Starting phenix.real_space_refine on Mon May 19 05:27:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ss4_40743/05_2025/8ss4_40743.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ss4_40743/05_2025/8ss4_40743.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ss4_40743/05_2025/8ss4_40743.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ss4_40743/05_2025/8ss4_40743.map" model { file = "/net/cci-nas-00/data/ceres_data/8ss4_40743/05_2025/8ss4_40743.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ss4_40743/05_2025/8ss4_40743.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.091 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 130 5.16 5 C 11763 2.51 5 N 2877 2.21 5 O 3208 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 17978 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4662 Classifications: {'peptide': 595} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 577} Chain breaks: 4 Chain: "B" Number of atoms: 3156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3156 Classifications: {'peptide': 404} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 390} Chain breaks: 2 Chain: "C" Number of atoms: 4662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4662 Classifications: {'peptide': 595} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 577} Chain breaks: 4 Chain: "D" Number of atoms: 3156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3156 Classifications: {'peptide': 404} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 390} Chain breaks: 2 Chain: "E" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1166 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain breaks: 1 Chain: "F" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1166 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain breaks: 1 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'SPD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.71, per 1000 atoms: 0.54 Number of scatterers: 17978 At special positions: 0 Unit cell: (115.54, 124.02, 139.92, 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 130 16.00 O 3208 8.00 N 2877 7.00 C 11763 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.02 Simple disulfide: pdb=" SG CYS A 890 " - pdb=" SG CYS A 900 " distance=2.04 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.01 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.02 Simple disulfide: pdb=" SG CYS C 890 " - pdb=" SG CYS C 900 " distance=2.04 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.01 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.06 Conformation dependent library (CDL) restraints added in 2.1 seconds 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4204 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 22 sheets defined 56.7% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing helix chain 'A' and resid 417 through 419 No H-bonds generated for 'chain 'A' and resid 417 through 419' Processing helix chain 'A' and resid 423 through 437 removed outlier: 3.648A pdb=" N ALA A 430 " --> pdb=" O VAL A 426 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS A 434 " --> pdb=" O ALA A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 469 removed outlier: 3.531A pdb=" N GLY A 465 " --> pdb=" O ASN A 461 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU A 467 " --> pdb=" O MET A 463 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 515 through 519 removed outlier: 3.636A pdb=" N LEU A 518 " --> pdb=" O PHE A 515 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP A 519 " --> pdb=" O SER A 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 515 through 519' Processing helix chain 'A' and resid 522 through 543 removed outlier: 3.821A pdb=" N VAL A 530 " --> pdb=" O TRP A 526 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL A 539 " --> pdb=" O GLY A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 585 removed outlier: 3.616A pdb=" N LEU A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TRP A 578 " --> pdb=" O PHE A 574 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N MET A 585 " --> pdb=" O LEU A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 629 removed outlier: 4.113A pdb=" N VAL A 601 " --> pdb=" O SER A 597 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE A 613 " --> pdb=" O THR A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 642 removed outlier: 3.683A pdb=" N LYS A 641 " --> pdb=" O GLU A 637 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLN A 642 " --> pdb=" O ASP A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 662 removed outlier: 3.993A pdb=" N PHE A 659 " --> pdb=" O THR A 655 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG A 660 " --> pdb=" O LYS A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 676 removed outlier: 3.979A pdb=" N SER A 676 " --> pdb=" O THR A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 695 Processing helix chain 'A' and resid 708 through 714 removed outlier: 3.740A pdb=" N GLN A 714 " --> pdb=" O GLU A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 754 removed outlier: 3.638A pdb=" N ASN A 747 " --> pdb=" O GLY A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 768 removed outlier: 3.751A pdb=" N LYS A 763 " --> pdb=" O LEU A 759 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN A 764 " --> pdb=" O ASP A 760 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TRP A 766 " --> pdb=" O LEU A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 822 removed outlier: 3.504A pdb=" N MET A 807 " --> pdb=" O LEU A 803 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER A 818 " --> pdb=" O PHE A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 856 Processing helix chain 'A' and resid 893 through 897 Processing helix chain 'A' and resid 929 through 952 removed outlier: 3.518A pdb=" N LEU A 933 " --> pdb=" O THR A 929 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N MET A 939 " --> pdb=" O SER A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 989 removed outlier: 3.774A pdb=" N ALA A 959 " --> pdb=" O ARG A 955 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL A 961 " --> pdb=" O ILE A 957 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE A 965 " --> pdb=" O VAL A 961 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE A 967 " --> pdb=" O GLY A 963 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL A 975 " --> pdb=" O LEU A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1035 removed outlier: 3.800A pdb=" N ALA A1008 " --> pdb=" O GLY A1004 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU A1015 " --> pdb=" O ALA A1011 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 436 Processing helix chain 'B' and resid 462 through 469 Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 524 through 546 removed outlier: 3.570A pdb=" N ALA B 532 " --> pdb=" O CYS B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 583 Processing helix chain 'B' and resid 595 through 626 removed outlier: 4.102A pdb=" N VAL B 601 " --> pdb=" O SER B 597 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU B 610 " --> pdb=" O TRP B 606 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE B 611 " --> pdb=" O PHE B 607 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA B 622 " --> pdb=" O ALA B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 642 removed outlier: 3.745A pdb=" N LYS B 641 " --> pdb=" O GLU B 637 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN B 642 " --> pdb=" O ASP B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 661 removed outlier: 3.788A pdb=" N PHE B 659 " --> pdb=" O THR B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 677 removed outlier: 3.505A pdb=" N SER B 676 " --> pdb=" O THR B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 696 Processing helix chain 'B' and resid 706 through 713 removed outlier: 3.530A pdb=" N GLU B 710 " --> pdb=" O SER B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 756 removed outlier: 3.674A pdb=" N ASN B 747 " --> pdb=" O GLY B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 767 removed outlier: 3.525A pdb=" N LYS B 763 " --> pdb=" O LEU B 759 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN B 764 " --> pdb=" O ASP B 760 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TRP B 766 " --> pdb=" O LEU B 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 790 through 792 No H-bonds generated for 'chain 'B' and resid 790 through 792' Processing helix chain 'B' and resid 793 through 820 removed outlier: 3.507A pdb=" N LEU B 808 " --> pdb=" O GLY B 804 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL B 809 " --> pdb=" O LEU B 805 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 419 No H-bonds generated for 'chain 'C' and resid 417 through 419' Processing helix chain 'C' and resid 423 through 437 removed outlier: 3.648A pdb=" N ALA C 430 " --> pdb=" O VAL C 426 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS C 434 " --> pdb=" O ALA C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 469 removed outlier: 3.530A pdb=" N GLY C 465 " --> pdb=" O ASN C 461 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU C 467 " --> pdb=" O MET C 463 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR C 469 " --> pdb=" O GLY C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 487 Processing helix chain 'C' and resid 515 through 519 removed outlier: 3.636A pdb=" N LEU C 518 " --> pdb=" O PHE C 515 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP C 519 " --> pdb=" O SER C 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 515 through 519' Processing helix chain 'C' and resid 522 through 543 removed outlier: 3.820A pdb=" N VAL C 530 " --> pdb=" O TRP C 526 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL C 539 " --> pdb=" O GLY C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 585 removed outlier: 3.616A pdb=" N LEU C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TRP C 578 " --> pdb=" O PHE C 574 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N MET C 585 " --> pdb=" O LEU C 581 " (cutoff:3.500A) Processing helix chain 'C' and resid 597 through 629 removed outlier: 4.113A pdb=" N VAL C 601 " --> pdb=" O SER C 597 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE C 613 " --> pdb=" O THR C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 642 removed outlier: 3.683A pdb=" N LYS C 641 " --> pdb=" O GLU C 637 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN C 642 " --> pdb=" O ASP C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 662 removed outlier: 3.993A pdb=" N PHE C 659 " --> pdb=" O THR C 655 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG C 660 " --> pdb=" O LYS C 656 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 676 removed outlier: 3.979A pdb=" N SER C 676 " --> pdb=" O THR C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 685 through 695 Processing helix chain 'C' and resid 708 through 714 removed outlier: 3.739A pdb=" N GLN C 714 " --> pdb=" O GLU C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 743 through 754 removed outlier: 3.639A pdb=" N ASN C 747 " --> pdb=" O GLY C 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 768 removed outlier: 3.751A pdb=" N LYS C 763 " --> pdb=" O LEU C 759 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN C 764 " --> pdb=" O ASP C 760 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TRP C 766 " --> pdb=" O LEU C 762 " (cutoff:3.500A) Processing helix chain 'C' and resid 793 through 822 removed outlier: 3.505A pdb=" N MET C 807 " --> pdb=" O LEU C 803 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER C 818 " --> pdb=" O PHE C 814 " (cutoff:3.500A) Processing helix chain 'C' and resid 834 through 856 Processing helix chain 'C' and resid 893 through 897 Processing helix chain 'C' and resid 929 through 952 removed outlier: 3.518A pdb=" N LEU C 933 " --> pdb=" O THR C 929 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N MET C 939 " --> pdb=" O SER C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 955 through 989 removed outlier: 3.773A pdb=" N ALA C 959 " --> pdb=" O ARG C 955 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL C 961 " --> pdb=" O ILE C 957 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE C 965 " --> pdb=" O VAL C 961 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE C 967 " --> pdb=" O GLY C 963 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL C 975 " --> pdb=" O LEU C 971 " (cutoff:3.500A) Processing helix chain 'C' and resid 1004 through 1035 removed outlier: 3.800A pdb=" N ALA C1008 " --> pdb=" O GLY C1004 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU C1015 " --> pdb=" O ALA C1011 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 436 Processing helix chain 'D' and resid 462 through 469 Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 515 through 519 Processing helix chain 'D' and resid 524 through 546 removed outlier: 3.570A pdb=" N ALA D 532 " --> pdb=" O CYS D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 583 Processing helix chain 'D' and resid 595 through 626 removed outlier: 4.103A pdb=" N VAL D 601 " --> pdb=" O SER D 597 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU D 610 " --> pdb=" O TRP D 606 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE D 611 " --> pdb=" O PHE D 607 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA D 622 " --> pdb=" O ALA D 618 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 642 removed outlier: 3.745A pdb=" N LYS D 641 " --> pdb=" O GLU D 637 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN D 642 " --> pdb=" O ASP D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 661 removed outlier: 3.789A pdb=" N PHE D 659 " --> pdb=" O THR D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 666 through 677 removed outlier: 3.505A pdb=" N SER D 676 " --> pdb=" O THR D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 696 Processing helix chain 'D' and resid 706 through 713 removed outlier: 3.531A pdb=" N GLU D 710 " --> pdb=" O SER D 706 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 756 removed outlier: 3.674A pdb=" N ASN D 747 " --> pdb=" O GLY D 743 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 767 removed outlier: 3.525A pdb=" N LYS D 763 " --> pdb=" O LEU D 759 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN D 764 " --> pdb=" O ASP D 760 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TRP D 766 " --> pdb=" O LEU D 762 " (cutoff:3.500A) Processing helix chain 'D' and resid 790 through 792 No H-bonds generated for 'chain 'D' and resid 790 through 792' Processing helix chain 'D' and resid 793 through 820 removed outlier: 3.507A pdb=" N LEU D 808 " --> pdb=" O GLY D 804 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL D 809 " --> pdb=" O LEU D 805 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 36 removed outlier: 4.287A pdb=" N SER E 19 " --> pdb=" O VAL E 15 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE E 22 " --> pdb=" O ALA E 18 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE E 29 " --> pdb=" O ILE E 25 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU E 34 " --> pdb=" O ALA E 30 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG E 35 " --> pdb=" O PHE E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 66 removed outlier: 3.624A pdb=" N LYS E 66 " --> pdb=" O CYS E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 85 removed outlier: 3.587A pdb=" N LEU E 80 " --> pdb=" O GLY E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 106 removed outlier: 4.154A pdb=" N ASN E 94 " --> pdb=" O THR E 90 " (cutoff:3.500A) Proline residue: E 96 - end of helix removed outlier: 3.675A pdb=" N ARG E 104 " --> pdb=" O TYR E 100 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N PHE E 106 " --> pdb=" O LEU E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 159 removed outlier: 3.611A pdb=" N TRP E 136 " --> pdb=" O GLN E 132 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU E 139 " --> pdb=" O SER E 135 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE E 147 " --> pdb=" O LEU E 143 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU E 150 " --> pdb=" O PHE E 146 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR E 151 " --> pdb=" O PHE E 147 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL E 154 " --> pdb=" O LEU E 150 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL E 158 " --> pdb=" O VAL E 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 36 removed outlier: 4.262A pdb=" N SER F 19 " --> pdb=" O VAL F 15 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE F 22 " --> pdb=" O ALA F 18 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE F 29 " --> pdb=" O ILE F 25 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU F 34 " --> pdb=" O ALA F 30 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG F 35 " --> pdb=" O PHE F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 66 Processing helix chain 'F' and resid 67 through 85 removed outlier: 3.890A pdb=" N GLU F 71 " --> pdb=" O LEU F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 106 removed outlier: 4.073A pdb=" N ASN F 94 " --> pdb=" O THR F 90 " (cutoff:3.500A) Proline residue: F 96 - end of helix removed outlier: 3.769A pdb=" N ARG F 104 " --> pdb=" O TYR F 100 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE F 106 " --> pdb=" O LEU F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 159 removed outlier: 3.661A pdb=" N SER F 135 " --> pdb=" O CYS F 131 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TRP F 136 " --> pdb=" O GLN F 132 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE F 141 " --> pdb=" O CYS F 137 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE F 147 " --> pdb=" O LEU F 143 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL F 154 " --> pdb=" O LEU F 150 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 396 through 399 Processing sheet with id=AA2, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AA3, first strand: chain 'A' and resid 490 through 491 Processing sheet with id=AA4, first strand: chain 'A' and resid 497 through 498 removed outlier: 3.655A pdb=" N LEU A 498 " --> pdb=" O LYS A 730 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 682 through 683 removed outlier: 7.525A pdb=" N VAL A 683 " --> pdb=" O TYR A 647 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N THR A 649 " --> pdb=" O VAL A 683 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 10.932A pdb=" N LEU A 650 " --> pdb=" O GLU A 705 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 862 through 864 Processing sheet with id=AA7, first strand: chain 'A' and resid 876 through 878 removed outlier: 3.658A pdb=" N TYR A 998 " --> pdb=" O GLY A 867 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 395 through 397 removed outlier: 6.715A pdb=" N VAL B 395 " --> pdb=" O LYS B 441 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AB1, first strand: chain 'B' and resid 475 through 480 removed outlier: 7.477A pdb=" N ALA B 477 " --> pdb=" O ALA B 735 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ALA B 735 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LEU B 479 " --> pdb=" O GLY B 733 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 702 through 705 removed outlier: 4.009A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 396 through 399 Processing sheet with id=AB4, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AB5, first strand: chain 'C' and resid 490 through 491 Processing sheet with id=AB6, first strand: chain 'C' and resid 497 through 498 removed outlier: 3.655A pdb=" N LEU C 498 " --> pdb=" O LYS C 730 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 682 through 683 removed outlier: 7.525A pdb=" N VAL C 683 " --> pdb=" O TYR C 647 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N THR C 649 " --> pdb=" O VAL C 683 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 10.932A pdb=" N LEU C 650 " --> pdb=" O GLU C 705 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 862 through 864 Processing sheet with id=AB9, first strand: chain 'C' and resid 876 through 878 removed outlier: 3.658A pdb=" N TYR C 998 " --> pdb=" O GLY C 867 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 395 through 397 removed outlier: 6.715A pdb=" N VAL D 395 " --> pdb=" O LYS D 441 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AC3, first strand: chain 'D' and resid 475 through 480 removed outlier: 7.476A pdb=" N ALA D 477 " --> pdb=" O ALA D 735 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ALA D 735 " --> pdb=" O ALA D 477 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LEU D 479 " --> pdb=" O GLY D 733 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 702 through 705 removed outlier: 4.009A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) 890 hydrogen bonds defined for protein. 2604 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: 5.00 Time building geometry restraints manager: 4.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 4949 1.33 - 1.45: 3583 1.45 - 1.57: 9651 1.57 - 1.69: 0 1.69 - 1.81: 210 Bond restraints: 18393 Sorted by residual: bond pdb=" C VAL F 69 " pdb=" N PRO F 70 " ideal model delta sigma weight residual 1.335 1.396 -0.061 1.28e-02 6.10e+03 2.30e+01 bond pdb=" C ALA C 735 " pdb=" N THR C 736 " ideal model delta sigma weight residual 1.331 1.227 0.104 2.83e-02 1.25e+03 1.35e+01 bond pdb=" C ALA A 735 " pdb=" N THR A 736 " ideal model delta sigma weight residual 1.331 1.228 0.103 2.83e-02 1.25e+03 1.33e+01 bond pdb=" C ASP D 519 " pdb=" N PRO D 520 " ideal model delta sigma weight residual 1.335 1.374 -0.039 1.19e-02 7.06e+03 1.07e+01 bond pdb=" C ASP B 519 " pdb=" N PRO B 520 " ideal model delta sigma weight residual 1.335 1.373 -0.039 1.19e-02 7.06e+03 1.06e+01 ... (remaining 18388 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 23805 2.74 - 5.49: 896 5.49 - 8.23: 120 8.23 - 10.97: 23 10.97 - 13.71: 6 Bond angle restraints: 24850 Sorted by residual: angle pdb=" C GLU A 678 " pdb=" N PRO A 679 " pdb=" CA PRO A 679 " ideal model delta sigma weight residual 119.84 109.06 10.78 1.25e+00 6.40e-01 7.43e+01 angle pdb=" C GLU C 678 " pdb=" N PRO C 679 " pdb=" CA PRO C 679 " ideal model delta sigma weight residual 119.84 109.10 10.74 1.25e+00 6.40e-01 7.39e+01 angle pdb=" C TYR F 117 " pdb=" N ASP F 118 " pdb=" CA ASP F 118 " ideal model delta sigma weight residual 122.74 134.31 -11.57 1.44e+00 4.82e-01 6.46e+01 angle pdb=" C TYR E 117 " pdb=" N ASP E 118 " pdb=" CA ASP E 118 " ideal model delta sigma weight residual 121.54 134.01 -12.47 1.91e+00 2.74e-01 4.26e+01 angle pdb=" C MET F 116 " pdb=" N TYR F 117 " pdb=" CA TYR F 117 " ideal model delta sigma weight residual 120.82 129.88 -9.06 1.47e+00 4.63e-01 3.80e+01 ... (remaining 24845 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.17: 9916 14.17 - 28.35: 670 28.35 - 42.52: 198 42.52 - 56.70: 21 56.70 - 70.87: 4 Dihedral angle restraints: 10809 sinusoidal: 4233 harmonic: 6576 Sorted by residual: dihedral pdb=" CA GLU C 413 " pdb=" C GLU C 413 " pdb=" N MET C 414 " pdb=" CA MET C 414 " ideal model delta harmonic sigma weight residual -180.00 -132.74 -47.26 0 5.00e+00 4.00e-02 8.93e+01 dihedral pdb=" CA GLU A 413 " pdb=" C GLU A 413 " pdb=" N MET A 414 " pdb=" CA MET A 414 " ideal model delta harmonic sigma weight residual -180.00 -132.76 -47.24 0 5.00e+00 4.00e-02 8.93e+01 dihedral pdb=" CA GLU C 678 " pdb=" C GLU C 678 " pdb=" N PRO C 679 " pdb=" CA PRO C 679 " ideal model delta harmonic sigma weight residual 180.00 133.16 46.84 0 5.00e+00 4.00e-02 8.78e+01 ... (remaining 10806 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 2355 0.076 - 0.152: 367 0.152 - 0.228: 63 0.228 - 0.304: 5 0.304 - 0.380: 4 Chirality restraints: 2794 Sorted by residual: chirality pdb=" CB ILE B 664 " pdb=" CA ILE B 664 " pdb=" CG1 ILE B 664 " pdb=" CG2 ILE B 664 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.61e+00 chirality pdb=" CB ILE D 664 " pdb=" CA ILE D 664 " pdb=" CG1 ILE D 664 " pdb=" CG2 ILE D 664 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.59e+00 chirality pdb=" CB ILE C 474 " pdb=" CA ILE C 474 " pdb=" CG1 ILE C 474 " pdb=" CG2 ILE C 474 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.43e+00 ... (remaining 2791 not shown) Planarity restraints: 3042 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 678 " 0.056 5.00e-02 4.00e+02 8.42e-02 1.13e+01 pdb=" N PRO A 679 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 679 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 679 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 678 " -0.055 5.00e-02 4.00e+02 8.41e-02 1.13e+01 pdb=" N PRO C 679 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO C 679 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 679 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG E 108 " -0.014 2.00e-02 2.50e+03 2.79e-02 7.78e+00 pdb=" C ARG E 108 " 0.048 2.00e-02 2.50e+03 pdb=" O ARG E 108 " -0.018 2.00e-02 2.50e+03 pdb=" N PRO E 109 " -0.016 2.00e-02 2.50e+03 ... (remaining 3039 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3850 2.77 - 3.30: 16208 3.30 - 3.84: 28153 3.84 - 4.37: 34120 4.37 - 4.90: 59144 Nonbonded interactions: 141475 Sorted by model distance: nonbonded pdb=" O LEU B 639 " pdb=" OH TYR B 647 " model vdw 2.238 3.040 nonbonded pdb=" O LEU D 639 " pdb=" OH TYR D 647 " model vdw 2.239 3.040 nonbonded pdb=" O ALA C 959 " pdb=" OG SER C 962 " model vdw 2.274 3.040 nonbonded pdb=" O ALA A 959 " pdb=" OG SER A 962 " model vdw 2.274 3.040 nonbonded pdb=" OE1 GLU B 402 " pdb=" OH TYR B 450 " model vdw 2.283 3.040 ... (remaining 141470 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 392 through 1035) selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 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: 0.690 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 36.840 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 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 : 0.009 0.104 18399 Z= 0.390 Angle : 1.233 13.714 24862 Z= 0.719 Chirality : 0.060 0.380 2794 Planarity : 0.007 0.084 3042 Dihedral : 10.768 70.869 6587 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.49 % Favored : 91.15 % Rotamer: Outliers : 0.36 % Allowed : 5.68 % Favored : 93.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.00 % Twisted Proline : 6.06 % Twisted General : 0.50 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.98 (0.12), residues: 2238 helix: -3.73 (0.08), residues: 1282 sheet: -3.97 (0.29), residues: 196 loop : -3.99 (0.17), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP A 861 HIS 0.014 0.002 HIS F 107 PHE 0.034 0.003 PHE B 667 TYR 0.031 0.003 TYR D 702 ARG 0.015 0.001 ARG D 628 Details of bonding type rmsd hydrogen bonds : bond 0.30924 ( 890) hydrogen bonds : angle 10.40833 ( 2604) SS BOND : bond 0.01272 ( 6) SS BOND : angle 1.30098 ( 12) covalent geometry : bond 0.00934 (18393) covalent geometry : angle 1.23269 (24850) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 391 time to evaluate : 1.890 Fit side-chains revert: symmetry clash REVERT: A 431 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7554 (mm-30) REVERT: A 592 SER cc_start: 0.8488 (t) cc_final: 0.7956 (p) REVERT: A 744 THR cc_start: 0.8906 (m) cc_final: 0.8583 (p) REVERT: A 907 MET cc_start: 0.5273 (ttt) cc_final: 0.4293 (mpp) REVERT: A 1002 LYS cc_start: 0.6778 (ttmp) cc_final: 0.6259 (mmtt) REVERT: B 393 LYS cc_start: 0.7086 (ttpt) cc_final: 0.6514 (tptp) REVERT: C 431 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7529 (mm-30) REVERT: C 651 ASP cc_start: 0.7324 (t70) cc_final: 0.7118 (t70) REVERT: C 695 LYS cc_start: 0.7982 (pptt) cc_final: 0.7552 (pttm) REVERT: C 729 SER cc_start: 0.8937 (t) cc_final: 0.8673 (p) REVERT: C 863 TYR cc_start: 0.5836 (m-10) cc_final: 0.5416 (m-80) REVERT: C 1005 TRP cc_start: 0.6828 (p-90) cc_final: 0.4064 (m-90) REVERT: C 1029 MET cc_start: 0.6407 (mmt) cc_final: 0.5655 (mmt) REVERT: D 393 LYS cc_start: 0.7015 (ttpt) cc_final: 0.6316 (tptp) REVERT: D 661 ARG cc_start: 0.8057 (ptp-110) cc_final: 0.7799 (ptm160) REVERT: D 761 LYS cc_start: 0.8328 (tmmt) cc_final: 0.8105 (tttm) REVERT: F 139 LEU cc_start: 0.5993 (tp) cc_final: 0.5248 (pp) outliers start: 7 outliers final: 1 residues processed: 398 average time/residue: 0.3124 time to fit residues: 184.0558 Evaluate side-chains 272 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 271 time to evaluate : 1.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 69 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 190 optimal weight: 0.9990 chunk 171 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 177 optimal weight: 0.8980 chunk 68 optimal weight: 0.5980 chunk 107 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 chunk 205 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS A 575 ASN A 747 ASN A 883 HIS A 990 ASN B 412 HIS C 412 HIS C 575 ASN C 586 GLN C 587 GLN C 747 ASN C 883 HIS C 990 ASN C1000 ASN ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 HIS ** E 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 ASN F 75 HIS F 107 HIS F 124 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.193923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.128996 restraints weight = 20091.698| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.81 r_work: 0.3159 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18399 Z= 0.156 Angle : 0.689 11.229 24862 Z= 0.363 Chirality : 0.042 0.191 2794 Planarity : 0.006 0.080 3042 Dihedral : 6.081 55.504 2468 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.37 % Favored : 92.45 % Rotamer: Outliers : 2.22 % Allowed : 10.01 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (0.15), residues: 2238 helix: -1.16 (0.13), residues: 1286 sheet: -3.53 (0.33), residues: 172 loop : -3.58 (0.18), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 766 HIS 0.006 0.001 HIS E 27 PHE 0.032 0.002 PHE E 31 TYR 0.018 0.001 TYR B 702 ARG 0.004 0.000 ARG C 545 Details of bonding type rmsd hydrogen bonds : bond 0.05110 ( 890) hydrogen bonds : angle 4.57917 ( 2604) SS BOND : bond 0.01279 ( 6) SS BOND : angle 1.68508 ( 12) covalent geometry : bond 0.00351 (18393) covalent geometry : angle 0.68845 (24850) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 297 time to evaluate : 2.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 MET cc_start: 0.7377 (tmm) cc_final: 0.7060 (tmm) REVERT: A 431 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8139 (mm-30) REVERT: A 467 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.7968 (pt) REVERT: A 637 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8098 (mt-10) REVERT: A 669 LYS cc_start: 0.7510 (mtmt) cc_final: 0.6940 (tttt) REVERT: A 907 MET cc_start: 0.4954 (ttt) cc_final: 0.4182 (mpp) REVERT: A 1002 LYS cc_start: 0.6510 (ttmp) cc_final: 0.6066 (mmtt) REVERT: B 393 LYS cc_start: 0.6929 (ttpt) cc_final: 0.5827 (tptp) REVERT: B 397 VAL cc_start: 0.8181 (OUTLIER) cc_final: 0.7965 (m) REVERT: B 695 LYS cc_start: 0.7616 (mtpm) cc_final: 0.7337 (mtmt) REVERT: B 708 MET cc_start: 0.8144 (tpt) cc_final: 0.7812 (mmt) REVERT: B 719 ASP cc_start: 0.7603 (t0) cc_final: 0.7359 (t0) REVERT: C 431 GLU cc_start: 0.8392 (mm-30) cc_final: 0.7928 (mm-30) REVERT: C 467 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8389 (pt) REVERT: C 637 GLU cc_start: 0.8321 (mt-10) cc_final: 0.8041 (mt-10) REVERT: C 651 ASP cc_start: 0.7603 (t70) cc_final: 0.7389 (t70) REVERT: C 688 GLU cc_start: 0.8263 (tt0) cc_final: 0.7738 (pt0) REVERT: C 729 SER cc_start: 0.9041 (t) cc_final: 0.8793 (p) REVERT: C 863 TYR cc_start: 0.5565 (m-10) cc_final: 0.4989 (m-80) REVERT: D 393 LYS cc_start: 0.6804 (ttpt) cc_final: 0.5760 (tptp) REVERT: D 397 VAL cc_start: 0.8067 (OUTLIER) cc_final: 0.7827 (m) REVERT: D 527 MET cc_start: 0.8236 (mmt) cc_final: 0.7885 (mmt) REVERT: D 545 ARG cc_start: 0.7898 (ttm-80) cc_final: 0.7454 (tpp80) REVERT: D 661 ARG cc_start: 0.7689 (ptp-110) cc_final: 0.7419 (ptm160) REVERT: D 719 ASP cc_start: 0.7716 (t0) cc_final: 0.7452 (t0) REVERT: D 813 GLU cc_start: 0.7794 (tt0) cc_final: 0.7577 (tt0) REVERT: E 102 LEU cc_start: 0.6843 (pp) cc_final: 0.6636 (pp) REVERT: F 139 LEU cc_start: 0.5966 (tp) cc_final: 0.4681 (pp) outliers start: 43 outliers final: 16 residues processed: 332 average time/residue: 0.2866 time to fit residues: 147.5912 Evaluate side-chains 280 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 260 time to evaluate : 1.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 527 MET Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 1013 SER Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 519 ASP Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 115 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 127 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 81 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 190 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 435 HIS B 756 GLN C 586 GLN ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.206595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.153415 restraints weight = 19899.320| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 4.82 r_work: 0.3253 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18399 Z= 0.182 Angle : 0.650 8.334 24862 Z= 0.338 Chirality : 0.042 0.191 2794 Planarity : 0.005 0.062 3042 Dihedral : 5.690 53.350 2468 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.36 % Favored : 91.47 % Rotamer: Outliers : 3.04 % Allowed : 10.78 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.00 % Twisted Proline : 6.06 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.17), residues: 2238 helix: 0.13 (0.14), residues: 1286 sheet: -3.35 (0.33), residues: 174 loop : -3.33 (0.20), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 766 HIS 0.007 0.002 HIS E 27 PHE 0.023 0.002 PHE E 141 TYR 0.025 0.001 TYR F 100 ARG 0.007 0.001 ARG D 628 Details of bonding type rmsd hydrogen bonds : bond 0.04262 ( 890) hydrogen bonds : angle 4.14514 ( 2604) SS BOND : bond 0.00779 ( 6) SS BOND : angle 1.38600 ( 12) covalent geometry : bond 0.00431 (18393) covalent geometry : angle 0.64901 (24850) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 295 time to evaluate : 2.015 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 414 MET cc_start: 0.7372 (tmm) cc_final: 0.7077 (tmm) REVERT: A 431 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8319 (mm-30) REVERT: A 434 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.8102 (tttm) REVERT: A 467 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8327 (pt) REVERT: A 669 LYS cc_start: 0.7587 (mtmt) cc_final: 0.7073 (tttt) REVERT: A 682 PHE cc_start: 0.8578 (m-10) cc_final: 0.8308 (m-80) REVERT: A 716 LYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7789 (tmtt) REVERT: A 863 TYR cc_start: 0.5586 (m-10) cc_final: 0.5084 (m-80) REVERT: A 907 MET cc_start: 0.4906 (ttt) cc_final: 0.4126 (mpp) REVERT: A 1002 LYS cc_start: 0.6381 (ttmp) cc_final: 0.6114 (mmtt) REVERT: A 1029 MET cc_start: 0.7486 (mmm) cc_final: 0.6869 (mtp) REVERT: B 393 LYS cc_start: 0.6929 (ttpt) cc_final: 0.5955 (tptp) REVERT: B 545 ARG cc_start: 0.6779 (ttm-80) cc_final: 0.6578 (ttt180) REVERT: B 695 LYS cc_start: 0.7727 (mtpm) cc_final: 0.7451 (mtmt) REVERT: B 719 ASP cc_start: 0.7887 (t0) cc_final: 0.7609 (t0) REVERT: C 467 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8360 (pt) REVERT: C 545 ARG cc_start: 0.7875 (mmm160) cc_final: 0.7013 (ttt-90) REVERT: C 630 VAL cc_start: 0.8626 (p) cc_final: 0.8258 (m) REVERT: C 651 ASP cc_start: 0.7790 (t70) cc_final: 0.7454 (t70) REVERT: C 729 SER cc_start: 0.9029 (t) cc_final: 0.8796 (p) REVERT: C 863 TYR cc_start: 0.5613 (m-10) cc_final: 0.5243 (m-80) REVERT: D 393 LYS cc_start: 0.6952 (ttpt) cc_final: 0.5999 (tptp) REVERT: D 397 VAL cc_start: 0.8201 (OUTLIER) cc_final: 0.7901 (m) REVERT: D 508 GLN cc_start: 0.7287 (mp10) cc_final: 0.6333 (mp10) REVERT: D 527 MET cc_start: 0.8442 (mmt) cc_final: 0.8036 (mmt) REVERT: D 545 ARG cc_start: 0.7891 (ttm-80) cc_final: 0.7451 (tpp80) REVERT: D 661 ARG cc_start: 0.7791 (ptp-110) cc_final: 0.7400 (ptm160) REVERT: D 719 ASP cc_start: 0.7929 (t0) cc_final: 0.7568 (t0) REVERT: D 813 GLU cc_start: 0.8023 (tt0) cc_final: 0.7756 (tt0) outliers start: 59 outliers final: 28 residues processed: 338 average time/residue: 0.2786 time to fit residues: 145.0952 Evaluate side-chains 292 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 259 time to evaluate : 1.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 527 MET Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 716 LYS Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 411 ASN Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 596 LEU Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 490 ASP Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain F residue 4 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 144 optimal weight: 9.9990 chunk 137 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 55 optimal weight: 0.0770 chunk 152 optimal weight: 2.9990 chunk 146 optimal weight: 20.0000 chunk 65 optimal weight: 0.7980 chunk 145 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 756 GLN C 435 HIS C 872 GLN D 587 GLN E 107 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.204157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.162914 restraints weight = 19582.778| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 3.00 r_work: 0.3285 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18399 Z= 0.160 Angle : 0.623 10.242 24862 Z= 0.321 Chirality : 0.042 0.191 2794 Planarity : 0.004 0.066 3042 Dihedral : 5.453 50.167 2468 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.28 % Favored : 92.54 % Rotamer: Outliers : 3.41 % Allowed : 12.18 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.00 % Twisted Proline : 6.06 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.18), residues: 2238 helix: 0.68 (0.14), residues: 1304 sheet: -2.68 (0.39), residues: 142 loop : -3.21 (0.20), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 766 HIS 0.009 0.002 HIS E 27 PHE 0.025 0.002 PHE F 78 TYR 0.026 0.001 TYR F 100 ARG 0.006 0.000 ARG C1031 Details of bonding type rmsd hydrogen bonds : bond 0.03791 ( 890) hydrogen bonds : angle 3.95246 ( 2604) SS BOND : bond 0.00486 ( 6) SS BOND : angle 1.07449 ( 12) covalent geometry : bond 0.00385 (18393) covalent geometry : angle 0.62281 (24850) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 273 time to evaluate : 2.053 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 467 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8261 (pt) REVERT: A 669 LYS cc_start: 0.7585 (mtmt) cc_final: 0.7156 (tttt) REVERT: A 716 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7818 (tmtt) REVERT: A 863 TYR cc_start: 0.5730 (m-10) cc_final: 0.5161 (m-80) REVERT: A 907 MET cc_start: 0.5060 (ttt) cc_final: 0.4217 (mpp) REVERT: A 1029 MET cc_start: 0.7316 (OUTLIER) cc_final: 0.6856 (mtp) REVERT: B 393 LYS cc_start: 0.7176 (ttpt) cc_final: 0.6386 (tptp) REVERT: B 695 LYS cc_start: 0.7712 (mtpm) cc_final: 0.7474 (mtmt) REVERT: B 719 ASP cc_start: 0.7865 (t0) cc_final: 0.7535 (t0) REVERT: C 434 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8268 (tttm) REVERT: C 467 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8309 (pt) REVERT: C 641 LYS cc_start: 0.7046 (OUTLIER) cc_final: 0.6482 (mmtp) REVERT: C 642 GLN cc_start: 0.6543 (OUTLIER) cc_final: 0.5555 (mp10) REVERT: C 651 ASP cc_start: 0.7781 (t70) cc_final: 0.7394 (t70) REVERT: C 669 LYS cc_start: 0.7570 (mtmt) cc_final: 0.7106 (tttt) REVERT: C 688 GLU cc_start: 0.7941 (tt0) cc_final: 0.7478 (pt0) REVERT: C 729 SER cc_start: 0.8997 (t) cc_final: 0.8738 (p) REVERT: C 863 TYR cc_start: 0.5906 (m-10) cc_final: 0.5460 (m-80) REVERT: C 1029 MET cc_start: 0.5984 (mmt) cc_final: 0.5421 (mmt) REVERT: D 393 LYS cc_start: 0.6977 (ttpt) cc_final: 0.5969 (tptp) REVERT: D 397 VAL cc_start: 0.8096 (OUTLIER) cc_final: 0.7788 (m) REVERT: D 527 MET cc_start: 0.8340 (mmt) cc_final: 0.8020 (mmt) REVERT: D 545 ARG cc_start: 0.7781 (ttm-80) cc_final: 0.7358 (tpp80) REVERT: D 661 ARG cc_start: 0.7814 (ptp-110) cc_final: 0.7418 (ptm160) REVERT: D 719 ASP cc_start: 0.7881 (t0) cc_final: 0.7543 (t0) REVERT: D 813 GLU cc_start: 0.8136 (tt0) cc_final: 0.7919 (tt0) REVERT: E 127 ILE cc_start: 0.6789 (OUTLIER) cc_final: 0.6522 (tp) REVERT: E 128 LEU cc_start: 0.4767 (tp) cc_final: 0.4344 (pp) outliers start: 66 outliers final: 39 residues processed: 321 average time/residue: 0.2777 time to fit residues: 137.5153 Evaluate side-chains 300 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 252 time to evaluate : 1.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 527 MET Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 641 LYS Chi-restraints excluded: chain A residue 716 LYS Chi-restraints excluded: chain A residue 718 CYS Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 411 ASN Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 647 TYR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 434 LYS Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 596 LEU Chi-restraints excluded: chain C residue 641 LYS Chi-restraints excluded: chain C residue 642 GLN Chi-restraints excluded: chain C residue 718 CYS Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 1013 SER Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 411 ASN Chi-restraints excluded: chain D residue 490 ASP Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 120 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 224 optimal weight: 0.9990 chunk 192 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 168 optimal weight: 0.5980 chunk 58 optimal weight: 4.9990 chunk 146 optimal weight: 0.7980 chunk 212 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 191 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.205801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.164142 restraints weight = 19820.587| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 3.12 r_work: 0.3299 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18399 Z= 0.129 Angle : 0.587 10.211 24862 Z= 0.302 Chirality : 0.040 0.179 2794 Planarity : 0.004 0.059 3042 Dihedral : 5.219 49.217 2468 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.46 % Favored : 92.36 % Rotamer: Outliers : 3.30 % Allowed : 13.26 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.18), residues: 2238 helix: 1.07 (0.15), residues: 1304 sheet: -2.35 (0.41), residues: 138 loop : -3.05 (0.20), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 766 HIS 0.010 0.001 HIS E 27 PHE 0.017 0.001 PHE E 141 TYR 0.026 0.001 TYR F 100 ARG 0.006 0.000 ARG C1031 Details of bonding type rmsd hydrogen bonds : bond 0.03505 ( 890) hydrogen bonds : angle 3.76373 ( 2604) SS BOND : bond 0.00650 ( 6) SS BOND : angle 0.99180 ( 12) covalent geometry : bond 0.00297 (18393) covalent geometry : angle 0.58660 (24850) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 280 time to evaluate : 2.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 434 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8232 (tttm) REVERT: A 467 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8272 (pt) REVERT: A 592 SER cc_start: 0.8980 (t) cc_final: 0.8703 (p) REVERT: A 669 LYS cc_start: 0.7488 (mtmt) cc_final: 0.7046 (tttt) REVERT: A 716 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7912 (tmtt) REVERT: A 734 ILE cc_start: 0.8979 (OUTLIER) cc_final: 0.8528 (mm) REVERT: A 863 TYR cc_start: 0.5745 (m-10) cc_final: 0.5151 (m-80) REVERT: A 907 MET cc_start: 0.5009 (ttt) cc_final: 0.4201 (mpp) REVERT: A 1029 MET cc_start: 0.7140 (OUTLIER) cc_final: 0.6732 (mtm) REVERT: B 393 LYS cc_start: 0.6840 (ttpt) cc_final: 0.6135 (tptp) REVERT: B 527 MET cc_start: 0.8213 (mmt) cc_final: 0.7878 (mmt) REVERT: B 719 ASP cc_start: 0.7819 (t0) cc_final: 0.7474 (t0) REVERT: C 434 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8389 (tttm) REVERT: C 467 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8310 (pt) REVERT: C 630 VAL cc_start: 0.8551 (p) cc_final: 0.8266 (m) REVERT: C 642 GLN cc_start: 0.6459 (OUTLIER) cc_final: 0.5773 (mp10) REVERT: C 651 ASP cc_start: 0.7722 (t70) cc_final: 0.7296 (t70) REVERT: C 669 LYS cc_start: 0.7508 (mtmt) cc_final: 0.7079 (tttt) REVERT: C 729 SER cc_start: 0.8969 (t) cc_final: 0.8714 (p) REVERT: C 734 ILE cc_start: 0.8961 (OUTLIER) cc_final: 0.8541 (mm) REVERT: C 863 TYR cc_start: 0.6025 (m-10) cc_final: 0.5543 (m-80) REVERT: C 901 PHE cc_start: 0.6078 (m-80) cc_final: 0.5479 (m-80) REVERT: C 1029 MET cc_start: 0.6052 (mmt) cc_final: 0.5380 (mmt) REVERT: D 393 LYS cc_start: 0.6954 (ttpt) cc_final: 0.5983 (tptp) REVERT: D 527 MET cc_start: 0.8378 (mmt) cc_final: 0.8087 (mmt) REVERT: D 545 ARG cc_start: 0.7811 (ttm-80) cc_final: 0.7425 (tpp80) REVERT: D 661 ARG cc_start: 0.7725 (ptp-110) cc_final: 0.7328 (ptm160) REVERT: D 678 GLU cc_start: 0.6157 (mm-30) cc_final: 0.5818 (mm-30) REVERT: D 719 ASP cc_start: 0.8009 (t0) cc_final: 0.7629 (t0) REVERT: D 813 GLU cc_start: 0.8178 (tt0) cc_final: 0.7978 (tt0) REVERT: E 100 TYR cc_start: 0.7335 (t80) cc_final: 0.7103 (t80) REVERT: E 127 ILE cc_start: 0.6663 (OUTLIER) cc_final: 0.6398 (tp) REVERT: E 128 LEU cc_start: 0.4490 (tp) cc_final: 0.3876 (pp) outliers start: 64 outliers final: 42 residues processed: 324 average time/residue: 0.2916 time to fit residues: 145.8734 Evaluate side-chains 314 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 262 time to evaluate : 2.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 716 LYS Chi-restraints excluded: chain A residue 718 CYS Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain B residue 411 ASN Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 647 TYR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 434 LYS Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 596 LEU Chi-restraints excluded: chain C residue 642 GLN Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 718 CYS Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 1013 SER Chi-restraints excluded: chain C residue 1023 MET Chi-restraints excluded: chain C residue 1026 TYR Chi-restraints excluded: chain D residue 411 ASN Chi-restraints excluded: chain D residue 490 ASP Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 792 VAL Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 116 MET Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 120 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 107 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 170 optimal weight: 2.9990 chunk 207 optimal weight: 0.2980 chunk 166 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 196 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 180 optimal weight: 0.1980 chunk 158 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4312 r_free = 0.4312 target = 0.209769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.156710 restraints weight = 20132.148| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 4.96 r_work: 0.3321 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18399 Z= 0.119 Angle : 0.571 7.932 24862 Z= 0.294 Chirality : 0.040 0.178 2794 Planarity : 0.004 0.064 3042 Dihedral : 5.066 44.366 2468 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.66 % Favored : 93.16 % Rotamer: Outliers : 3.25 % Allowed : 14.04 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.18), residues: 2238 helix: 1.30 (0.15), residues: 1298 sheet: -2.16 (0.41), residues: 138 loop : -2.94 (0.20), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 766 HIS 0.010 0.001 HIS E 27 PHE 0.033 0.001 PHE F 78 TYR 0.025 0.001 TYR F 100 ARG 0.003 0.000 ARG D 628 Details of bonding type rmsd hydrogen bonds : bond 0.03362 ( 890) hydrogen bonds : angle 3.67022 ( 2604) SS BOND : bond 0.00307 ( 6) SS BOND : angle 0.85780 ( 12) covalent geometry : bond 0.00272 (18393) covalent geometry : angle 0.57098 (24850) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 281 time to evaluate : 1.918 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 434 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8327 (tttm) REVERT: A 467 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8210 (pt) REVERT: A 592 SER cc_start: 0.8934 (t) cc_final: 0.8657 (p) REVERT: A 669 LYS cc_start: 0.7371 (mtmt) cc_final: 0.6961 (tttt) REVERT: A 715 ARG cc_start: 0.7025 (OUTLIER) cc_final: 0.6615 (mmp-170) REVERT: A 716 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7940 (tmtt) REVERT: A 734 ILE cc_start: 0.8943 (OUTLIER) cc_final: 0.8495 (mm) REVERT: A 863 TYR cc_start: 0.5627 (m-10) cc_final: 0.5018 (m-80) REVERT: A 1026 TYR cc_start: 0.7358 (OUTLIER) cc_final: 0.7138 (m-10) REVERT: A 1029 MET cc_start: 0.6867 (OUTLIER) cc_final: 0.5602 (mmm) REVERT: B 393 LYS cc_start: 0.6855 (ttpt) cc_final: 0.5985 (tptp) REVERT: B 527 MET cc_start: 0.8238 (mmt) cc_final: 0.7945 (mmt) REVERT: B 678 GLU cc_start: 0.6313 (mm-30) cc_final: 0.6085 (mm-30) REVERT: B 719 ASP cc_start: 0.7849 (t0) cc_final: 0.7506 (t0) REVERT: C 434 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8341 (tttm) REVERT: C 467 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8231 (pt) REVERT: C 630 VAL cc_start: 0.8488 (p) cc_final: 0.8183 (m) REVERT: C 642 GLN cc_start: 0.6560 (OUTLIER) cc_final: 0.5877 (mp10) REVERT: C 651 ASP cc_start: 0.7617 (t70) cc_final: 0.7252 (p0) REVERT: C 734 ILE cc_start: 0.8932 (OUTLIER) cc_final: 0.8511 (mm) REVERT: C 901 PHE cc_start: 0.6009 (m-80) cc_final: 0.5413 (m-80) REVERT: C 1029 MET cc_start: 0.6037 (mmt) cc_final: 0.5351 (mmt) REVERT: D 393 LYS cc_start: 0.6908 (ttpt) cc_final: 0.5795 (tptp) REVERT: D 527 MET cc_start: 0.8374 (mmt) cc_final: 0.8051 (mmt) REVERT: D 545 ARG cc_start: 0.7745 (ttm-80) cc_final: 0.7390 (tpp80) REVERT: D 661 ARG cc_start: 0.7704 (ptp-110) cc_final: 0.7332 (ptm160) REVERT: D 678 GLU cc_start: 0.6030 (mm-30) cc_final: 0.5704 (mm-30) REVERT: D 719 ASP cc_start: 0.7902 (t0) cc_final: 0.7533 (t0) REVERT: E 100 TYR cc_start: 0.7436 (t80) cc_final: 0.7176 (t80) REVERT: E 127 ILE cc_start: 0.6636 (OUTLIER) cc_final: 0.6340 (tp) REVERT: E 128 LEU cc_start: 0.4662 (tp) cc_final: 0.3922 (pp) REVERT: F 27 HIS cc_start: 0.7500 (OUTLIER) cc_final: 0.7031 (p-80) REVERT: F 143 LEU cc_start: 0.8017 (mm) cc_final: 0.7787 (mm) outliers start: 63 outliers final: 36 residues processed: 322 average time/residue: 0.2808 time to fit residues: 138.8557 Evaluate side-chains 321 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 272 time to evaluate : 1.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 715 ARG Chi-restraints excluded: chain A residue 716 LYS Chi-restraints excluded: chain A residue 718 CYS Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 1026 TYR Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 411 ASN Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 647 TYR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 434 LYS Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 596 LEU Chi-restraints excluded: chain C residue 642 GLN Chi-restraints excluded: chain C residue 718 CYS Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 1023 MET Chi-restraints excluded: chain C residue 1026 TYR Chi-restraints excluded: chain D residue 411 ASN Chi-restraints excluded: chain D residue 490 ASP Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 792 VAL Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain F residue 120 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 3 optimal weight: 1.9990 chunk 103 optimal weight: 0.0570 chunk 63 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 147 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 chunk 220 optimal weight: 20.0000 chunk 208 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 191 optimal weight: 0.8980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 642 GLN ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.212940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.164257 restraints weight = 20297.903| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 3.65 r_work: 0.3306 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18399 Z= 0.121 Angle : 0.574 7.871 24862 Z= 0.294 Chirality : 0.040 0.179 2794 Planarity : 0.004 0.061 3042 Dihedral : 4.987 51.343 2468 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.93 % Favored : 92.98 % Rotamer: Outliers : 2.99 % Allowed : 14.34 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.18), residues: 2238 helix: 1.43 (0.15), residues: 1298 sheet: -2.09 (0.41), residues: 138 loop : -2.87 (0.20), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 88 HIS 0.010 0.001 HIS E 27 PHE 0.017 0.001 PHE E 78 TYR 0.024 0.001 TYR F 100 ARG 0.002 0.000 ARG C1031 Details of bonding type rmsd hydrogen bonds : bond 0.03312 ( 890) hydrogen bonds : angle 3.61736 ( 2604) SS BOND : bond 0.00275 ( 6) SS BOND : angle 0.79455 ( 12) covalent geometry : bond 0.00278 (18393) covalent geometry : angle 0.57347 (24850) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 284 time to evaluate : 2.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8319 (tttm) REVERT: A 467 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8219 (pt) REVERT: A 545 ARG cc_start: 0.7555 (ttm-80) cc_final: 0.7288 (tmm-80) REVERT: A 592 SER cc_start: 0.8941 (t) cc_final: 0.8696 (p) REVERT: A 669 LYS cc_start: 0.7365 (mtmt) cc_final: 0.6980 (tttt) REVERT: A 715 ARG cc_start: 0.7101 (OUTLIER) cc_final: 0.6723 (mmp-170) REVERT: A 734 ILE cc_start: 0.8943 (OUTLIER) cc_final: 0.8491 (mm) REVERT: A 863 TYR cc_start: 0.5794 (m-10) cc_final: 0.5114 (m-80) REVERT: A 1026 TYR cc_start: 0.7370 (OUTLIER) cc_final: 0.7135 (m-10) REVERT: B 393 LYS cc_start: 0.6855 (ttpt) cc_final: 0.6590 (ttmt) REVERT: B 527 MET cc_start: 0.8253 (mmt) cc_final: 0.8040 (mmt) REVERT: B 719 ASP cc_start: 0.7817 (t0) cc_final: 0.7473 (t0) REVERT: C 434 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8367 (tttm) REVERT: C 467 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8223 (pt) REVERT: C 630 VAL cc_start: 0.8477 (p) cc_final: 0.8162 (m) REVERT: C 638 ASP cc_start: 0.7802 (m-30) cc_final: 0.6898 (m-30) REVERT: C 641 LYS cc_start: 0.7068 (OUTLIER) cc_final: 0.6464 (mmtp) REVERT: C 642 GLN cc_start: 0.6510 (OUTLIER) cc_final: 0.5798 (mp10) REVERT: C 651 ASP cc_start: 0.7525 (t70) cc_final: 0.7280 (p0) REVERT: C 716 LYS cc_start: 0.7740 (OUTLIER) cc_final: 0.7399 (tptt) REVERT: C 734 ILE cc_start: 0.8938 (OUTLIER) cc_final: 0.8508 (mm) REVERT: C 901 PHE cc_start: 0.6263 (m-80) cc_final: 0.5695 (m-80) REVERT: C 924 MET cc_start: 0.6787 (pmm) cc_final: 0.6113 (ptt) REVERT: C 1029 MET cc_start: 0.6081 (mmt) cc_final: 0.5448 (mmt) REVERT: D 393 LYS cc_start: 0.6909 (ttpt) cc_final: 0.6027 (tptp) REVERT: D 545 ARG cc_start: 0.7652 (ttm-80) cc_final: 0.7357 (tpp80) REVERT: D 661 ARG cc_start: 0.7741 (ptp-110) cc_final: 0.7366 (ptm160) REVERT: D 678 GLU cc_start: 0.6072 (mm-30) cc_final: 0.5824 (mm-30) REVERT: D 719 ASP cc_start: 0.7901 (t0) cc_final: 0.7537 (t0) REVERT: E 127 ILE cc_start: 0.6738 (OUTLIER) cc_final: 0.6495 (tp) REVERT: E 128 LEU cc_start: 0.4424 (tp) cc_final: 0.3795 (pp) REVERT: F 27 HIS cc_start: 0.7471 (OUTLIER) cc_final: 0.6590 (p-80) outliers start: 58 outliers final: 40 residues processed: 324 average time/residue: 0.2933 time to fit residues: 146.3058 Evaluate side-chains 326 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 273 time to evaluate : 2.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 715 ARG Chi-restraints excluded: chain A residue 718 CYS Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 1026 TYR Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 411 ASN Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 647 TYR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 434 LYS Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 596 LEU Chi-restraints excluded: chain C residue 641 LYS Chi-restraints excluded: chain C residue 642 GLN Chi-restraints excluded: chain C residue 716 LYS Chi-restraints excluded: chain C residue 718 CYS Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 1023 MET Chi-restraints excluded: chain C residue 1026 TYR Chi-restraints excluded: chain D residue 411 ASN Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 792 VAL Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 120 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 16 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 131 optimal weight: 0.7980 chunk 220 optimal weight: 20.0000 chunk 40 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 192 optimal weight: 0.9990 chunk 166 optimal weight: 0.7980 chunk 148 optimal weight: 0.8980 chunk 168 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.211794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.164038 restraints weight = 20336.280| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 3.67 r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18399 Z= 0.138 Angle : 0.590 8.322 24862 Z= 0.302 Chirality : 0.041 0.175 2794 Planarity : 0.004 0.066 3042 Dihedral : 4.966 51.881 2468 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.97 % Favored : 92.94 % Rotamer: Outliers : 3.20 % Allowed : 14.60 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.18), residues: 2238 helix: 1.46 (0.15), residues: 1296 sheet: -2.05 (0.41), residues: 138 loop : -2.82 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 88 HIS 0.011 0.001 HIS E 27 PHE 0.029 0.001 PHE F 78 TYR 0.023 0.001 TYR F 100 ARG 0.004 0.000 ARG B 545 Details of bonding type rmsd hydrogen bonds : bond 0.03403 ( 890) hydrogen bonds : angle 3.62706 ( 2604) SS BOND : bond 0.00293 ( 6) SS BOND : angle 0.75005 ( 12) covalent geometry : bond 0.00326 (18393) covalent geometry : angle 0.58953 (24850) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 285 time to evaluate : 2.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7856 (tttm) REVERT: A 467 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8105 (pt) REVERT: A 592 SER cc_start: 0.8790 (t) cc_final: 0.8586 (p) REVERT: A 641 LYS cc_start: 0.7687 (OUTLIER) cc_final: 0.7232 (mmtp) REVERT: A 715 ARG cc_start: 0.6693 (OUTLIER) cc_final: 0.6370 (mmp-170) REVERT: A 734 ILE cc_start: 0.8477 (OUTLIER) cc_final: 0.7983 (mm) REVERT: A 863 TYR cc_start: 0.6595 (m-10) cc_final: 0.6003 (m-80) REVERT: B 393 LYS cc_start: 0.6849 (ttpt) cc_final: 0.6618 (ttmt) REVERT: B 527 MET cc_start: 0.6942 (mmt) cc_final: 0.6682 (mmt) REVERT: B 719 ASP cc_start: 0.7365 (t0) cc_final: 0.7129 (t0) REVERT: C 434 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7893 (tttm) REVERT: C 467 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8093 (pt) REVERT: C 630 VAL cc_start: 0.8607 (p) cc_final: 0.8380 (m) REVERT: C 641 LYS cc_start: 0.7271 (OUTLIER) cc_final: 0.6614 (mmtp) REVERT: C 642 GLN cc_start: 0.6690 (OUTLIER) cc_final: 0.5994 (mp10) REVERT: C 734 ILE cc_start: 0.8428 (OUTLIER) cc_final: 0.7949 (mm) REVERT: C 924 MET cc_start: 0.6577 (pmm) cc_final: 0.5824 (ptt) REVERT: C 1029 MET cc_start: 0.5394 (mmt) cc_final: 0.4675 (mmt) REVERT: D 393 LYS cc_start: 0.6708 (ttpt) cc_final: 0.6480 (ttmt) REVERT: D 661 ARG cc_start: 0.7765 (ptp-110) cc_final: 0.7458 (ptm160) REVERT: D 719 ASP cc_start: 0.7530 (t0) cc_final: 0.7203 (t0) REVERT: F 27 HIS cc_start: 0.6668 (OUTLIER) cc_final: 0.6271 (p-80) outliers start: 62 outliers final: 44 residues processed: 324 average time/residue: 0.2915 time to fit residues: 145.2617 Evaluate side-chains 331 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 276 time to evaluate : 1.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 641 LYS Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 715 ARG Chi-restraints excluded: chain A residue 716 LYS Chi-restraints excluded: chain A residue 718 CYS Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 411 ASN Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 647 TYR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 434 LYS Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 596 LEU Chi-restraints excluded: chain C residue 641 LYS Chi-restraints excluded: chain C residue 642 GLN Chi-restraints excluded: chain C residue 716 LYS Chi-restraints excluded: chain C residue 718 CYS Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 1023 MET Chi-restraints excluded: chain D residue 411 ASN Chi-restraints excluded: chain D residue 490 ASP Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 792 VAL Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 120 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 212 optimal weight: 0.4980 chunk 213 optimal weight: 0.9990 chunk 165 optimal weight: 3.9990 chunk 71 optimal weight: 0.0170 chunk 66 optimal weight: 1.9990 chunk 225 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 147 optimal weight: 8.9990 chunk 200 optimal weight: 9.9990 overall best weight: 0.7020 ------------------------------------------------------------------------------- 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 = 0.4330 r_free = 0.4330 target = 0.212792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.168114 restraints weight = 20460.837| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 3.56 r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.4302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18399 Z= 0.125 Angle : 0.594 10.944 24862 Z= 0.303 Chirality : 0.040 0.174 2794 Planarity : 0.004 0.066 3042 Dihedral : 4.933 53.653 2468 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.06 % Favored : 92.81 % Rotamer: Outliers : 3.20 % Allowed : 15.02 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.18), residues: 2238 helix: 1.58 (0.15), residues: 1290 sheet: -1.98 (0.41), residues: 138 loop : -2.79 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 88 HIS 0.011 0.001 HIS E 27 PHE 0.023 0.001 PHE F 141 TYR 0.023 0.001 TYR F 100 ARG 0.009 0.000 ARG A 545 Details of bonding type rmsd hydrogen bonds : bond 0.03299 ( 890) hydrogen bonds : angle 3.59081 ( 2604) SS BOND : bond 0.00229 ( 6) SS BOND : angle 0.73919 ( 12) covalent geometry : bond 0.00291 (18393) covalent geometry : angle 0.59383 (24850) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 286 time to evaluate : 2.114 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 434 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7967 (tttm) REVERT: A 467 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8032 (pt) REVERT: A 715 ARG cc_start: 0.6804 (OUTLIER) cc_final: 0.6521 (mmp-170) REVERT: A 734 ILE cc_start: 0.8444 (OUTLIER) cc_final: 0.7967 (mm) REVERT: A 863 TYR cc_start: 0.6799 (m-10) cc_final: 0.6235 (m-80) REVERT: B 393 LYS cc_start: 0.6767 (ttpt) cc_final: 0.6530 (ttmt) REVERT: B 719 ASP cc_start: 0.7375 (t0) cc_final: 0.7115 (t0) REVERT: C 434 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7986 (tttm) REVERT: C 467 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8057 (pt) REVERT: C 630 VAL cc_start: 0.8591 (p) cc_final: 0.8347 (m) REVERT: C 641 LYS cc_start: 0.7337 (OUTLIER) cc_final: 0.6668 (mmtp) REVERT: C 642 GLN cc_start: 0.6601 (OUTLIER) cc_final: 0.5901 (mp10) REVERT: C 734 ILE cc_start: 0.8372 (OUTLIER) cc_final: 0.7901 (mm) REVERT: C 924 MET cc_start: 0.6743 (pmm) cc_final: 0.6078 (ptt) REVERT: C 1029 MET cc_start: 0.5170 (mmt) cc_final: 0.4480 (mmt) REVERT: D 393 LYS cc_start: 0.6635 (ttpt) cc_final: 0.6425 (ttmt) REVERT: D 642 GLN cc_start: 0.6910 (mt0) cc_final: 0.6662 (mt0) REVERT: D 661 ARG cc_start: 0.7734 (ptp-110) cc_final: 0.7427 (ptm160) REVERT: D 719 ASP cc_start: 0.7437 (t0) cc_final: 0.7136 (t0) REVERT: E 128 LEU cc_start: 0.4066 (tp) cc_final: 0.3821 (mt) REVERT: F 27 HIS cc_start: 0.6726 (OUTLIER) cc_final: 0.6244 (p-80) REVERT: F 116 MET cc_start: 0.5296 (tpt) cc_final: 0.4525 (tpt) outliers start: 62 outliers final: 43 residues processed: 326 average time/residue: 0.2810 time to fit residues: 142.4133 Evaluate side-chains 327 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 274 time to evaluate : 1.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 715 ARG Chi-restraints excluded: chain A residue 716 LYS Chi-restraints excluded: chain A residue 718 CYS Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 411 ASN Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 647 TYR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 434 LYS Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 596 LEU Chi-restraints excluded: chain C residue 641 LYS Chi-restraints excluded: chain C residue 642 GLN Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 716 LYS Chi-restraints excluded: chain C residue 718 CYS Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 1015 LEU Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 411 ASN Chi-restraints excluded: chain D residue 490 ASP Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 792 VAL Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 120 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 140 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 167 optimal weight: 0.4980 chunk 170 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 165 optimal weight: 0.8980 chunk 185 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 435 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.209059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.155292 restraints weight = 20306.006| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 4.94 r_work: 0.3279 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.4306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 18399 Z= 0.186 Angle : 0.640 12.969 24862 Z= 0.327 Chirality : 0.043 0.177 2794 Planarity : 0.004 0.063 3042 Dihedral : 5.096 54.478 2468 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.95 % Favored : 91.91 % Rotamer: Outliers : 2.84 % Allowed : 15.63 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.18), residues: 2238 helix: 1.38 (0.15), residues: 1294 sheet: -2.14 (0.40), residues: 138 loop : -2.79 (0.20), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 88 HIS 0.011 0.002 HIS E 27 PHE 0.020 0.002 PHE E 78 TYR 0.021 0.001 TYR B 647 ARG 0.009 0.000 ARG B 628 Details of bonding type rmsd hydrogen bonds : bond 0.03656 ( 890) hydrogen bonds : angle 3.75246 ( 2604) SS BOND : bond 0.00574 ( 6) SS BOND : angle 0.92562 ( 12) covalent geometry : bond 0.00457 (18393) covalent geometry : angle 0.64012 (24850) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 280 time to evaluate : 1.986 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 434 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8329 (tttm) REVERT: A 467 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8513 (pp) REVERT: A 641 LYS cc_start: 0.7724 (OUTLIER) cc_final: 0.7489 (ptpt) REVERT: A 669 LYS cc_start: 0.7346 (mtmt) cc_final: 0.6903 (tttt) REVERT: A 715 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.7050 (mmp-170) REVERT: A 734 ILE cc_start: 0.9041 (OUTLIER) cc_final: 0.8530 (mm) REVERT: A 863 TYR cc_start: 0.5892 (m-10) cc_final: 0.5110 (m-80) REVERT: A 1029 MET cc_start: 0.7209 (mtm) cc_final: 0.6498 (mtp) REVERT: B 393 LYS cc_start: 0.6935 (ttpt) cc_final: 0.6633 (ttmt) REVERT: B 719 ASP cc_start: 0.7761 (t0) cc_final: 0.7415 (t0) REVERT: C 434 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8324 (tttm) REVERT: C 467 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8527 (pp) REVERT: C 630 VAL cc_start: 0.8393 (p) cc_final: 0.8049 (m) REVERT: C 641 LYS cc_start: 0.7331 (OUTLIER) cc_final: 0.6677 (mmtp) REVERT: C 642 GLN cc_start: 0.6378 (OUTLIER) cc_final: 0.5473 (mp10) REVERT: C 734 ILE cc_start: 0.9035 (OUTLIER) cc_final: 0.8534 (mm) REVERT: C 924 MET cc_start: 0.7036 (pmm) cc_final: 0.6491 (ptt) REVERT: C 1029 MET cc_start: 0.6050 (mmt) cc_final: 0.4727 (mmt) REVERT: D 393 LYS cc_start: 0.6897 (ttpt) cc_final: 0.6261 (ttpt) REVERT: D 642 GLN cc_start: 0.6965 (mt0) cc_final: 0.6746 (mt0) REVERT: D 661 ARG cc_start: 0.7732 (ptp-110) cc_final: 0.7377 (ptm160) REVERT: D 719 ASP cc_start: 0.7988 (t0) cc_final: 0.7559 (t0) REVERT: D 772 GLU cc_start: 0.8289 (mp0) cc_final: 0.7574 (mt-10) REVERT: E 128 LEU cc_start: 0.4704 (tp) cc_final: 0.3980 (mt) REVERT: F 27 HIS cc_start: 0.7308 (OUTLIER) cc_final: 0.6627 (p-80) REVERT: F 83 LEU cc_start: 0.7349 (tp) cc_final: 0.7051 (tp) REVERT: F 116 MET cc_start: 0.3733 (tpt) cc_final: 0.3372 (tpt) outliers start: 55 outliers final: 40 residues processed: 316 average time/residue: 0.2954 time to fit residues: 142.5522 Evaluate side-chains 318 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 267 time to evaluate : 2.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 641 LYS Chi-restraints excluded: chain A residue 715 ARG Chi-restraints excluded: chain A residue 716 LYS Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 411 ASN Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 647 TYR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 434 LYS Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 596 LEU Chi-restraints excluded: chain C residue 641 LYS Chi-restraints excluded: chain C residue 642 GLN Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 716 LYS Chi-restraints excluded: chain C residue 718 CYS Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 411 ASN Chi-restraints excluded: chain D residue 490 ASP Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 792 VAL Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 120 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 190 optimal weight: 1.9990 chunk 68 optimal weight: 0.0980 chunk 138 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 119 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 203 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 187 optimal weight: 4.9990 chunk 181 optimal weight: 1.9990 chunk 171 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4328 r_free = 0.4328 target = 0.212470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.168181 restraints weight = 20242.839| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 3.71 r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18399 Z= 0.122 Angle : 0.593 12.295 24862 Z= 0.303 Chirality : 0.040 0.173 2794 Planarity : 0.004 0.063 3042 Dihedral : 4.922 53.473 2468 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.75 % Favored : 93.07 % Rotamer: Outliers : 2.53 % Allowed : 16.20 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.18), residues: 2238 helix: 1.58 (0.15), residues: 1290 sheet: -1.98 (0.41), residues: 138 loop : -2.70 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 88 HIS 0.011 0.001 HIS E 27 PHE 0.023 0.001 PHE E 78 TYR 0.022 0.001 TYR F 100 ARG 0.004 0.000 ARG B 545 Details of bonding type rmsd hydrogen bonds : bond 0.03261 ( 890) hydrogen bonds : angle 3.60194 ( 2604) SS BOND : bond 0.00509 ( 6) SS BOND : angle 0.84923 ( 12) covalent geometry : bond 0.00280 (18393) covalent geometry : angle 0.59289 (24850) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8033.11 seconds wall clock time: 140 minutes 9.00 seconds (8409.00 seconds total)