REVERT: E 684 MET cc_start: 0.2895 (tpp) cc_final: 0.2013 (tpp) REVERT: E 702 ILE cc_start: 0.5500 (OUTLIER) cc_final: 0.5089 (tp) REVERT: F 554 PHE cc_start: 0.7550 (OUTLIER) cc_final: 0.5864 (m-80) REVERT: F 656 ASP cc_start: 0.7331 (OUTLIER) cc_final: 0.7036 (t0) REVERT: F 699 TYR cc_start: 0.7239 (OUTLIER) cc_final: 0.6890 (m-80) REVERT: F 707 VAL cc_start: 0.5935 (OUTLIER) cc_final: 0.5734 (p) outliers start: 123 outliers final: 73 residues processed: 326 average time/residue: 0.3473 time to fit residues: 175.4678 Evaluate side-chains 300 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 212 time to evaluate : 2.771 ------------------------------------------------------------------------------- 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 436 TYR Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 561 PHE Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 636 ARG Chi-restraints excluded: chain A residue 645 TYR Chi-restraints excluded: chain A residue 723 LYS Chi-restraints excluded: chain A residue 757 GLU Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain B residue 426 MET 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 554 PHE Chi-restraints excluded: chain B residue 581 CYS Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 733 THR Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain C residue 334 LEU 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 455 SER Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 483 GLU Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 575 LYS Chi-restraints excluded: chain C residue 581 CYS Chi-restraints excluded: chain C residue 656 ASP 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 431 ASP Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 512 THR Chi-restraints excluded: chain D residue 607 LYS Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 693 ILE Chi-restraints excluded: chain D residue 723 LYS Chi-restraints excluded: chain D residue 757 GLU Chi-restraints excluded: chain E residue 324 ASN Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain E residue 337 ASN Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 462 MET Chi-restraints excluded: chain E residue 463 ASN Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain E residue 546 ASN Chi-restraints excluded: chain E residue 561 PHE Chi-restraints excluded: chain E residue 582 VAL Chi-restraints excluded: chain E residue 592 ILE Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 650 LEU Chi-restraints excluded: chain E residue 691 GLU Chi-restraints excluded: chain E residue 702 ILE Chi-restraints excluded: chain F residue 354 SER 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 525 VAL 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 625 ARG 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 Chi-restraints excluded: chain F residue 707 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 247 optimal weight: 6.9990 chunk 251 optimal weight: 9.9990 chunk 211 optimal weight: 10.0000 chunk 101 optimal weight: 3.9990 chunk 270 optimal weight: 30.0000 chunk 125 optimal weight: 4.9990 chunk 143 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 106 optimal weight: 8.9990 chunk 121 optimal weight: 9.9990 chunk 7 optimal weight: 0.5980 overall best weight: 2.8586 ------------------------------------------------------------------------------- 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** ** B 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 661 ASN ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 324 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.251311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.225178 restraints weight = 25145.896| |-----------------------------------------------------------------------------| r_work (start): 0.4439 rms_B_bonded: 1.35 r_work: 0.4060 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3899 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 22841 Z= 0.211 Angle : 0.593 10.004 30892 Z= 0.308 Chirality : 0.045 0.231 3472 Planarity : 0.004 0.052 3940 Dihedral : 7.873 166.270 3090 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 5.64 % Allowed : 27.09 % Favored : 67.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.16), residues: 2766 helix: 0.46 (0.17), residues: 1039 sheet: -0.72 (0.28), residues: 364 loop : -0.95 (0.16), residues: 1363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 350 HIS 0.006 0.001 HIS D 680 PHE 0.018 0.002 PHE E 501 TYR 0.016 0.001 TYR A 699 ARG 0.004 0.000 ARG E 387 Details of bonding type rmsd hydrogen bonds : bond 0.04819 ( 788) hydrogen bonds : angle 5.00541 ( 2244) covalent geometry : bond 0.00534 (22841) covalent geometry : angle 0.59276 (30892) *********************** 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 354 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 214 time to evaluate : 2.486 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: 0.5645 (m) cc_final: 0.5352 (m) REVERT: A 684 MET cc_start: 0.8091 (tmt) cc_final: 0.7503 (tmt) REVERT: B 351 ILE cc_start: 0.8460 (OUTLIER) cc_final: 0.7984 (mt) REVERT: B 481 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.7914 (tt) REVERT: B 554 PHE cc_start: 0.8995 (OUTLIER) cc_final: 0.7754 (t80) REVERT: B 583 ILE cc_start: 0.7890 (OUTLIER) cc_final: 0.7458 (mp) REVERT: C 361 GLU cc_start: 0.7029 (OUTLIER) cc_final: 0.6637 (pt0) REVERT: C 426 MET cc_start: 0.7665 (OUTLIER) cc_final: 0.7429 (ttm) REVERT: C 736 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.7306 (tt) REVERT: D 475 ASN cc_start: 0.7115 (t0) cc_final: 0.6901 (t0) REVERT: E 339 VAL cc_start: 0.8834 (OUTLIER) cc_final: 0.8596 (t) REVERT: E 458 MET cc_start: 0.4616 (tmm) cc_final: 0.3388 (tmm) REVERT: E 462 MET cc_start: 0.5637 (OUTLIER) cc_final: 0.5378 (pmt) REVERT: E 548 HIS cc_start: 0.6383 (OUTLIER) cc_final: 0.5176 (t-170) REVERT: E 561 PHE cc_start: 0.3153 (OUTLIER) cc_final: 0.1725 (m-80) REVERT: E 592 ILE cc_start: 0.3903 (OUTLIER) cc_final: 0.3675 (tt) REVERT: E 610 PHE cc_start: 0.3601 (OUTLIER) cc_final: 0.3205 (m-80) REVERT: E 650 LEU cc_start: 0.1673 (OUTLIER) cc_final: 0.0857 (tt) REVERT: E 702 ILE cc_start: 0.5416 (OUTLIER) cc_final: 0.5109 (tp) REVERT: F 554 PHE cc_start: 0.7502 (OUTLIER) cc_final: 0.5937 (m-80) REVERT: F 656 ASP cc_start: 0.7040 (OUTLIER) cc_final: 0.6810 (t0) REVERT: F 660 GLN cc_start: 0.7702 (OUTLIER) cc_final: 0.7468 (mp10) REVERT: F 699 TYR cc_start: 0.7101 (OUTLIER) cc_final: 0.6752 (m-80) REVERT: F 710 SER cc_start: 0.3449 (OUTLIER) cc_final: 0.2890 (m) outliers start: 140 outliers final: 92 residues processed: 327 average time/residue: 0.3245 time to fit residues: 167.4229 Evaluate side-chains 317 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 205 time to evaluate : 2.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 436 TYR Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 488 SER 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 645 TYR Chi-restraints excluded: chain A residue 723 LYS 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 419 VAL Chi-restraints excluded: chain B residue 426 MET 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 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 561 PHE Chi-restraints excluded: chain B residue 581 CYS Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 733 THR Chi-restraints excluded: chain C residue 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 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 486 LEU Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 575 LYS Chi-restraints excluded: chain C residue 581 CYS Chi-restraints excluded: chain C residue 583 ILE Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 656 ASP Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 699 TYR Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 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 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 D residue 723 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 339 VAL Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 436 TYR Chi-restraints excluded: chain E residue 462 MET Chi-restraints excluded: chain E residue 463 ASN Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain E residue 546 ASN Chi-restraints excluded: chain E residue 548 HIS Chi-restraints excluded: chain E residue 561 PHE Chi-restraints excluded: chain E residue 582 VAL Chi-restraints excluded: chain E residue 592 ILE Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 610 PHE 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 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 494 THR Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 525 VAL Chi-restraints excluded: chain F residue 547 MET Chi-restraints excluded: chain F residue 554 PHE Chi-restraints excluded: chain F residue 578 THR Chi-restraints excluded: chain F residue 581 CYS Chi-restraints excluded: chain F residue 625 ARG 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 660 GLN Chi-restraints excluded: chain F residue 680 HIS Chi-restraints excluded: chain F residue 699 TYR Chi-restraints excluded: chain F residue 710 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 213 optimal weight: 7.9990 chunk 148 optimal weight: 7.9990 chunk 70 optimal weight: 9.9990 chunk 249 optimal weight: 4.9990 chunk 212 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 142 optimal weight: 0.8980 chunk 234 optimal weight: 0.6980 chunk 188 optimal weight: 0.9980 chunk 79 optimal weight: 8.9990 chunk 71 optimal weight: 7.9990 overall best weight: 2.7184 ------------------------------------------------------------------------------- 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** B 469 GLN ** B 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 ASN C 740 GLN ** D 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 662 ASN ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 324 ASN ** F 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.251608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.214265 restraints weight = 25339.692| |-----------------------------------------------------------------------------| r_work (start): 0.4335 rms_B_bonded: 2.43 r_work: 0.4091 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.4052 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.4052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.1924 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 : 0.586 9.174 30892 Z= 0.305 Chirality : 0.044 0.219 3472 Planarity : 0.004 0.050 3940 Dihedral : 7.776 167.003 3087 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 5.56 % Allowed : 27.29 % Favored : 67.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.16), residues: 2766 helix: 0.41 (0.16), residues: 1044 sheet: -0.73 (0.29), residues: 360 loop : -0.97 (0.16), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 350 HIS 0.006 0.001 HIS D 680 PHE 0.039 0.002 PHE E 501 TYR 0.014 0.001 TYR C 482 ARG 0.004 0.000 ARG E 387 Details of bonding type rmsd hydrogen bonds : bond 0.04601 ( 788) hydrogen bonds : angle 4.96758 ( 2244) covalent geometry : bond 0.00513 (22841) covalent geometry : angle 0.58593 (30892) *********************** 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 357 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 219 time to evaluate : 2.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 581 CYS cc_start: 0.5011 (m) cc_final: 0.4793 (m) REVERT: A 684 MET cc_start: 0.7969 (tmt) cc_final: 0.7379 (tmt) REVERT: B 351 ILE cc_start: 0.8511 (OUTLIER) cc_final: 0.8003 (mt) REVERT: B 481 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.7952 (tt) REVERT: B 554 PHE cc_start: 0.8968 (OUTLIER) cc_final: 0.7751 (t80) REVERT: B 583 ILE cc_start: 0.7847 (OUTLIER) cc_final: 0.7408 (mp) REVERT: C 426 MET cc_start: 0.7465 (OUTLIER) cc_final: 0.7255 (ttm) REVERT: C 483 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.6207 (pt0) REVERT: C 692 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6690 (mp0) REVERT: E 339 VAL cc_start: 0.8971 (OUTLIER) cc_final: 0.8722 (t) REVERT: E 458 MET cc_start: 0.4232 (tmm) cc_final: 0.3085 (tmm) REVERT: E 548 HIS cc_start: 0.6167 (OUTLIER) cc_final: 0.4942 (t-170) REVERT: E 561 PHE cc_start: 0.3015 (OUTLIER) cc_final: 0.1936 (m-10) REVERT: E 592 ILE cc_start: 0.3580 (OUTLIER) cc_final: 0.3366 (pt) REVERT: E 610 PHE cc_start: 0.3257 (OUTLIER) cc_final: 0.2926 (m-80) REVERT: E 650 LEU cc_start: 0.1718 (OUTLIER) cc_final: 0.0819 (tt) REVERT: E 702 ILE cc_start: 0.5328 (OUTLIER) cc_final: 0.5048 (tp) REVERT: F 554 PHE cc_start: 0.7462 (OUTLIER) cc_final: 0.5881 (m-80) REVERT: F 656 ASP cc_start: 0.6701 (OUTLIER) cc_final: 0.6498 (t0) REVERT: F 660 GLN cc_start: 0.7466 (OUTLIER) cc_final: 0.7252 (mp10) REVERT: F 699 TYR cc_start: 0.6866 (OUTLIER) cc_final: 0.6633 (m-80) outliers start: 138 outliers final: 97 residues processed: 327 average time/residue: 0.4554 time to fit residues: 234.6715 Evaluate side-chains 327 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 212 time to evaluate : 2.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 436 TYR Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain A residue 501 PHE 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 645 TYR Chi-restraints excluded: chain A residue 723 LYS 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 419 VAL Chi-restraints excluded: chain B residue 426 MET 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 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 561 PHE Chi-restraints excluded: chain B residue 581 CYS Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 733 THR Chi-restraints excluded: chain C residue 334 LEU 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 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 581 CYS Chi-restraints excluded: chain C residue 583 ILE Chi-restraints excluded: chain C residue 656 ASP Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 689 THR Chi-restraints excluded: chain C residue 692 GLU Chi-restraints excluded: chain C residue 699 TYR Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 324 ASN Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 499 THR 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 D residue 723 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 339 VAL Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 390 LYS Chi-restraints excluded: chain E residue 436 TYR Chi-restraints excluded: chain E residue 463 ASN Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain E residue 546 ASN Chi-restraints excluded: chain E residue 548 HIS Chi-restraints excluded: chain E residue 561 PHE Chi-restraints excluded: chain E residue 582 VAL Chi-restraints excluded: chain E residue 592 ILE Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 610 PHE 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 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 494 THR Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 525 VAL Chi-restraints excluded: chain F residue 547 MET Chi-restraints excluded: chain F residue 554 PHE Chi-restraints excluded: chain F residue 578 THR Chi-restraints excluded: chain F residue 581 CYS Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 656 ASP Chi-restraints excluded: chain F residue 659 ILE Chi-restraints excluded: chain F residue 660 GLN Chi-restraints excluded: chain F residue 680 HIS Chi-restraints excluded: chain F residue 695 ASP Chi-restraints excluded: chain F residue 699 TYR Chi-restraints excluded: chain F residue 700 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 160 optimal weight: 0.0020 chunk 22 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 236 optimal weight: 0.5980 chunk 188 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 143 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 228 optimal weight: 9.9990 chunk 18 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- 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** ** B 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN ** D 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 661 ASN ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 324 ASN F 475 ASN ** F 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.254456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.230131 restraints weight = 25357.413| |-----------------------------------------------------------------------------| r_work (start): 0.4483 rms_B_bonded: 1.31 r_work: 0.4081 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3864 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 22841 Z= 0.103 Angle : 0.525 14.374 30892 Z= 0.273 Chirality : 0.041 0.195 3472 Planarity : 0.004 0.047 3940 Dihedral : 7.425 166.704 3087 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.70 % Allowed : 28.99 % Favored : 67.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.16), residues: 2766 helix: 0.69 (0.17), residues: 1053 sheet: -0.65 (0.29), residues: 358 loop : -0.81 (0.16), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 675 HIS 0.006 0.000 HIS D 680 PHE 0.037 0.001 PHE E 501 TYR 0.013 0.001 TYR C 679 ARG 0.004 0.000 ARG F 514 Details of bonding type rmsd hydrogen bonds : bond 0.02959 ( 788) hydrogen bonds : angle 4.62446 ( 2244) covalent geometry : bond 0.00241 (22841) covalent geometry : angle 0.52467 (30892) *********************** 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 317 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 225 time to evaluate : 3.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 780 GLU cc_start: 0.6454 (OUTLIER) cc_final: 0.5973 (mt-10) REVERT: B 481 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.7833 (tt) REVERT: B 554 PHE cc_start: 0.9019 (OUTLIER) cc_final: 0.7782 (t80) REVERT: B 583 ILE cc_start: 0.7804 (OUTLIER) cc_final: 0.7389 (mp) REVERT: C 483 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.6464 (pt0) REVERT: E 548 HIS cc_start: 0.6490 (OUTLIER) cc_final: 0.5319 (t-170) REVERT: E 561 PHE cc_start: 0.3060 (OUTLIER) cc_final: 0.1827 (m-10) REVERT: E 592 ILE cc_start: 0.4137 (OUTLIER) cc_final: 0.3886 (tt) REVERT: E 650 LEU cc_start: 0.1672 (OUTLIER) cc_final: 0.0821 (tt) REVERT: E 702 ILE cc_start: 0.5483 (OUTLIER) cc_final: 0.5042 (tp) REVERT: F 547 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.7784 (ttm) REVERT: F 554 PHE cc_start: 0.7565 (OUTLIER) cc_final: 0.5877 (m-80) REVERT: F 656 ASP cc_start: 0.7185 (OUTLIER) cc_final: 0.6933 (t0) REVERT: F 660 GLN cc_start: 0.7846 (OUTLIER) cc_final: 0.7621 (mp10) outliers start: 92 outliers final: 59 residues processed: 296 average time/residue: 0.4681 time to fit residues: 221.4343 Evaluate side-chains 281 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 208 time to evaluate : 3.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 561 PHE Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 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 426 MET Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 581 CYS Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 733 THR Chi-restraints excluded: chain C residue 334 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 656 ASP 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 512 THR 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 337 ASN 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 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 650 LEU Chi-restraints excluded: chain E residue 702 ILE Chi-restraints excluded: chain F residue 324 ASN Chi-restraints excluded: chain F residue 356 LYS Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 447 ASP Chi-restraints excluded: chain F residue 471 LEU Chi-restraints excluded: chain F residue 475 ASN Chi-restraints excluded: chain F residue 483 GLU Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 525 VAL Chi-restraints excluded: chain F residue 547 MET Chi-restraints excluded: chain F residue 554 PHE Chi-restraints excluded: chain F residue 656 ASP Chi-restraints excluded: chain F residue 659 ILE Chi-restraints excluded: chain F residue 660 GLN Chi-restraints excluded: chain F residue 680 HIS Chi-restraints excluded: chain F residue 695 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 42 optimal weight: 40.0000 chunk 109 optimal weight: 10.0000 chunk 135 optimal weight: 9.9990 chunk 123 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 171 optimal weight: 6.9990 chunk 241 optimal weight: 5.9990 chunk 98 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 226 optimal weight: 1.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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** B 324 ASN B 529 GLN ** D 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 324 ASN F 475 ASN ** F 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 546 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.252071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.219671 restraints weight = 25241.404| |-----------------------------------------------------------------------------| r_work (start): 0.4384 rms_B_bonded: 1.72 r_work: 0.4021 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3749 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 22841 Z= 0.192 Angle : 0.588 8.902 30892 Z= 0.306 Chirality : 0.045 0.182 3472 Planarity : 0.004 0.046 3940 Dihedral : 7.530 167.098 3079 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.99 % Allowed : 28.54 % Favored : 67.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.16), residues: 2766 helix: 0.54 (0.17), residues: 1051 sheet: -0.75 (0.29), residues: 366 loop : -0.86 (0.17), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 675 HIS 0.005 0.001 HIS D 680 PHE 0.036 0.002 PHE E 501 TYR 0.019 0.001 TYR D 645 ARG 0.004 0.000 ARG F 514 Details of bonding type rmsd hydrogen bonds : bond 0.04607 ( 788) hydrogen bonds : angle 4.89569 ( 2244) covalent geometry : bond 0.00485 (22841) covalent geometry : angle 0.58798 (30892) *********************** 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 311 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 212 time to evaluate : 2.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 382 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8039 (tt0) REVERT: B 481 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7819 (tt) REVERT: B 554 PHE cc_start: 0.9018 (OUTLIER) cc_final: 0.7814 (t80) REVERT: B 583 ILE cc_start: 0.7855 (OUTLIER) cc_final: 0.7445 (mp) REVERT: C 426 MET cc_start: 0.7745 (OUTLIER) cc_final: 0.7501 (ttm) REVERT: C 483 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.6765 (pm20) REVERT: E 339 VAL cc_start: 0.9070 (OUTLIER) cc_final: 0.8799 (t) REVERT: E 548 HIS cc_start: 0.6720 (OUTLIER) cc_final: 0.5521 (t-170) REVERT: E 561 PHE cc_start: 0.3120 (OUTLIER) cc_final: 0.1795 (m-80) REVERT: E 592 ILE cc_start: 0.4372 (OUTLIER) cc_final: 0.4040 (pt) REVERT: E 650 LEU cc_start: 0.1723 (OUTLIER) cc_final: 0.0881 (tt) REVERT: F 547 MET cc_start: 0.8191 (OUTLIER) cc_final: 0.7874 (ttm) REVERT: F 554 PHE cc_start: 0.7578 (OUTLIER) cc_final: 0.5908 (m-80) REVERT: F 656 ASP cc_start: 0.7304 (OUTLIER) cc_final: 0.6960 (t0) REVERT: F 660 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.7520 (mp10) REVERT: F 710 SER cc_start: 0.3411 (OUTLIER) cc_final: 0.2974 (m) outliers start: 99 outliers final: 72 residues processed: 291 average time/residue: 0.3281 time to fit residues: 150.7114 Evaluate side-chains 298 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 210 time to evaluate : 2.501 ------------------------------------------------------------------------------- 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 488 SER Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 561 PHE Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 636 ARG Chi-restraints excluded: chain A residue 645 TYR Chi-restraints excluded: chain A residue 723 LYS Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 426 MET 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 499 THR Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 529 GLN Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 581 CYS Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 702 ILE Chi-restraints excluded: chain B residue 733 THR Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 483 GLU Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 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 512 THR 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 D residue 723 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 339 VAL Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 419 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 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 650 LEU Chi-restraints excluded: chain F residue 324 ASN Chi-restraints excluded: chain F residue 356 LYS Chi-restraints excluded: chain F residue 402 ASP Chi-restraints excluded: chain F residue 447 ASP Chi-restraints excluded: chain F residue 471 LEU Chi-restraints excluded: chain F residue 483 GLU Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 525 VAL Chi-restraints excluded: chain F residue 547 MET Chi-restraints excluded: chain F residue 554 PHE 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 660 GLN Chi-restraints excluded: chain F residue 680 HIS Chi-restraints excluded: chain F residue 695 ASP Chi-restraints excluded: chain F residue 700 LEU Chi-restraints excluded: chain F residue 710 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 87 optimal weight: 0.0470 chunk 268 optimal weight: 40.0000 chunk 194 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 212 optimal weight: 9.9990 chunk 9 optimal weight: 0.9990 chunk 208 optimal weight: 9.9990 chunk 219 optimal weight: 8.9990 chunk 214 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 160 optimal weight: 6.9990 overall best weight: 2.4086 ------------------------------------------------------------------------------- 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** B 529 GLN C 740 GLN ** D 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 324 ASN ** F 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 546 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.251945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.219535 restraints weight = 25383.597| |-----------------------------------------------------------------------------| r_work (start): 0.4382 rms_B_bonded: 1.80 r_work: 0.4026 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3865 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 22841 Z= 0.185 Angle : 0.583 9.013 30892 Z= 0.303 Chirality : 0.044 0.182 3472 Planarity : 0.004 0.045 3940 Dihedral : 7.546 167.394 3079 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.70 % Allowed : 28.74 % Favored : 67.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.16), residues: 2766 helix: 0.50 (0.17), residues: 1048 sheet: -0.74 (0.29), residues: 356 loop : -0.89 (0.16), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 675 HIS 0.005 0.001 HIS D 680 PHE 0.034 0.001 PHE E 501 TYR 0.022 0.001 TYR C 664 ARG 0.004 0.000 ARG F 514 Details of bonding type rmsd hydrogen bonds : bond 0.04440 ( 788) hydrogen bonds : angle 4.87397 ( 2244) covalent geometry : bond 0.00466 (22841) covalent geometry : angle 0.58321 (30892) ********************** 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 305 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 213 time to evaluate : 2.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 618 MET cc_start: 0.7724 (ptp) cc_final: 0.7518 (ptp) REVERT: B 481 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.7912 (tt) REVERT: B 554 PHE cc_start: 0.8998 (OUTLIER) cc_final: 0.7843 (t80) REVERT: B 583 ILE cc_start: 0.7871 (OUTLIER) cc_final: 0.7463 (mp) REVERT: C 361 GLU cc_start: 0.7071 (OUTLIER) cc_final: 0.6729 (pt0) REVERT: D 361 GLU cc_start: 0.5415 (tm-30) cc_final: 0.4773 (tt0) REVERT: D 757 GLU cc_start: 0.4968 (OUTLIER) cc_final: 0.4120 (tp30) REVERT: E 339 VAL cc_start: 0.8898 (OUTLIER) cc_final: 0.8625 (t) REVERT: E 459 GLU cc_start: 0.5953 (mm-30) cc_final: 0.5712 (mm-30) REVERT: E 548 HIS cc_start: 0.6538 (OUTLIER) cc_final: 0.5324 (t-170) REVERT: E 561 PHE cc_start: 0.3151 (OUTLIER) cc_final: 0.1897 (m-80) REVERT: E 592 ILE cc_start: 0.4172 (OUTLIER) cc_final: 0.3893 (pt) REVERT: E 650 LEU cc_start: 0.1810 (OUTLIER) cc_final: 0.0927 (tt) REVERT: F 554 PHE cc_start: 0.7608 (OUTLIER) cc_final: 0.5928 (m-80) REVERT: F 656 ASP cc_start: 0.7099 (OUTLIER) cc_final: 0.6805 (t0) REVERT: F 660 GLN cc_start: 0.7768 (OUTLIER) cc_final: 0.7501 (mp10) outliers start: 92 outliers final: 75 residues processed: 285 average time/residue: 0.3239 time to fit residues: 148.3050 Evaluate side-chains 299 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 211 time to evaluate : 2.511 ------------------------------------------------------------------------------- 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 488 SER 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 609 VAL 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 426 MET 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 529 GLN Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 581 CYS Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 702 ILE Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 733 THR Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 483 GLU Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 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 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 D residue 723 LYS Chi-restraints excluded: chain D residue 757 GLU Chi-restraints excluded: chain E residue 324 ASN Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain E residue 337 ASN Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 419 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 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 650 LEU Chi-restraints excluded: chain F residue 324 ASN Chi-restraints excluded: chain F residue 356 LYS Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 402 ASP Chi-restraints excluded: chain F residue 447 ASP Chi-restraints excluded: chain F residue 471 LEU Chi-restraints excluded: chain F residue 483 GLU Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 525 VAL Chi-restraints excluded: chain F residue 547 MET Chi-restraints excluded: chain F residue 554 PHE Chi-restraints excluded: chain F residue 651 LEU 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 700 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 104 optimal weight: 1.9990 chunk 218 optimal weight: 10.0000 chunk 207 optimal weight: 10.0000 chunk 222 optimal weight: 50.0000 chunk 50 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 11 optimal weight: 0.0670 chunk 176 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 154 optimal weight: 9.9990 chunk 168 optimal weight: 5.9990 overall best weight: 1.7522 ------------------------------------------------------------------------------- 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** B 529 GLN ** D 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 324 ASN ** F 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 546 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.252767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.220235 restraints weight = 25329.809| |-----------------------------------------------------------------------------| r_work (start): 0.4389 rms_B_bonded: 1.86 r_work: 0.4024 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3885 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.2260 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= 0.148 Angle : 0.560 9.761 30892 Z= 0.292 Chirality : 0.043 0.178 3472 Planarity : 0.004 0.044 3940 Dihedral : 7.469 167.613 3079 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.74 % Allowed : 28.78 % Favored : 67.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.16), residues: 2766 helix: 0.57 (0.17), residues: 1051 sheet: -0.67 (0.30), residues: 352 loop : -0.86 (0.16), residues: 1363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 675 HIS 0.004 0.001 HIS D 680 PHE 0.032 0.001 PHE E 501 TYR 0.022 0.001 TYR E 670 ARG 0.004 0.000 ARG F 514 Details of bonding type rmsd hydrogen bonds : bond 0.03950 ( 788) hydrogen bonds : angle 4.78255 ( 2244) covalent geometry : bond 0.00371 (22841) covalent geometry : angle 0.56038 (30892) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12670.76 seconds wall clock time: 222 minutes 2.02 seconds (13322.02 seconds total)