Starting phenix.real_space_refine on Sun May 3 09:39:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mzo_48763/05_2026/9mzo_48763.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mzo_48763/05_2026/9mzo_48763.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mzo_48763/05_2026/9mzo_48763.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mzo_48763/05_2026/9mzo_48763.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mzo_48763/05_2026/9mzo_48763.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mzo_48763/05_2026/9mzo_48763.map" } resolution = 3.86 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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: 4 Type Number sf(0) Gaussians S 71 5.16 5 C 7697 2.51 5 N 1895 2.21 5 O 2228 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11891 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2915 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 12, 'TRANS': 357} Chain breaks: 1 Chain: "B" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2938 Classifications: {'peptide': 373} Link IDs: {'PTRANS': 13, 'TRANS': 359} Chain breaks: 1 Chain: "C" Number of atoms: 2939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2939 Classifications: {'peptide': 373} Link IDs: {'PTRANS': 13, 'TRANS': 359} Chain breaks: 1 Chain: "D" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2933 Classifications: {'peptide': 372} Link IDs: {'PTRANS': 13, 'TRANS': 358} Chain breaks: 1 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'NAG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'NAG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'NAG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.31, per 1000 atoms: 0.28 Number of scatterers: 11891 At special positions: 0 Unit cell: (127.2, 90.1, 124.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 71 16.00 O 2228 8.00 N 1895 7.00 C 7697 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 676 " - pdb=" SG CYS B 802 " distance=2.03 Simple disulfide: pdb=" SG CYS A 750 " - pdb=" SG CYS A 804 " distance=2.03 Simple disulfide: pdb=" SG CYS B 750 " - pdb=" SG CYS B 804 " distance=2.03 Simple disulfide: pdb=" SG CYS C 676 " - pdb=" SG CYS D 802 " distance=2.03 Simple disulfide: pdb=" SG CYS C 750 " - pdb=" SG CYS C 804 " distance=2.03 Simple disulfide: pdb=" SG CYS D 750 " - pdb=" SG CYS D 804 " distance=2.03 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 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1001 " - " ASN A 546 " " NAG A1002 " - " ASN A 749 " " NAG B1001 " - " ASN B 751 " " NAG C1001 " - " ASN C 751 " " NAG D1001 " - " ASN D 751 " " NAG E 1 " - " ASN B 546 " " NAG F 1 " - " ASN D 546 " Time building additional restraints: 1.00 Conformation dependent library (CDL) restraints added in 512.5 milliseconds 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2744 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 17 sheets defined 53.4% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 461 through 474 Processing helix chain 'A' and resid 499 through 507 removed outlier: 3.537A pdb=" N ASP A 507 " --> pdb=" O ARG A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 527 removed outlier: 4.202A pdb=" N VAL A 526 " --> pdb=" O VAL A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 584 removed outlier: 3.691A pdb=" N PHE A 584 " --> pdb=" O VAL A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 665 removed outlier: 4.027A pdb=" N GLY A 638 " --> pdb=" O ARG A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 677 removed outlier: 3.685A pdb=" N LEU A 674 " --> pdb=" O SER A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 697 Processing helix chain 'A' and resid 699 through 711 Processing helix chain 'A' and resid 720 through 731 removed outlier: 3.547A pdb=" N GLN A 726 " --> pdb=" O GLU A 722 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER A 731 " --> pdb=" O ARG A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 749 removed outlier: 3.864A pdb=" N PHE A 744 " --> pdb=" O THR A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 788 removed outlier: 4.148A pdb=" N LYS A 777 " --> pdb=" O PRO A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 798 removed outlier: 3.837A pdb=" N MET A 793 " --> pdb=" O GLY A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 846 removed outlier: 5.821A pdb=" N GLY A 822 " --> pdb=" O GLN A 818 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE A 823 " --> pdb=" O ASN A 819 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE A 824 " --> pdb=" O ILE A 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 457 No H-bonds generated for 'chain 'B' and resid 455 through 457' Processing helix chain 'B' and resid 461 through 474 Processing helix chain 'B' and resid 500 through 506 Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 553 through 557 removed outlier: 3.586A pdb=" N ASN B 557 " --> pdb=" O SER B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 584 Processing helix chain 'B' and resid 630 through 661 removed outlier: 3.984A pdb=" N VAL B 636 " --> pdb=" O SER B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 677 removed outlier: 3.651A pdb=" N GLN B 677 " --> pdb=" O ASP B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 697 removed outlier: 4.010A pdb=" N THR B 692 " --> pdb=" O GLY B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 712 removed outlier: 3.645A pdb=" N LYS B 704 " --> pdb=" O SER B 700 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG B 712 " --> pdb=" O PHE B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 731 removed outlier: 3.540A pdb=" N GLY B 724 " --> pdb=" O SER B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 749 Processing helix chain 'B' and resid 773 through 788 removed outlier: 3.786A pdb=" N LYS B 777 " --> pdb=" O PRO B 773 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU B 788 " --> pdb=" O GLN B 784 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 799 Processing helix chain 'B' and resid 816 through 821 removed outlier: 4.007A pdb=" N GLY B 821 " --> pdb=" O VAL B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 844 Processing helix chain 'C' and resid 454 through 458 removed outlier: 3.698A pdb=" N ARG C 458 " --> pdb=" O GLY C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 474 removed outlier: 3.534A pdb=" N THR C 472 " --> pdb=" O ARG C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 507 Processing helix chain 'C' and resid 520 through 525 Processing helix chain 'C' and resid 560 through 584 removed outlier: 3.701A pdb=" N PHE C 584 " --> pdb=" O VAL C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 665 Processing helix chain 'C' and resid 670 through 677 Processing helix chain 'C' and resid 688 through 696 Processing helix chain 'C' and resid 699 through 712 removed outlier: 3.915A pdb=" N ARG C 712 " --> pdb=" O PHE C 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 720 through 731 removed outlier: 4.568A pdb=" N GLN C 726 " --> pdb=" O GLU C 722 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG C 727 " --> pdb=" O GLU C 723 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 749 removed outlier: 3.785A pdb=" N PHE C 744 " --> pdb=" O THR C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 774 through 789 Processing helix chain 'C' and resid 790 through 800 removed outlier: 3.670A pdb=" N MET C 794 " --> pdb=" O LYS C 790 " (cutoff:3.500A) Processing helix chain 'C' and resid 820 through 844 removed outlier: 4.032A pdb=" N PHE C 824 " --> pdb=" O ILE C 820 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 459 removed outlier: 3.567A pdb=" N PHE D 459 " --> pdb=" O ASN D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 474 Processing helix chain 'D' and resid 499 through 506 removed outlier: 3.770A pdb=" N ARG D 503 " --> pdb=" O ASN D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 584 removed outlier: 3.539A pdb=" N TRP D 564 " --> pdb=" O SER D 560 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE D 584 " --> pdb=" O VAL D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 632 through 661 removed outlier: 3.830A pdb=" N VAL D 636 " --> pdb=" O SER D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 671 through 677 removed outlier: 4.199A pdb=" N ALA D 675 " --> pdb=" O ALA D 671 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN D 677 " --> pdb=" O ASP D 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 697 removed outlier: 3.896A pdb=" N THR D 692 " --> pdb=" O GLY D 688 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 712 removed outlier: 3.540A pdb=" N LYS D 704 " --> pdb=" O SER D 700 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG D 712 " --> pdb=" O PHE D 708 " (cutoff:3.500A) Processing helix chain 'D' and resid 712 through 717 removed outlier: 3.717A pdb=" N VAL D 716 " --> pdb=" O ARG D 712 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 731 removed outlier: 3.646A pdb=" N SER D 731 " --> pdb=" O ARG D 727 " (cutoff:3.500A) Processing helix chain 'D' and resid 739 through 749 Processing helix chain 'D' and resid 775 through 788 removed outlier: 3.999A pdb=" N THR D 779 " --> pdb=" O ARG D 775 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLU D 788 " --> pdb=" O GLN D 784 " (cutoff:3.500A) Processing helix chain 'D' and resid 791 through 793 No H-bonds generated for 'chain 'D' and resid 791 through 793' Processing helix chain 'D' and resid 794 through 799 removed outlier: 3.677A pdb=" N TRP D 799 " --> pdb=" O LYS D 795 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 845 removed outlier: 3.681A pdb=" N ILE D 820 " --> pdb=" O GLY D 816 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N GLY D 822 " --> pdb=" O GLN D 818 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE D 823 " --> pdb=" O ASN D 819 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE D 824 " --> pdb=" O ILE D 820 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 436 through 437 removed outlier: 3.617A pdb=" N THR A 437 " --> pdb=" O ARG A 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 445 through 446 Processing sheet with id=AA3, first strand: chain 'A' and resid 513 through 514 Processing sheet with id=AA4, first strand: chain 'A' and resid 681 through 683 removed outlier: 6.610A pdb=" N GLU A 681 " --> pdb=" O ALA A 734 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N LEU A 736 " --> pdb=" O GLU A 681 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLY A 683 " --> pdb=" O LEU A 736 " (cutoff:3.500A) removed outlier: 9.152A pdb=" N GLU A 738 " --> pdb=" O GLY A 683 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N TYR A 733 " --> pdb=" O ARG A 543 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ARG A 543 " --> pdb=" O TYR A 733 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ILE A 540 " --> pdb=" O ILE A 755 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE A 755 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N TYR A 542 " --> pdb=" O THR A 753 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N THR A 753 " --> pdb=" O TYR A 542 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 681 through 683 removed outlier: 6.610A pdb=" N GLU A 681 " --> pdb=" O ALA A 734 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N LEU A 736 " --> pdb=" O GLU A 681 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLY A 683 " --> pdb=" O LEU A 736 " (cutoff:3.500A) removed outlier: 9.152A pdb=" N GLU A 738 " --> pdb=" O GLY A 683 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N TYR A 733 " --> pdb=" O ARG A 543 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ARG A 543 " --> pdb=" O TYR A 733 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 433 through 435 Processing sheet with id=AA7, first strand: chain 'B' and resid 445 through 446 Processing sheet with id=AA8, first strand: chain 'B' and resid 528 through 529 removed outlier: 3.804A pdb=" N ASP B 528 " --> pdb=" O THR B 768 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR B 768 " --> pdb=" O ASP B 528 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 534 through 536 removed outlier: 3.972A pdb=" N MET B 534 " --> pdb=" O TYR B 764 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 682 through 683 removed outlier: 6.402A pdb=" N GLY B 683 " --> pdb=" O LEU B 736 " (cutoff:3.500A) removed outlier: 8.696A pdb=" N GLU B 738 " --> pdb=" O GLY B 683 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 433 through 437 removed outlier: 6.696A pdb=" N LEU C 433 " --> pdb=" O GLU C 479 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N ARG C 481 " --> pdb=" O LEU C 433 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL C 435 " --> pdb=" O ARG C 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 490 through 491 Processing sheet with id=AB4, first strand: chain 'C' and resid 513 through 514 Processing sheet with id=AB5, first strand: chain 'C' and resid 682 through 684 removed outlier: 7.044A pdb=" N GLY C 683 " --> pdb=" O LEU C 736 " (cutoff:3.500A) removed outlier: 9.182A pdb=" N GLU C 738 " --> pdb=" O GLY C 683 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N TYR C 542 " --> pdb=" O THR C 753 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N THR C 753 " --> pdb=" O TYR C 542 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 682 through 684 removed outlier: 7.044A pdb=" N GLY C 683 " --> pdb=" O LEU C 736 " (cutoff:3.500A) removed outlier: 9.182A pdb=" N GLU C 738 " --> pdb=" O GLY C 683 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 513 through 519 removed outlier: 4.246A pdb=" N ALA D 515 " --> pdb=" O GLY D 765 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N GLY D 765 " --> pdb=" O ALA D 515 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU D 517 " --> pdb=" O GLY D 763 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLY D 763 " --> pdb=" O LEU D 517 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 682 through 683 removed outlier: 6.292A pdb=" N GLY D 683 " --> pdb=" O LEU D 736 " (cutoff:3.500A) removed outlier: 8.798A pdb=" N GLU D 738 " --> pdb=" O GLY D 683 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ILE D 540 " --> pdb=" O ILE D 755 " (cutoff:3.500A) 573 hydrogen bonds defined for protein. 1686 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: 1.77 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3683 1.34 - 1.46: 2666 1.46 - 1.58: 5671 1.58 - 1.70: 0 1.70 - 1.82: 118 Bond restraints: 12138 Sorted by residual: bond pdb=" N MET A 664 " pdb=" CA MET A 664 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.33e-02 5.65e+03 5.73e+00 bond pdb=" N MET C 664 " pdb=" CA MET C 664 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.33e-02 5.65e+03 4.88e+00 bond pdb=" N THR A 660 " pdb=" CA THR A 660 " ideal model delta sigma weight residual 1.459 1.482 -0.023 1.23e-02 6.61e+03 3.45e+00 bond pdb=" N THR C 660 " pdb=" CA THR C 660 " ideal model delta sigma weight residual 1.459 1.481 -0.021 1.23e-02 6.61e+03 3.04e+00 bond pdb=" N THR B 652 " pdb=" CA THR B 652 " ideal model delta sigma weight residual 1.459 1.478 -0.019 1.19e-02 7.06e+03 2.54e+00 ... (remaining 12133 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 16151 2.01 - 4.02: 222 4.02 - 6.04: 35 6.04 - 8.05: 9 8.05 - 10.06: 5 Bond angle restraints: 16422 Sorted by residual: angle pdb=" C TYR B 651 " pdb=" N THR B 652 " pdb=" CA THR B 652 " ideal model delta sigma weight residual 120.44 114.27 6.17 1.30e+00 5.92e-01 2.25e+01 angle pdb=" N THR B 652 " pdb=" CA THR B 652 " pdb=" C THR B 652 " ideal model delta sigma weight residual 111.07 106.88 4.19 1.07e+00 8.73e-01 1.54e+01 angle pdb=" N ILE B 820 " pdb=" CA ILE B 820 " pdb=" C ILE B 820 " ideal model delta sigma weight residual 111.09 106.76 4.33 1.25e+00 6.40e-01 1.20e+01 angle pdb=" C TYR D 651 " pdb=" N THR D 652 " pdb=" CA THR D 652 " ideal model delta sigma weight residual 120.44 116.32 4.12 1.30e+00 5.92e-01 1.00e+01 angle pdb=" CA LEU B 569 " pdb=" CB LEU B 569 " pdb=" CG LEU B 569 " ideal model delta sigma weight residual 116.30 126.36 -10.06 3.50e+00 8.16e-02 8.26e+00 ... (remaining 16417 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 6299 17.94 - 35.88: 783 35.88 - 53.82: 193 53.82 - 71.76: 34 71.76 - 89.71: 17 Dihedral angle restraints: 7326 sinusoidal: 3038 harmonic: 4288 Sorted by residual: dihedral pdb=" CB CYS C 676 " pdb=" SG CYS C 676 " pdb=" SG CYS D 802 " pdb=" CB CYS D 802 " ideal model delta sinusoidal sigma weight residual 93.00 27.97 65.03 1 1.00e+01 1.00e-02 5.55e+01 dihedral pdb=" CB CYS D 750 " pdb=" SG CYS D 750 " pdb=" SG CYS D 804 " pdb=" CB CYS D 804 " ideal model delta sinusoidal sigma weight residual -86.00 -25.13 -60.87 1 1.00e+01 1.00e-02 4.93e+01 dihedral pdb=" CB CYS B 750 " pdb=" SG CYS B 750 " pdb=" SG CYS B 804 " pdb=" CB CYS B 804 " ideal model delta sinusoidal sigma weight residual 93.00 32.89 60.11 1 1.00e+01 1.00e-02 4.82e+01 ... (remaining 7323 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1789 0.087 - 0.173: 94 0.173 - 0.260: 2 0.260 - 0.347: 0 0.347 - 0.434: 1 Chirality restraints: 1886 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN D 546 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.70e+00 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.37 -0.03 2.00e-02 2.50e+03 2.36e+00 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.38 -0.02 2.00e-02 2.50e+03 1.35e+00 ... (remaining 1883 not shown) Planarity restraints: 2047 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 798 " -0.018 2.00e-02 2.50e+03 1.23e-02 3.81e+00 pdb=" CG TRP D 798 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP D 798 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP D 798 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 798 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 798 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 798 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 798 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 798 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP D 798 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 723 " 0.009 2.00e-02 2.50e+03 1.92e-02 3.67e+00 pdb=" CD GLU A 723 " -0.033 2.00e-02 2.50e+03 pdb=" OE1 GLU A 723 " 0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU A 723 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 555 " 0.012 2.00e-02 2.50e+03 1.27e-02 2.84e+00 pdb=" CG PHE B 555 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE B 555 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE B 555 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE B 555 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 555 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE B 555 " 0.001 2.00e-02 2.50e+03 ... (remaining 2044 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 4986 2.92 - 3.41: 12795 3.41 - 3.91: 19246 3.91 - 4.40: 21579 4.40 - 4.90: 34195 Nonbonded interactions: 92801 Sorted by model distance: nonbonded pdb=" OG1 THR B 652 " pdb=" OG1 THR C 652 " model vdw 2.421 3.040 nonbonded pdb=" OG1 THR B 652 " pdb=" N ALA B 653 " model vdw 2.522 3.120 nonbonded pdb=" N ASP C 562 " pdb=" OD1 ASP C 562 " model vdw 2.534 3.120 nonbonded pdb=" N ASN D 549 " pdb=" OD1 ASN D 549 " model vdw 2.556 3.120 nonbonded pdb=" O GLN B 784 " pdb=" OE1 GLN B 784 " model vdw 2.557 3.040 ... (remaining 92796 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' and (resid 432 through 844 or resid 1003)) selection = (chain 'B' and (resid 432 through 584 or resid 630 through 844 or resid 1002)) selection = (chain 'C' and (resid 432 through 584 or resid 630 through 844 or resid 1002)) selection = (chain 'D' and (resid 432 through 584 or resid 630 through 844 or resid 1002)) } ncs_group { reference = 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 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: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.210 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 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 : 0.002 0.036 12153 Z= 0.124 Angle : 0.652 19.589 16461 Z= 0.330 Chirality : 0.042 0.434 1886 Planarity : 0.003 0.036 2040 Dihedral : 16.754 89.705 4564 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.33 % Allowed : 22.11 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.22), residues: 1472 helix: 0.07 (0.18), residues: 735 sheet: -1.63 (0.56), residues: 92 loop : -1.64 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 663 TYR 0.021 0.001 TYR C 682 PHE 0.030 0.001 PHE B 555 TRP 0.033 0.001 TRP D 798 HIS 0.002 0.001 HIS D 792 Details of bonding type rmsd covalent geometry : bond 0.00249 (12138) covalent geometry : angle 0.62188 (16422) SS BOND : bond 0.00269 ( 6) SS BOND : angle 0.95655 ( 12) hydrogen bonds : bond 0.19570 ( 565) hydrogen bonds : angle 7.58790 ( 1686) link_BETA1-4 : bond 0.00138 ( 2) link_BETA1-4 : angle 1.72666 ( 6) link_NAG-ASN : bond 0.01024 ( 7) link_NAG-ASN : angle 5.45494 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 209 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 441 GLU cc_start: 0.8268 (mp0) cc_final: 0.7795 (mp0) REVERT: A 511 ASP cc_start: 0.7618 (t70) cc_final: 0.7369 (t0) REVERT: A 658 PHE cc_start: 0.8189 (t80) cc_final: 0.7952 (t80) REVERT: A 686 GLU cc_start: 0.8024 (tp30) cc_final: 0.7548 (tp30) REVERT: A 793 MET cc_start: 0.8351 (pmm) cc_final: 0.7698 (tmm) REVERT: B 544 LYS cc_start: 0.9073 (mmmt) cc_final: 0.8638 (mtpp) REVERT: B 709 MET cc_start: 0.9498 (mmm) cc_final: 0.9293 (mmm) REVERT: B 737 MET cc_start: 0.7471 (ppp) cc_final: 0.7207 (ppp) REVERT: B 793 MET cc_start: 0.8681 (tpp) cc_final: 0.8166 (ptp) REVERT: C 662 GLU cc_start: 0.8376 (mm-30) cc_final: 0.7886 (mp0) REVERT: C 737 MET cc_start: 0.8284 (ptm) cc_final: 0.7968 (ptm) REVERT: C 827 LEU cc_start: 0.8809 (tt) cc_final: 0.8441 (tp) REVERT: C 833 LEU cc_start: 0.9219 (mm) cc_final: 0.8850 (tt) REVERT: D 524 GLU cc_start: 0.7755 (tm-30) cc_final: 0.7394 (tm-30) REVERT: D 635 ILE cc_start: 0.9314 (mp) cc_final: 0.8979 (tp) outliers start: 17 outliers final: 13 residues processed: 216 average time/residue: 0.0886 time to fit residues: 29.7841 Evaluate side-chains 206 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 193 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 673 ASP Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 799 TRP Chi-restraints excluded: chain A residue 834 SER Chi-restraints excluded: chain B residue 701 THR Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 647 ILE Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain D residue 483 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.120420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.092015 restraints weight = 30467.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.095117 restraints weight = 17558.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.097126 restraints weight = 12766.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.098442 restraints weight = 10518.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.099110 restraints weight = 9313.298| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12153 Z= 0.163 Angle : 0.621 19.425 16461 Z= 0.311 Chirality : 0.042 0.457 1886 Planarity : 0.003 0.034 2040 Dihedral : 5.570 62.875 1817 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 3.67 % Allowed : 21.95 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.23), residues: 1472 helix: 0.99 (0.19), residues: 750 sheet: -1.69 (0.56), residues: 94 loop : -1.57 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 503 TYR 0.014 0.001 TYR B 764 PHE 0.017 0.001 PHE D 744 TRP 0.023 0.002 TRP D 798 HIS 0.002 0.000 HIS B 792 Details of bonding type rmsd covalent geometry : bond 0.00367 (12138) covalent geometry : angle 0.58978 (16422) SS BOND : bond 0.00373 ( 6) SS BOND : angle 0.89032 ( 12) hydrogen bonds : bond 0.03842 ( 565) hydrogen bonds : angle 4.83368 ( 1686) link_BETA1-4 : bond 0.00307 ( 2) link_BETA1-4 : angle 1.91168 ( 6) link_NAG-ASN : bond 0.00980 ( 7) link_NAG-ASN : angle 5.40741 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 198 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 441 GLU cc_start: 0.8464 (mp0) cc_final: 0.7975 (mp0) REVERT: A 487 LYS cc_start: 0.9259 (OUTLIER) cc_final: 0.8933 (pttt) REVERT: A 511 ASP cc_start: 0.7833 (t70) cc_final: 0.7482 (t0) REVERT: A 686 GLU cc_start: 0.8072 (tp30) cc_final: 0.7673 (tp30) REVERT: A 748 ARG cc_start: 0.8516 (mmp-170) cc_final: 0.8243 (mmp80) REVERT: A 793 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.7907 (tmm) REVERT: A 794 MET cc_start: 0.8447 (mtt) cc_final: 0.8222 (mtt) REVERT: A 818 GLN cc_start: 0.8489 (pm20) cc_final: 0.7682 (tt0) REVERT: B 544 LYS cc_start: 0.9247 (mmmt) cc_final: 0.8764 (mtpp) REVERT: B 686 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.6993 (pm20) REVERT: B 691 MET cc_start: 0.9234 (OUTLIER) cc_final: 0.8987 (ptt) REVERT: B 737 MET cc_start: 0.7885 (ppp) cc_final: 0.7399 (ppp) REVERT: B 784 GLN cc_start: 0.8799 (tp-100) cc_final: 0.8359 (tp-100) REVERT: B 793 MET cc_start: 0.8718 (tpp) cc_final: 0.8213 (ptp) REVERT: C 503 ARG cc_start: 0.8536 (tpt-90) cc_final: 0.7531 (mmm-85) REVERT: D 524 GLU cc_start: 0.7864 (tm-30) cc_final: 0.7530 (tm-30) REVERT: D 635 ILE cc_start: 0.9336 (mp) cc_final: 0.9061 (tp) REVERT: D 793 MET cc_start: 0.8264 (ptp) cc_final: 0.7846 (ptp) outliers start: 47 outliers final: 31 residues processed: 228 average time/residue: 0.0862 time to fit residues: 30.7420 Evaluate side-chains 218 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 183 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 487 LYS Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 745 VAL Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 799 TRP Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain B residue 691 MET Chi-restraints excluded: chain B residue 701 THR Chi-restraints excluded: chain B residue 745 VAL Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 647 ILE Chi-restraints excluded: chain C residue 677 GLN Chi-restraints excluded: chain C residue 691 MET Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 692 THR Chi-restraints excluded: chain D residue 827 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 72 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 56 optimal weight: 9.9990 chunk 143 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 114 optimal weight: 8.9990 chunk 106 optimal weight: 0.7980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.119621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.092498 restraints weight = 29539.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.095594 restraints weight = 16454.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.097602 restraints weight = 11688.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.098975 restraints weight = 9487.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.099686 restraints weight = 8281.225| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12153 Z= 0.144 Angle : 0.616 19.490 16461 Z= 0.303 Chirality : 0.042 0.467 1886 Planarity : 0.003 0.032 2040 Dihedral : 5.541 64.824 1812 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.83 % Allowed : 23.36 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.23), residues: 1472 helix: 1.19 (0.19), residues: 750 sheet: -1.61 (0.57), residues: 90 loop : -1.57 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 503 TYR 0.013 0.001 TYR C 462 PHE 0.011 0.001 PHE A 658 TRP 0.030 0.002 TRP A 798 HIS 0.002 0.000 HIS B 792 Details of bonding type rmsd covalent geometry : bond 0.00329 (12138) covalent geometry : angle 0.58435 (16422) SS BOND : bond 0.00304 ( 6) SS BOND : angle 0.97439 ( 12) hydrogen bonds : bond 0.03501 ( 565) hydrogen bonds : angle 4.61076 ( 1686) link_BETA1-4 : bond 0.00136 ( 2) link_BETA1-4 : angle 1.76333 ( 6) link_NAG-ASN : bond 0.01002 ( 7) link_NAG-ASN : angle 5.38065 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 197 time to evaluate : 0.525 Fit side-chains revert: symmetry clash REVERT: A 441 GLU cc_start: 0.8425 (mp0) cc_final: 0.7935 (mp0) REVERT: A 511 ASP cc_start: 0.7845 (t70) cc_final: 0.7551 (t0) REVERT: A 748 ARG cc_start: 0.8569 (mmp-170) cc_final: 0.8259 (mmp80) REVERT: A 793 MET cc_start: 0.8520 (OUTLIER) cc_final: 0.7924 (tmm) REVERT: A 794 MET cc_start: 0.8417 (mtt) cc_final: 0.8187 (mtt) REVERT: B 544 LYS cc_start: 0.9258 (mmmt) cc_final: 0.8764 (mtpp) REVERT: B 686 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7208 (pm20) REVERT: B 691 MET cc_start: 0.9314 (OUTLIER) cc_final: 0.8926 (ptt) REVERT: B 737 MET cc_start: 0.7831 (ppp) cc_final: 0.7352 (ppp) REVERT: B 776 ASP cc_start: 0.8275 (m-30) cc_final: 0.8026 (m-30) REVERT: B 784 GLN cc_start: 0.8776 (tp-100) cc_final: 0.8217 (tp-100) REVERT: B 793 MET cc_start: 0.8696 (tpp) cc_final: 0.8270 (ptp) REVERT: C 833 LEU cc_start: 0.9241 (mm) cc_final: 0.8753 (tt) REVERT: D 524 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7553 (tm-30) REVERT: D 564 TRP cc_start: 0.7786 (OUTLIER) cc_final: 0.7539 (m-10) REVERT: D 733 TYR cc_start: 0.7857 (t80) cc_final: 0.7504 (t80) outliers start: 49 outliers final: 32 residues processed: 227 average time/residue: 0.0891 time to fit residues: 31.6050 Evaluate side-chains 225 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 189 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 799 TRP Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain B residue 691 MET Chi-restraints excluded: chain B residue 701 THR Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 647 ILE Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 677 GLN Chi-restraints excluded: chain C residue 691 MET Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 776 ASP Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 540 ILE Chi-restraints excluded: chain D residue 564 TRP Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 692 THR Chi-restraints excluded: chain D residue 827 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 58 optimal weight: 9.9990 chunk 2 optimal weight: 0.9980 chunk 141 optimal weight: 0.8980 chunk 89 optimal weight: 9.9990 chunk 40 optimal weight: 8.9990 chunk 134 optimal weight: 8.9990 chunk 94 optimal weight: 7.9990 chunk 49 optimal weight: 7.9990 chunk 144 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.120104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.092066 restraints weight = 30012.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.095249 restraints weight = 16776.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.097303 restraints weight = 12004.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.098697 restraints weight = 9788.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.099615 restraints weight = 8598.120| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12153 Z= 0.134 Angle : 0.618 18.850 16461 Z= 0.301 Chirality : 0.043 0.461 1886 Planarity : 0.003 0.032 2040 Dihedral : 5.601 65.225 1812 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 4.84 % Allowed : 23.44 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.23), residues: 1472 helix: 1.22 (0.19), residues: 752 sheet: -1.70 (0.53), residues: 100 loop : -1.56 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 663 TYR 0.018 0.001 TYR C 462 PHE 0.009 0.001 PHE B 533 TRP 0.024 0.002 TRP D 798 HIS 0.003 0.001 HIS B 792 Details of bonding type rmsd covalent geometry : bond 0.00308 (12138) covalent geometry : angle 0.58639 (16422) SS BOND : bond 0.00334 ( 6) SS BOND : angle 1.44671 ( 12) hydrogen bonds : bond 0.03231 ( 565) hydrogen bonds : angle 4.47315 ( 1686) link_BETA1-4 : bond 0.00260 ( 2) link_BETA1-4 : angle 1.74280 ( 6) link_NAG-ASN : bond 0.01038 ( 7) link_NAG-ASN : angle 5.29269 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 207 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 442 PRO cc_start: 0.9311 (Cg_endo) cc_final: 0.8976 (Cg_exo) REVERT: A 505 LEU cc_start: 0.9111 (tp) cc_final: 0.8529 (tp) REVERT: A 511 ASP cc_start: 0.7836 (t70) cc_final: 0.7559 (t0) REVERT: A 748 ARG cc_start: 0.8562 (mmp-170) cc_final: 0.8254 (mmp80) REVERT: A 793 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.7892 (tmm) REVERT: A 794 MET cc_start: 0.8485 (mtt) cc_final: 0.8219 (mtt) REVERT: A 818 GLN cc_start: 0.8537 (pm20) cc_final: 0.7632 (tt0) REVERT: B 544 LYS cc_start: 0.9252 (mmmt) cc_final: 0.8737 (mtpp) REVERT: B 686 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7210 (pm20) REVERT: B 691 MET cc_start: 0.9300 (OUTLIER) cc_final: 0.8879 (ptt) REVERT: B 709 MET cc_start: 0.9467 (mmm) cc_final: 0.8631 (mmt) REVERT: B 784 GLN cc_start: 0.8806 (tp-100) cc_final: 0.8225 (tp-100) REVERT: B 793 MET cc_start: 0.8719 (tpp) cc_final: 0.8272 (ptp) REVERT: B 813 SER cc_start: 0.8438 (OUTLIER) cc_final: 0.8237 (m) REVERT: C 833 LEU cc_start: 0.9222 (mm) cc_final: 0.8778 (tt) REVERT: D 524 GLU cc_start: 0.7903 (tm-30) cc_final: 0.7575 (tm-30) REVERT: D 564 TRP cc_start: 0.7729 (OUTLIER) cc_final: 0.7520 (m-10) REVERT: D 635 ILE cc_start: 0.9377 (mp) cc_final: 0.9073 (tp) REVERT: D 733 TYR cc_start: 0.7857 (t80) cc_final: 0.7487 (t80) REVERT: D 793 MET cc_start: 0.8426 (ptp) cc_final: 0.7380 (ptp) outliers start: 62 outliers final: 35 residues processed: 249 average time/residue: 0.0882 time to fit residues: 34.4038 Evaluate side-chains 235 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 195 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 673 ASP Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 745 VAL Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 799 TRP Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain B residue 691 MET Chi-restraints excluded: chain B residue 701 THR Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 774 TYR Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 647 ILE Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 677 GLN Chi-restraints excluded: chain C residue 691 MET Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 776 ASP Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 540 ILE Chi-restraints excluded: chain D residue 564 TRP Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 794 MET Chi-restraints excluded: chain D residue 827 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 143 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 chunk 133 optimal weight: 0.4980 chunk 12 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 792 HIS D 721 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.120758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.092547 restraints weight = 30222.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.095728 restraints weight = 17164.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.097796 restraints weight = 12355.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.099211 restraints weight = 10118.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.100124 restraints weight = 8885.899| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12153 Z= 0.132 Angle : 0.625 19.405 16461 Z= 0.304 Chirality : 0.043 0.467 1886 Planarity : 0.003 0.031 2040 Dihedral : 5.585 65.752 1811 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.98 % Allowed : 24.38 % Favored : 71.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.23), residues: 1472 helix: 1.30 (0.19), residues: 746 sheet: -1.90 (0.49), residues: 115 loop : -1.48 (0.26), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 663 TYR 0.015 0.001 TYR C 462 PHE 0.014 0.001 PHE A 836 TRP 0.041 0.002 TRP B 799 HIS 0.002 0.001 HIS B 792 Details of bonding type rmsd covalent geometry : bond 0.00304 (12138) covalent geometry : angle 0.59399 (16422) SS BOND : bond 0.00353 ( 6) SS BOND : angle 1.27818 ( 12) hydrogen bonds : bond 0.03091 ( 565) hydrogen bonds : angle 4.39455 ( 1686) link_BETA1-4 : bond 0.00179 ( 2) link_BETA1-4 : angle 1.76178 ( 6) link_NAG-ASN : bond 0.00998 ( 7) link_NAG-ASN : angle 5.33353 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 213 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 442 PRO cc_start: 0.9314 (Cg_endo) cc_final: 0.8961 (Cg_exo) REVERT: A 505 LEU cc_start: 0.9091 (tp) cc_final: 0.8502 (tp) REVERT: A 511 ASP cc_start: 0.7809 (t70) cc_final: 0.7557 (t0) REVERT: A 706 TRP cc_start: 0.9368 (t-100) cc_final: 0.8989 (t-100) REVERT: A 793 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.7877 (tmm) REVERT: A 794 MET cc_start: 0.8485 (mtt) cc_final: 0.8187 (mtt) REVERT: A 818 GLN cc_start: 0.8483 (pm20) cc_final: 0.7638 (tt0) REVERT: B 544 LYS cc_start: 0.9250 (mmmt) cc_final: 0.8699 (mtpp) REVERT: B 686 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7277 (pm20) REVERT: B 691 MET cc_start: 0.9298 (OUTLIER) cc_final: 0.8809 (ptt) REVERT: B 747 GLN cc_start: 0.9334 (mm-40) cc_final: 0.9107 (mm-40) REVERT: B 784 GLN cc_start: 0.8798 (tp-100) cc_final: 0.8201 (tp-100) REVERT: B 793 MET cc_start: 0.8708 (tpp) cc_final: 0.8270 (ptp) REVERT: B 813 SER cc_start: 0.8483 (OUTLIER) cc_final: 0.8282 (m) REVERT: C 793 MET cc_start: 0.8767 (ptp) cc_final: 0.8528 (mpp) REVERT: D 524 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7552 (tm-30) REVERT: D 733 TYR cc_start: 0.7869 (t80) cc_final: 0.7522 (t80) outliers start: 51 outliers final: 36 residues processed: 247 average time/residue: 0.0908 time to fit residues: 34.7728 Evaluate side-chains 242 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 202 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 673 ASP Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 745 VAL Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 799 TRP Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain B residue 691 MET Chi-restraints excluded: chain B residue 701 THR Chi-restraints excluded: chain B residue 750 CYS Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 800 ARG Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 647 ILE Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 677 GLN Chi-restraints excluded: chain C residue 691 MET Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 776 ASP Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 540 ILE Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 827 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 128 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 85 optimal weight: 7.9990 chunk 145 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 105 optimal weight: 0.5980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.120437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.092268 restraints weight = 30479.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.095403 restraints weight = 17380.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.097438 restraints weight = 12556.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.098840 restraints weight = 10318.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.099736 restraints weight = 9080.653| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12153 Z= 0.134 Angle : 0.634 19.519 16461 Z= 0.307 Chirality : 0.043 0.455 1886 Planarity : 0.003 0.032 2040 Dihedral : 5.616 66.260 1811 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 4.06 % Allowed : 25.31 % Favored : 70.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.23), residues: 1472 helix: 1.27 (0.19), residues: 752 sheet: -1.95 (0.47), residues: 121 loop : -1.55 (0.26), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 663 TYR 0.012 0.001 TYR B 764 PHE 0.032 0.001 PHE B 555 TRP 0.037 0.002 TRP B 799 HIS 0.002 0.001 HIS B 792 Details of bonding type rmsd covalent geometry : bond 0.00310 (12138) covalent geometry : angle 0.60307 (16422) SS BOND : bond 0.00350 ( 6) SS BOND : angle 1.29242 ( 12) hydrogen bonds : bond 0.03070 ( 565) hydrogen bonds : angle 4.39845 ( 1686) link_BETA1-4 : bond 0.00311 ( 2) link_BETA1-4 : angle 1.76932 ( 6) link_NAG-ASN : bond 0.00937 ( 7) link_NAG-ASN : angle 5.34018 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 204 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 442 PRO cc_start: 0.9305 (Cg_endo) cc_final: 0.8926 (Cg_exo) REVERT: A 505 LEU cc_start: 0.9087 (tp) cc_final: 0.8497 (tp) REVERT: A 511 ASP cc_start: 0.7786 (t70) cc_final: 0.7489 (t0) REVERT: A 706 TRP cc_start: 0.9379 (t-100) cc_final: 0.8907 (t-100) REVERT: A 793 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.7904 (tmm) REVERT: A 794 MET cc_start: 0.8506 (mtt) cc_final: 0.8261 (mtt) REVERT: B 544 LYS cc_start: 0.9224 (mmmt) cc_final: 0.8704 (mtpp) REVERT: B 686 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7465 (pm20) REVERT: B 747 GLN cc_start: 0.9276 (mm-40) cc_final: 0.9013 (mm-40) REVERT: B 784 GLN cc_start: 0.8774 (tp-100) cc_final: 0.8142 (tp-100) REVERT: B 793 MET cc_start: 0.8688 (tpp) cc_final: 0.8271 (ptp) REVERT: B 813 SER cc_start: 0.8494 (OUTLIER) cc_final: 0.8281 (m) REVERT: C 793 MET cc_start: 0.8779 (ptp) cc_final: 0.8524 (mpp) REVERT: C 833 LEU cc_start: 0.9259 (mm) cc_final: 0.8794 (tt) REVERT: D 524 GLU cc_start: 0.7907 (tm-30) cc_final: 0.7560 (tm-30) REVERT: D 635 ILE cc_start: 0.9319 (mp) cc_final: 0.9023 (tp) REVERT: D 664 MET cc_start: 0.6963 (mtp) cc_final: 0.6748 (mmp) REVERT: D 733 TYR cc_start: 0.7860 (t80) cc_final: 0.7521 (t80) REVERT: D 793 MET cc_start: 0.8104 (ptp) cc_final: 0.7710 (ptp) outliers start: 52 outliers final: 38 residues processed: 239 average time/residue: 0.0886 time to fit residues: 33.0734 Evaluate side-chains 239 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 198 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 673 ASP Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 745 VAL Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 799 TRP Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain B residue 691 MET Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 738 GLU Chi-restraints excluded: chain B residue 745 VAL Chi-restraints excluded: chain B residue 750 CYS Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 800 ARG Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 647 ILE Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 677 GLN Chi-restraints excluded: chain C residue 691 MET Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 776 ASP Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 540 ILE Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 827 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 0 optimal weight: 6.9990 chunk 143 optimal weight: 3.9990 chunk 71 optimal weight: 0.3980 chunk 139 optimal weight: 10.0000 chunk 147 optimal weight: 9.9990 chunk 122 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 117 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 133 optimal weight: 0.7980 chunk 100 optimal weight: 6.9990 overall best weight: 2.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 721 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.118221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.089515 restraints weight = 30519.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.092526 restraints weight = 17807.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.094473 restraints weight = 13044.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.095756 restraints weight = 10803.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.096558 restraints weight = 9602.930| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 12153 Z= 0.200 Angle : 0.675 19.259 16461 Z= 0.333 Chirality : 0.045 0.482 1886 Planarity : 0.003 0.033 2040 Dihedral : 5.785 70.319 1810 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 4.45 % Allowed : 26.02 % Favored : 69.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.23), residues: 1472 helix: 1.20 (0.19), residues: 753 sheet: -2.18 (0.47), residues: 117 loop : -1.58 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 663 TYR 0.015 0.001 TYR B 764 PHE 0.027 0.001 PHE B 555 TRP 0.028 0.002 TRP B 799 HIS 0.003 0.001 HIS A 792 Details of bonding type rmsd covalent geometry : bond 0.00455 (12138) covalent geometry : angle 0.64639 (16422) SS BOND : bond 0.00319 ( 6) SS BOND : angle 1.33655 ( 12) hydrogen bonds : bond 0.03207 ( 565) hydrogen bonds : angle 4.52275 ( 1686) link_BETA1-4 : bond 0.00285 ( 2) link_BETA1-4 : angle 1.87310 ( 6) link_NAG-ASN : bond 0.00889 ( 7) link_NAG-ASN : angle 5.34503 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 192 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 441 GLU cc_start: 0.8569 (mp0) cc_final: 0.8355 (mp0) REVERT: A 442 PRO cc_start: 0.9374 (Cg_endo) cc_final: 0.8933 (Cg_exo) REVERT: A 505 LEU cc_start: 0.9169 (tp) cc_final: 0.8607 (tp) REVERT: A 511 ASP cc_start: 0.7910 (t70) cc_final: 0.7653 (t0) REVERT: A 793 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.7960 (tmm) REVERT: A 794 MET cc_start: 0.8574 (mtt) cc_final: 0.8322 (mtt) REVERT: A 818 GLN cc_start: 0.8525 (pm20) cc_final: 0.7655 (tt0) REVERT: B 544 LYS cc_start: 0.9255 (mmmt) cc_final: 0.8707 (mtpp) REVERT: B 686 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7720 (pm20) REVERT: B 691 MET cc_start: 0.9392 (OUTLIER) cc_final: 0.9101 (ptt) REVERT: B 709 MET cc_start: 0.9463 (mmm) cc_final: 0.8746 (mmt) REVERT: B 737 MET cc_start: 0.8006 (ppp) cc_final: 0.7643 (ppp) REVERT: B 747 GLN cc_start: 0.9289 (mm-40) cc_final: 0.9015 (mm-40) REVERT: B 784 GLN cc_start: 0.8780 (tp-100) cc_final: 0.8135 (tp-100) REVERT: B 793 MET cc_start: 0.8736 (tpp) cc_final: 0.8308 (ptp) REVERT: B 794 MET cc_start: 0.8907 (ttm) cc_final: 0.8553 (mtp) REVERT: B 813 SER cc_start: 0.8546 (OUTLIER) cc_final: 0.8337 (m) REVERT: C 793 MET cc_start: 0.8832 (ptp) cc_final: 0.8587 (mpp) REVERT: C 833 LEU cc_start: 0.9249 (mm) cc_final: 0.8771 (tt) REVERT: D 524 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7562 (tm-30) REVERT: D 635 ILE cc_start: 0.9372 (mp) cc_final: 0.9079 (tp) REVERT: D 664 MET cc_start: 0.7100 (mtp) cc_final: 0.6828 (mmp) REVERT: D 737 MET cc_start: 0.8010 (OUTLIER) cc_final: 0.7538 (ptt) outliers start: 57 outliers final: 39 residues processed: 230 average time/residue: 0.0830 time to fit residues: 30.5534 Evaluate side-chains 227 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 183 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 673 ASP Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 745 VAL Chi-restraints excluded: chain A residue 746 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 799 TRP Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain B residue 691 MET Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 741 THR Chi-restraints excluded: chain B residue 745 VAL Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 800 ARG Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 647 ILE Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 677 GLN Chi-restraints excluded: chain C residue 691 MET Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 776 ASP Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 540 ILE Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 737 MET Chi-restraints excluded: chain D residue 827 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 12 optimal weight: 0.0770 chunk 83 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 43 optimal weight: 9.9990 chunk 91 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 chunk 55 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 chunk 101 optimal weight: 10.0000 chunk 112 optimal weight: 0.4980 overall best weight: 1.0340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.119849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.091547 restraints weight = 30334.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.094631 restraints weight = 17451.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.096625 restraints weight = 12671.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.097997 restraints weight = 10435.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.098801 restraints weight = 9198.868| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12153 Z= 0.131 Angle : 0.672 19.483 16461 Z= 0.324 Chirality : 0.044 0.471 1886 Planarity : 0.003 0.031 2040 Dihedral : 5.727 67.593 1810 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 4.14 % Allowed : 26.64 % Favored : 69.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.22), residues: 1472 helix: 1.20 (0.19), residues: 757 sheet: -2.10 (0.48), residues: 117 loop : -1.65 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 663 TYR 0.025 0.001 TYR C 462 PHE 0.027 0.001 PHE B 555 TRP 0.043 0.002 TRP A 798 HIS 0.002 0.001 HIS D 792 Details of bonding type rmsd covalent geometry : bond 0.00306 (12138) covalent geometry : angle 0.64230 (16422) SS BOND : bond 0.00516 ( 6) SS BOND : angle 2.05795 ( 12) hydrogen bonds : bond 0.03069 ( 565) hydrogen bonds : angle 4.46752 ( 1686) link_BETA1-4 : bond 0.00186 ( 2) link_BETA1-4 : angle 1.71307 ( 6) link_NAG-ASN : bond 0.00954 ( 7) link_NAG-ASN : angle 5.33920 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 208 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 442 PRO cc_start: 0.9249 (Cg_endo) cc_final: 0.8872 (Cg_exo) REVERT: A 505 LEU cc_start: 0.9060 (tp) cc_final: 0.8440 (tp) REVERT: A 511 ASP cc_start: 0.7820 (t70) cc_final: 0.7548 (t0) REVERT: A 706 TRP cc_start: 0.9376 (t-100) cc_final: 0.8963 (t-100) REVERT: A 738 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.7788 (mp0) REVERT: A 793 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.7993 (tmm) REVERT: A 794 MET cc_start: 0.8590 (mtt) cc_final: 0.8364 (mtt) REVERT: A 818 GLN cc_start: 0.8445 (pm20) cc_final: 0.7597 (tt0) REVERT: B 544 LYS cc_start: 0.9290 (mmmt) cc_final: 0.8807 (mttt) REVERT: B 686 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7591 (pm20) REVERT: B 709 MET cc_start: 0.9462 (mmm) cc_final: 0.8704 (mmt) REVERT: B 725 ILE cc_start: 0.9122 (mp) cc_final: 0.8660 (mm) REVERT: B 784 GLN cc_start: 0.8759 (tp-100) cc_final: 0.8130 (tp-100) REVERT: B 793 MET cc_start: 0.8704 (tpp) cc_final: 0.8230 (ptp) REVERT: B 813 SER cc_start: 0.8507 (OUTLIER) cc_final: 0.8295 (m) REVERT: C 833 LEU cc_start: 0.9251 (mm) cc_final: 0.8793 (tt) REVERT: D 441 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7931 (tp30) REVERT: D 524 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7587 (tm-30) REVERT: D 635 ILE cc_start: 0.9319 (mp) cc_final: 0.9011 (tp) REVERT: D 664 MET cc_start: 0.7124 (mtp) cc_final: 0.6814 (mmp) REVERT: D 737 MET cc_start: 0.8034 (OUTLIER) cc_final: 0.7682 (ptt) outliers start: 53 outliers final: 38 residues processed: 240 average time/residue: 0.0824 time to fit residues: 31.3877 Evaluate side-chains 242 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 198 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 673 ASP Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 738 GLU Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 745 VAL Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 799 TRP Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain B residue 741 THR Chi-restraints excluded: chain B residue 745 VAL Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 800 ARG Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 647 ILE Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 677 GLN Chi-restraints excluded: chain C residue 691 MET Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 776 ASP Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain D residue 441 GLU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 540 ILE Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 691 MET Chi-restraints excluded: chain D residue 737 MET Chi-restraints excluded: chain D residue 827 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 127 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 142 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 119 optimal weight: 8.9990 chunk 88 optimal weight: 7.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.115782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.088168 restraints weight = 29744.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.091027 restraints weight = 17067.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.092926 restraints weight = 12366.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.094108 restraints weight = 10155.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.094961 restraints weight = 9020.683| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 12153 Z= 0.234 Angle : 0.728 19.334 16461 Z= 0.362 Chirality : 0.046 0.502 1886 Planarity : 0.004 0.034 2040 Dihedral : 5.928 71.653 1810 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 3.83 % Allowed : 27.50 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.22), residues: 1472 helix: 1.12 (0.19), residues: 753 sheet: -2.27 (0.46), residues: 117 loop : -1.70 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 663 TYR 0.022 0.002 TYR C 462 PHE 0.025 0.001 PHE B 555 TRP 0.037 0.003 TRP A 798 HIS 0.003 0.001 HIS A 792 Details of bonding type rmsd covalent geometry : bond 0.00528 (12138) covalent geometry : angle 0.70054 (16422) SS BOND : bond 0.00329 ( 6) SS BOND : angle 1.64998 ( 12) hydrogen bonds : bond 0.03317 ( 565) hydrogen bonds : angle 4.63291 ( 1686) link_BETA1-4 : bond 0.00322 ( 2) link_BETA1-4 : angle 1.92235 ( 6) link_NAG-ASN : bond 0.00866 ( 7) link_NAG-ASN : angle 5.36917 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 189 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 442 PRO cc_start: 0.9379 (Cg_endo) cc_final: 0.8996 (Cg_exo) REVERT: A 505 LEU cc_start: 0.9178 (tp) cc_final: 0.8612 (tp) REVERT: A 511 ASP cc_start: 0.7964 (t70) cc_final: 0.7728 (t0) REVERT: A 738 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.8529 (mp0) REVERT: A 793 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.7957 (tmm) REVERT: A 794 MET cc_start: 0.8600 (mtt) cc_final: 0.8335 (mtt) REVERT: A 818 GLN cc_start: 0.8401 (pm20) cc_final: 0.7594 (tt0) REVERT: B 544 LYS cc_start: 0.9276 (mmmt) cc_final: 0.8729 (mtpp) REVERT: B 686 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7754 (pm20) REVERT: B 691 MET cc_start: 0.9380 (OUTLIER) cc_final: 0.9009 (ptt) REVERT: B 784 GLN cc_start: 0.8812 (tp-100) cc_final: 0.8196 (tp-100) REVERT: B 793 MET cc_start: 0.8731 (tpp) cc_final: 0.8325 (ptp) REVERT: B 794 MET cc_start: 0.8927 (ttm) cc_final: 0.8579 (mtp) REVERT: B 813 SER cc_start: 0.8568 (OUTLIER) cc_final: 0.8365 (m) REVERT: C 833 LEU cc_start: 0.9257 (mm) cc_final: 0.8798 (tt) REVERT: D 524 GLU cc_start: 0.7900 (tm-30) cc_final: 0.7579 (tm-30) REVERT: D 664 MET cc_start: 0.7002 (mtp) cc_final: 0.6792 (mmp) REVERT: D 737 MET cc_start: 0.8066 (OUTLIER) cc_final: 0.7697 (ptt) REVERT: D 793 MET cc_start: 0.8355 (ptp) cc_final: 0.7641 (ptp) outliers start: 49 outliers final: 37 residues processed: 223 average time/residue: 0.0796 time to fit residues: 28.3751 Evaluate side-chains 229 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 186 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 673 ASP Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 738 GLU Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 745 VAL Chi-restraints excluded: chain A residue 746 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 799 TRP Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain B residue 691 MET Chi-restraints excluded: chain B residue 741 THR Chi-restraints excluded: chain B residue 745 VAL Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 800 ARG Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 647 ILE Chi-restraints excluded: chain C residue 677 GLN Chi-restraints excluded: chain C residue 691 MET Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 776 ASP Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 540 ILE Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 737 MET Chi-restraints excluded: chain D residue 827 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 115 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 chunk 110 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 138 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.119372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.091249 restraints weight = 30353.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.094365 restraints weight = 17129.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.096430 restraints weight = 12294.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.097789 restraints weight = 10023.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.098700 restraints weight = 8806.979| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12153 Z= 0.139 Angle : 0.689 19.598 16461 Z= 0.335 Chirality : 0.045 0.478 1886 Planarity : 0.003 0.031 2040 Dihedral : 5.747 67.110 1810 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.52 % Allowed : 28.05 % Favored : 68.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.23), residues: 1472 helix: 1.18 (0.19), residues: 752 sheet: -2.19 (0.51), residues: 102 loop : -1.62 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 663 TYR 0.016 0.001 TYR C 462 PHE 0.026 0.001 PHE B 555 TRP 0.031 0.002 TRP A 798 HIS 0.004 0.001 HIS D 792 Details of bonding type rmsd covalent geometry : bond 0.00324 (12138) covalent geometry : angle 0.66061 (16422) SS BOND : bond 0.00390 ( 6) SS BOND : angle 1.34295 ( 12) hydrogen bonds : bond 0.03101 ( 565) hydrogen bonds : angle 4.51491 ( 1686) link_BETA1-4 : bond 0.00146 ( 2) link_BETA1-4 : angle 1.75055 ( 6) link_NAG-ASN : bond 0.00982 ( 7) link_NAG-ASN : angle 5.36390 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 201 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 442 PRO cc_start: 0.9290 (Cg_endo) cc_final: 0.8911 (Cg_exo) REVERT: A 505 LEU cc_start: 0.9089 (tp) cc_final: 0.8454 (tp) REVERT: A 511 ASP cc_start: 0.7833 (t70) cc_final: 0.7577 (t0) REVERT: A 793 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.8003 (tmm) REVERT: A 794 MET cc_start: 0.8576 (mtt) cc_final: 0.8373 (mtt) REVERT: A 818 GLN cc_start: 0.8335 (pm20) cc_final: 0.7480 (tt0) REVERT: B 544 LYS cc_start: 0.9286 (mmmt) cc_final: 0.8749 (mtpp) REVERT: B 686 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7588 (pm20) REVERT: B 691 MET cc_start: 0.9273 (OUTLIER) cc_final: 0.8925 (ptt) REVERT: B 776 ASP cc_start: 0.8183 (m-30) cc_final: 0.7598 (t70) REVERT: B 784 GLN cc_start: 0.8764 (tp-100) cc_final: 0.8111 (tp-100) REVERT: B 793 MET cc_start: 0.8720 (tpp) cc_final: 0.8217 (ptp) REVERT: B 794 MET cc_start: 0.8945 (ttm) cc_final: 0.8583 (mtp) REVERT: B 813 SER cc_start: 0.8547 (OUTLIER) cc_final: 0.8337 (m) REVERT: C 770 MET cc_start: 0.8719 (mmm) cc_final: 0.8426 (mmt) REVERT: C 833 LEU cc_start: 0.9248 (mm) cc_final: 0.8822 (tt) REVERT: D 501 MET cc_start: 0.9051 (mmt) cc_final: 0.8818 (mmt) REVERT: D 524 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7534 (tm-30) REVERT: D 635 ILE cc_start: 0.9306 (mp) cc_final: 0.9031 (tp) REVERT: D 664 MET cc_start: 0.7086 (mtp) cc_final: 0.6842 (mmp) REVERT: D 737 MET cc_start: 0.8142 (OUTLIER) cc_final: 0.7818 (ptt) REVERT: A 1003 GLU cc_start: 0.5850 (pt0) cc_final: 0.5638 (pt0) outliers start: 45 outliers final: 34 residues processed: 230 average time/residue: 0.0858 time to fit residues: 30.8661 Evaluate side-chains 237 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 198 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 745 VAL Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 799 TRP Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain B residue 691 MET Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 800 ARG Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 647 ILE Chi-restraints excluded: chain C residue 677 GLN Chi-restraints excluded: chain C residue 691 MET Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 776 ASP Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain C residue 792 HIS Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain C residue 835 VAL Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 540 ILE Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 691 MET Chi-restraints excluded: chain D residue 737 MET Chi-restraints excluded: chain D residue 827 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 66 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 132 optimal weight: 8.9990 chunk 145 optimal weight: 0.7980 chunk 135 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.119566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.091293 restraints weight = 30494.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.094373 restraints weight = 17564.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.096430 restraints weight = 12712.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.097810 restraints weight = 10406.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.098620 restraints weight = 9157.823| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12153 Z= 0.137 Angle : 0.687 19.516 16461 Z= 0.334 Chirality : 0.045 0.480 1886 Planarity : 0.003 0.031 2040 Dihedral : 5.619 65.878 1808 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.36 % Allowed : 28.12 % Favored : 68.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.22), residues: 1472 helix: 1.14 (0.19), residues: 758 sheet: -2.19 (0.51), residues: 102 loop : -1.64 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 663 TYR 0.019 0.001 TYR C 462 PHE 0.024 0.001 PHE B 555 TRP 0.025 0.002 TRP D 798 HIS 0.004 0.001 HIS D 792 Details of bonding type rmsd covalent geometry : bond 0.00320 (12138) covalent geometry : angle 0.65936 (16422) SS BOND : bond 0.00349 ( 6) SS BOND : angle 1.12524 ( 12) hydrogen bonds : bond 0.03091 ( 565) hydrogen bonds : angle 4.51578 ( 1686) link_BETA1-4 : bond 0.00191 ( 2) link_BETA1-4 : angle 1.76804 ( 6) link_NAG-ASN : bond 0.00967 ( 7) link_NAG-ASN : angle 5.36176 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1935.09 seconds wall clock time: 34 minutes 21.41 seconds (2061.41 seconds total)