Starting phenix.real_space_refine on Mon Jun 16 01:40:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ss4_40743/06_2025/8ss4_40743.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ss4_40743/06_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_40743/06_2025/8ss4_40743.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ss4_40743/06_2025/8ss4_40743.map" model { file = "/net/cci-nas-00/data/ceres_data/8ss4_40743/06_2025/8ss4_40743.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ss4_40743/06_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-5710/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: 10.26, per 1000 atoms: 0.57 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: 4.19 Conformation dependent library (CDL) restraints added in 2.3 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: 1.98 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: 5.62 Time building geometry restraints manager: 4.79 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: 2.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.620 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 39.250 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.330 ------------------------------------------------------------------------------- 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 : 1.945 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: 0.3274 time to fit residues: 195.3749 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 : 2.021 ------------------------------------------------------------------------------- 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 = 0.129002 restraints weight = 20091.693| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.81 r_work: 0.3160 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 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 4.57916 ( 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 : 2.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 MET cc_start: 0.7382 (tmm) cc_final: 0.7066 (tmm) REVERT: A 431 GLU cc_start: 0.8499 (mm-30) cc_final: 0.8133 (mm-30) REVERT: A 467 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.7966 (pt) REVERT: A 637 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8103 (mt-10) REVERT: A 669 LYS cc_start: 0.7491 (mtmt) cc_final: 0.6924 (tttt) REVERT: A 907 MET cc_start: 0.4954 (ttt) cc_final: 0.4179 (mpp) REVERT: A 1002 LYS cc_start: 0.6488 (ttmp) cc_final: 0.6045 (mmtt) REVERT: B 393 LYS cc_start: 0.6927 (ttpt) cc_final: 0.5826 (tptp) REVERT: B 397 VAL cc_start: 0.8188 (OUTLIER) cc_final: 0.7972 (m) REVERT: B 695 LYS cc_start: 0.7610 (mtpm) cc_final: 0.7329 (mtmt) REVERT: B 708 MET cc_start: 0.8143 (tpt) cc_final: 0.7812 (mmt) REVERT: B 719 ASP cc_start: 0.7606 (t0) cc_final: 0.7364 (t0) REVERT: C 431 GLU cc_start: 0.8388 (mm-30) cc_final: 0.7921 (mm-30) REVERT: C 467 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8385 (pt) REVERT: C 637 GLU cc_start: 0.8329 (mt-10) cc_final: 0.8048 (mt-10) REVERT: C 651 ASP cc_start: 0.7598 (t70) cc_final: 0.7384 (t70) REVERT: C 688 GLU cc_start: 0.8257 (tt0) cc_final: 0.7730 (pt0) REVERT: C 729 SER cc_start: 0.9039 (t) cc_final: 0.8790 (p) REVERT: C 863 TYR cc_start: 0.5527 (m-10) cc_final: 0.4955 (m-80) REVERT: D 393 LYS cc_start: 0.6800 (ttpt) cc_final: 0.5757 (tptp) REVERT: D 397 VAL cc_start: 0.8072 (OUTLIER) cc_final: 0.7831 (m) REVERT: D 527 MET cc_start: 0.8232 (mmt) cc_final: 0.7882 (mmt) REVERT: D 545 ARG cc_start: 0.7907 (ttm-80) cc_final: 0.7471 (tpp80) REVERT: D 661 ARG cc_start: 0.7691 (ptp-110) cc_final: 0.7420 (ptm160) REVERT: D 719 ASP cc_start: 0.7723 (t0) cc_final: 0.7460 (t0) REVERT: D 813 GLU cc_start: 0.7798 (tt0) cc_final: 0.7583 (tt0) REVERT: E 102 LEU cc_start: 0.6844 (pp) cc_final: 0.6640 (pp) REVERT: F 139 LEU cc_start: 0.5968 (tp) cc_final: 0.4683 (pp) outliers start: 43 outliers final: 16 residues processed: 332 average time/residue: 0.4013 time to fit residues: 211.1077 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 : 2.922 ------------------------------------------------------------------------------- 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: 4.9990 chunk 81 optimal weight: 0.7980 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: 6.9990 chunk 190 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 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 = 0.4286 r_free = 0.4286 target = 0.206641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.154709 restraints weight = 19899.980| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 5.07 r_work: 0.3280 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3006 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= 0.180 Angle : 0.649 8.306 24862 Z= 0.337 Chirality : 0.042 0.192 2794 Planarity : 0.005 0.062 3042 Dihedral : 5.691 53.325 2468 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.45 % Favored : 91.38 % Rotamer: Outliers : 3.10 % Allowed : 10.78 % Favored : 86.12 % 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: -1.97 (0.17), residues: 2238 helix: 0.15 (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 0.008 0.002 HIS E 27 PHE 0.023 0.002 PHE E 141 TYR 0.026 0.001 TYR F 100 ARG 0.006 0.000 ARG D 628 Details of bonding type rmsd hydrogen bonds : bond 0.04261 ( 890) hydrogen bonds : angle 4.14112 ( 2604) SS BOND : bond 0.00818 ( 6) SS BOND : angle 1.34735 ( 12) covalent geometry : bond 0.00434 (18393) covalent geometry : angle 0.64859 (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 357 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 297 time to evaluate : 5.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 414 MET cc_start: 0.7326 (tmm) cc_final: 0.7025 (tmm) REVERT: A 431 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8254 (mm-30) REVERT: A 434 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.8056 (tttm) REVERT: A 467 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8291 (pt) REVERT: A 669 LYS cc_start: 0.7544 (mtmt) cc_final: 0.7037 (tttt) REVERT: A 716 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7776 (tmtt) REVERT: A 863 TYR cc_start: 0.5398 (m-10) cc_final: 0.4909 (m-80) REVERT: A 907 MET cc_start: 0.4859 (ttt) cc_final: 0.4101 (mpp) REVERT: A 1002 LYS cc_start: 0.6268 (ttmp) cc_final: 0.6014 (mmtt) REVERT: A 1029 MET cc_start: 0.7445 (mmm) cc_final: 0.6816 (mtp) REVERT: B 393 LYS cc_start: 0.6901 (ttpt) cc_final: 0.6176 (tptp) REVERT: B 397 VAL cc_start: 0.8310 (OUTLIER) cc_final: 0.8088 (m) REVERT: B 545 ARG cc_start: 0.6763 (ttm-80) cc_final: 0.6555 (ttt180) REVERT: B 695 LYS cc_start: 0.7671 (mtpm) cc_final: 0.7402 (mtmt) REVERT: B 719 ASP cc_start: 0.7844 (t0) cc_final: 0.7561 (t0) REVERT: C 467 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8324 (pt) REVERT: C 545 ARG cc_start: 0.7850 (mmm160) cc_final: 0.7002 (ttt-90) REVERT: C 630 VAL cc_start: 0.8571 (p) cc_final: 0.8208 (m) REVERT: C 651 ASP cc_start: 0.7759 (t70) cc_final: 0.7414 (t70) REVERT: C 729 SER cc_start: 0.9008 (t) cc_final: 0.8764 (p) REVERT: C 863 TYR cc_start: 0.5382 (m-10) cc_final: 0.5012 (m-80) REVERT: D 393 LYS cc_start: 0.6893 (ttpt) cc_final: 0.5954 (tptp) REVERT: D 397 VAL cc_start: 0.8151 (OUTLIER) cc_final: 0.7850 (m) REVERT: D 508 GLN cc_start: 0.7251 (mp10) cc_final: 0.6345 (mp10) REVERT: D 527 MET cc_start: 0.8375 (mmt) cc_final: 0.7941 (mmt) REVERT: D 545 ARG cc_start: 0.7899 (ttm-80) cc_final: 0.7466 (tpp80) REVERT: D 661 ARG cc_start: 0.7781 (ptp-110) cc_final: 0.7388 (ptm160) REVERT: D 719 ASP cc_start: 0.7880 (t0) cc_final: 0.7510 (t0) outliers start: 60 outliers final: 29 residues processed: 340 average time/residue: 0.4442 time to fit residues: 239.5856 Evaluate side-chains 292 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 257 time to evaluate : 3.488 ------------------------------------------------------------------------------- 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 397 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 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 Chi-restraints excluded: chain F residue 120 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 144 optimal weight: 20.0000 chunk 137 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 152 optimal weight: 0.8980 chunk 146 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 145 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 756 GLN C 872 GLN D 587 GLN E 107 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.208197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.158590 restraints weight = 20223.534| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 3.70 r_work: 0.3232 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 18399 Z= 0.194 Angle : 0.647 10.578 24862 Z= 0.334 Chirality : 0.043 0.194 2794 Planarity : 0.004 0.067 3042 Dihedral : 5.540 50.678 2468 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.09 % Favored : 91.73 % Rotamer: Outliers : 3.61 % Allowed : 12.18 % Favored : 84.21 % 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: -1.42 (0.18), residues: 2238 helix: 0.57 (0.14), residues: 1304 sheet: -2.78 (0.39), residues: 144 loop : -3.25 (0.20), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 766 HIS 0.010 0.002 HIS E 27 PHE 0.024 0.002 PHE F 78 TYR 0.026 0.001 TYR F 100 ARG 0.006 0.001 ARG C1031 Details of bonding type rmsd hydrogen bonds : bond 0.03968 ( 890) hydrogen bonds : angle 4.04235 ( 2604) SS BOND : bond 0.00521 ( 6) SS BOND : angle 1.09698 ( 12) covalent geometry : bond 0.00471 (18393) covalent geometry : angle 0.64699 (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 342 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 272 time to evaluate : 1.922 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 431 GLU cc_start: 0.8760 (mm-30) cc_final: 0.8505 (mm-30) REVERT: A 434 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8104 (tttm) REVERT: A 467 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8371 (pt) REVERT: A 641 LYS cc_start: 0.7429 (OUTLIER) cc_final: 0.6936 (mmtp) REVERT: A 669 LYS cc_start: 0.7596 (mtmt) cc_final: 0.7157 (tttt) REVERT: A 716 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7815 (tmtt) REVERT: A 863 TYR cc_start: 0.5641 (m-10) cc_final: 0.5072 (m-80) REVERT: A 907 MET cc_start: 0.5141 (ttt) cc_final: 0.4283 (mpp) REVERT: A 1029 MET cc_start: 0.7307 (OUTLIER) cc_final: 0.6781 (mtp) REVERT: B 393 LYS cc_start: 0.7180 (ttpt) cc_final: 0.6352 (tptp) REVERT: B 695 LYS cc_start: 0.7693 (mtpm) cc_final: 0.7435 (mtmt) REVERT: B 719 ASP cc_start: 0.7945 (t0) cc_final: 0.7666 (t0) REVERT: C 434 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8273 (tttm) REVERT: C 467 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8389 (pt) REVERT: C 641 LYS cc_start: 0.7095 (OUTLIER) cc_final: 0.6479 (mmtp) REVERT: C 642 GLN cc_start: 0.6550 (OUTLIER) cc_final: 0.5571 (mp10) REVERT: C 651 ASP cc_start: 0.7857 (t70) cc_final: 0.7485 (t70) REVERT: C 669 LYS cc_start: 0.7572 (mtmt) cc_final: 0.7095 (tttt) REVERT: C 729 SER cc_start: 0.9042 (t) cc_final: 0.8805 (p) REVERT: C 863 TYR cc_start: 0.5777 (m-10) cc_final: 0.5337 (m-80) REVERT: C 1029 MET cc_start: 0.6153 (mmt) cc_final: 0.5533 (mmt) REVERT: D 393 LYS cc_start: 0.7014 (ttpt) cc_final: 0.5952 (tptp) REVERT: D 397 VAL cc_start: 0.8187 (OUTLIER) cc_final: 0.7890 (m) REVERT: D 527 MET cc_start: 0.8449 (mmt) cc_final: 0.8135 (mmt) REVERT: D 545 ARG cc_start: 0.7838 (ttm-80) cc_final: 0.7378 (tpp80) REVERT: D 661 ARG cc_start: 0.7802 (ptp-110) cc_final: 0.7416 (ptm160) REVERT: D 719 ASP cc_start: 0.7916 (t0) cc_final: 0.7575 (t0) REVERT: E 100 TYR cc_start: 0.7411 (t80) cc_final: 0.7089 (t80) REVERT: E 127 ILE cc_start: 0.6791 (OUTLIER) cc_final: 0.6510 (tp) REVERT: E 128 LEU cc_start: 0.4910 (tp) cc_final: 0.4482 (pp) outliers start: 70 outliers final: 38 residues processed: 321 average time/residue: 0.3000 time to fit residues: 150.0777 Evaluate side-chains 304 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 255 time to evaluate : 1.998 ------------------------------------------------------------------------------- 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 503 MET 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 973 LEU 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 683 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 434 LYS Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 589 CYS 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 224 optimal weight: 9.9990 chunk 192 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 136 optimal weight: 0.9980 chunk 168 optimal weight: 0.9980 chunk 58 optimal weight: 7.9990 chunk 146 optimal weight: 3.9990 chunk 212 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 191 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS C 435 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.204967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.162880 restraints weight = 19767.228| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 3.09 r_work: 0.3288 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18399 Z= 0.137 Angle : 0.594 10.161 24862 Z= 0.307 Chirality : 0.041 0.180 2794 Planarity : 0.004 0.059 3042 Dihedral : 5.279 50.040 2468 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.33 % Favored : 92.49 % Rotamer: Outliers : 3.25 % Allowed : 13.62 % Favored : 83.13 % 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: -0.92 (0.18), residues: 2238 helix: 0.98 (0.15), residues: 1304 sheet: -2.44 (0.40), residues: 138 loop : -3.08 (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 0.025 0.001 TYR F 100 ARG 0.004 0.000 ARG D 628 Details of bonding type rmsd hydrogen bonds : bond 0.03598 ( 890) hydrogen bonds : angle 3.82557 ( 2604) SS BOND : bond 0.00438 ( 6) SS BOND : angle 0.92925 ( 12) covalent geometry : bond 0.00321 (18393) covalent geometry : angle 0.59411 (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 336 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 273 time to evaluate : 1.982 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 467 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8032 (pt) REVERT: A 592 SER cc_start: 0.8983 (t) cc_final: 0.8739 (p) REVERT: A 669 LYS cc_start: 0.7492 (mtmt) cc_final: 0.7062 (tttt) REVERT: A 716 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7863 (tmtt) REVERT: A 734 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8541 (mm) REVERT: A 863 TYR cc_start: 0.5671 (m-10) cc_final: 0.5050 (m-80) REVERT: A 907 MET cc_start: 0.5026 (ttt) cc_final: 0.4206 (mpp) REVERT: A 1026 TYR cc_start: 0.7508 (OUTLIER) cc_final: 0.7229 (m-10) REVERT: A 1029 MET cc_start: 0.7148 (OUTLIER) cc_final: 0.6700 (mtm) REVERT: B 393 LYS cc_start: 0.6836 (ttpt) cc_final: 0.6105 (tptp) REVERT: B 719 ASP cc_start: 0.7837 (t0) cc_final: 0.7426 (t0) REVERT: C 434 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8304 (tttm) REVERT: C 467 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8359 (pt) REVERT: C 642 GLN cc_start: 0.6446 (OUTLIER) cc_final: 0.5281 (mp-120) REVERT: C 651 ASP cc_start: 0.7772 (t70) cc_final: 0.7381 (p0) REVERT: C 669 LYS cc_start: 0.7484 (mtmt) cc_final: 0.7064 (tttt) REVERT: C 729 SER cc_start: 0.9002 (t) cc_final: 0.8746 (p) REVERT: C 734 ILE cc_start: 0.8969 (OUTLIER) cc_final: 0.8530 (mm) REVERT: C 863 TYR cc_start: 0.5820 (m-10) cc_final: 0.5287 (m-80) REVERT: C 901 PHE cc_start: 0.6114 (m-80) cc_final: 0.5449 (m-80) REVERT: C 1029 MET cc_start: 0.6059 (mmt) cc_final: 0.5344 (mmt) REVERT: D 393 LYS cc_start: 0.6935 (ttpt) cc_final: 0.5937 (tptp) REVERT: D 397 VAL cc_start: 0.8012 (OUTLIER) cc_final: 0.7749 (m) REVERT: D 527 MET cc_start: 0.8375 (mmt) cc_final: 0.8072 (mmt) REVERT: D 545 ARG cc_start: 0.7740 (ttm-80) cc_final: 0.7369 (tpp80) REVERT: D 661 ARG cc_start: 0.7709 (ptp-110) cc_final: 0.7313 (ptm160) REVERT: D 719 ASP cc_start: 0.7994 (t0) cc_final: 0.7608 (t0) REVERT: E 100 TYR cc_start: 0.7445 (t80) cc_final: 0.7188 (t80) REVERT: E 127 ILE cc_start: 0.6651 (OUTLIER) cc_final: 0.6401 (tp) REVERT: E 128 LEU cc_start: 0.4663 (tp) cc_final: 0.4259 (pp) REVERT: F 143 LEU cc_start: 0.8093 (mm) cc_final: 0.7837 (mm) outliers start: 63 outliers final: 39 residues processed: 315 average time/residue: 0.2942 time to fit residues: 143.4966 Evaluate side-chains 308 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 258 time to evaluate : 1.817 ------------------------------------------------------------------------------- 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 467 LEU Chi-restraints excluded: chain A residue 629 MET 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 1026 TYR Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain B residue 399 THR 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 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 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 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: 0.8980 chunk 31 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 170 optimal weight: 1.9990 chunk 207 optimal weight: 0.0270 chunk 166 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 196 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 180 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 overall best weight: 0.7438 ------------------------------------------------------------------------------- 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 = 0.4321 r_free = 0.4321 target = 0.211808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.166611 restraints weight = 20416.856| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 3.52 r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.3904 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= 0.128 Angle : 0.581 8.068 24862 Z= 0.299 Chirality : 0.040 0.180 2794 Planarity : 0.004 0.062 3042 Dihedral : 5.120 45.448 2468 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.88 % Favored : 92.94 % Rotamer: Outliers : 3.41 % Allowed : 13.93 % Favored : 82.66 % 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: -0.65 (0.18), residues: 2238 helix: 1.19 (0.15), residues: 1302 sheet: -2.23 (0.41), residues: 138 loop : -2.98 (0.20), residues: 798 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 0.016 0.001 PHE C 960 TYR 0.023 0.001 TYR F 100 ARG 0.004 0.000 ARG D 628 Details of bonding type rmsd hydrogen bonds : bond 0.03457 ( 890) hydrogen bonds : angle 3.73006 ( 2604) SS BOND : bond 0.00310 ( 6) SS BOND : angle 0.86227 ( 12) covalent geometry : bond 0.00297 (18393) covalent geometry : angle 0.58090 (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 352 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 286 time to evaluate : 2.038 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 434 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.8095 (tttm) REVERT: A 467 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8074 (pt) REVERT: A 592 SER cc_start: 0.8815 (t) cc_final: 0.8609 (p) REVERT: A 734 ILE cc_start: 0.8423 (OUTLIER) cc_final: 0.7921 (mm) REVERT: A 863 TYR cc_start: 0.6549 (m-10) cc_final: 0.6112 (m-80) REVERT: B 393 LYS cc_start: 0.6787 (ttpt) cc_final: 0.6523 (ttmt) REVERT: B 719 ASP cc_start: 0.7284 (t0) cc_final: 0.7017 (t0) REVERT: C 434 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.8064 (tttm) REVERT: C 467 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8101 (pt) REVERT: C 641 LYS cc_start: 0.7170 (OUTLIER) cc_final: 0.6718 (mmtp) REVERT: C 642 GLN cc_start: 0.6768 (OUTLIER) cc_final: 0.5797 (mp-120) REVERT: C 729 SER cc_start: 0.8685 (t) cc_final: 0.8410 (p) REVERT: C 734 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.7930 (mm) REVERT: C 863 TYR cc_start: 0.6928 (m-10) cc_final: 0.6417 (m-80) REVERT: C 1029 MET cc_start: 0.5238 (mmt) cc_final: 0.4489 (mmt) REVERT: D 393 LYS cc_start: 0.6672 (ttpt) cc_final: 0.6236 (tptp) REVERT: D 527 MET cc_start: 0.7189 (mmt) cc_final: 0.6968 (mmt) REVERT: D 545 ARG cc_start: 0.7522 (ttm-80) cc_final: 0.7319 (tpp80) REVERT: D 661 ARG cc_start: 0.7710 (ptp-110) cc_final: 0.7403 (ptm160) REVERT: D 719 ASP cc_start: 0.7502 (t0) cc_final: 0.7201 (t0) REVERT: F 27 HIS cc_start: 0.6626 (OUTLIER) cc_final: 0.6368 (p-80) REVERT: F 83 LEU cc_start: 0.7675 (tp) cc_final: 0.7350 (tp) REVERT: F 143 LEU cc_start: 0.8222 (mm) cc_final: 0.8020 (mm) outliers start: 66 outliers final: 41 residues processed: 330 average time/residue: 0.2831 time to fit residues: 146.0622 Evaluate side-chains 314 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 264 time to evaluate : 2.001 ------------------------------------------------------------------------------- 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 683 VAL 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 1023 MET Chi-restraints excluded: chain B residue 408 MET 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 416 GLU 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 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 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 D residue 408 MET 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 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: 0.4980 chunk 63 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 60 optimal weight: 0.6980 chunk 147 optimal weight: 10.0000 chunk 12 optimal weight: 0.7980 chunk 220 optimal weight: 20.0000 chunk 208 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 191 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 642 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.209442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.163651 restraints weight = 19971.992| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 3.60 r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.4086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18399 Z= 0.122 Angle : 0.581 8.720 24862 Z= 0.298 Chirality : 0.040 0.191 2794 Planarity : 0.004 0.062 3042 Dihedral : 5.021 52.391 2468 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.88 % Favored : 93.03 % Rotamer: Outliers : 2.73 % Allowed : 14.65 % Favored : 82.61 % 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: -0.43 (0.18), residues: 2238 helix: 1.39 (0.15), residues: 1298 sheet: -2.13 (0.41), residues: 138 loop : -2.89 (0.20), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 88 HIS 0.010 0.001 HIS E 27 PHE 0.021 0.001 PHE C 901 TYR 0.022 0.001 TYR F 100 ARG 0.002 0.000 ARG C 991 Details of bonding type rmsd hydrogen bonds : bond 0.03355 ( 890) hydrogen bonds : angle 3.65026 ( 2604) SS BOND : bond 0.00269 ( 6) SS BOND : angle 0.75667 ( 12) covalent geometry : bond 0.00281 (18393) covalent geometry : angle 0.58073 (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 333 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 280 time to evaluate : 1.949 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 467 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8015 (pt) REVERT: A 592 SER cc_start: 0.8773 (t) cc_final: 0.8558 (p) REVERT: A 734 ILE cc_start: 0.8412 (OUTLIER) cc_final: 0.7947 (mm) REVERT: A 863 TYR cc_start: 0.6611 (m-10) cc_final: 0.6018 (m-80) REVERT: B 393 LYS cc_start: 0.6701 (ttpt) cc_final: 0.6481 (ttmt) REVERT: B 719 ASP cc_start: 0.7388 (t0) cc_final: 0.7128 (t0) REVERT: C 434 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7948 (tttm) REVERT: C 467 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7931 (pt) REVERT: C 641 LYS cc_start: 0.7237 (OUTLIER) cc_final: 0.6624 (mmtp) REVERT: C 642 GLN cc_start: 0.6681 (OUTLIER) cc_final: 0.5993 (mp10) REVERT: C 729 SER cc_start: 0.8596 (t) cc_final: 0.8339 (p) REVERT: C 734 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.7951 (mm) REVERT: C 1029 MET cc_start: 0.5389 (mmt) cc_final: 0.4728 (mmt) REVERT: D 393 LYS cc_start: 0.6739 (ttpt) cc_final: 0.6133 (tptp) REVERT: D 661 ARG cc_start: 0.7712 (ptp-110) cc_final: 0.7401 (ptm160) REVERT: D 719 ASP cc_start: 0.7560 (t0) cc_final: 0.7230 (t0) REVERT: F 27 HIS cc_start: 0.6761 (OUTLIER) cc_final: 0.6241 (p-80) outliers start: 53 outliers final: 41 residues processed: 312 average time/residue: 0.3249 time to fit residues: 159.2861 Evaluate side-chains 318 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 269 time to evaluate : 2.308 ------------------------------------------------------------------------------- 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 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 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 1023 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 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 416 GLU 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 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 408 MET 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 14 LEU 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 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: 2.9990 chunk 220 optimal weight: 20.0000 chunk 40 optimal weight: 7.9990 chunk 49 optimal weight: 4.9990 chunk 192 optimal weight: 0.7980 chunk 166 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 chunk 168 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 = 0.4261 r_free = 0.4261 target = 0.202232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.161832 restraints weight = 19646.524| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 3.09 r_work: 0.3254 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 18399 Z= 0.211 Angle : 0.648 9.797 24862 Z= 0.332 Chirality : 0.043 0.197 2794 Planarity : 0.004 0.064 3042 Dihedral : 5.237 53.613 2468 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.53 % Favored : 91.38 % Rotamer: Outliers : 3.66 % Allowed : 14.71 % Favored : 81.63 % 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: -0.64 (0.18), residues: 2238 helix: 1.22 (0.15), residues: 1296 sheet: -2.29 (0.40), residues: 140 loop : -2.95 (0.20), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 88 HIS 0.010 0.002 HIS E 27 PHE 0.018 0.002 PHE A 495 TYR 0.020 0.001 TYR F 100 ARG 0.005 0.000 ARG D 628 Details of bonding type rmsd hydrogen bonds : bond 0.03873 ( 890) hydrogen bonds : angle 3.84733 ( 2604) SS BOND : bond 0.00382 ( 6) SS BOND : angle 0.69948 ( 12) covalent geometry : bond 0.00523 (18393) covalent geometry : angle 0.64826 (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 350 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 279 time to evaluate : 2.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8314 (tttm) REVERT: A 467 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8408 (pt) REVERT: A 641 LYS cc_start: 0.7763 (OUTLIER) cc_final: 0.7343 (mmtp) REVERT: A 734 ILE cc_start: 0.9052 (OUTLIER) cc_final: 0.8546 (mm) REVERT: A 863 TYR cc_start: 0.5988 (m-10) cc_final: 0.5225 (m-80) REVERT: A 1029 MET cc_start: 0.7140 (mtm) cc_final: 0.6897 (mtp) REVERT: B 393 LYS cc_start: 0.6990 (ttpt) cc_final: 0.6688 (ttmt) REVERT: B 719 ASP cc_start: 0.7853 (t0) cc_final: 0.7429 (t0) REVERT: C 434 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8350 (tttm) REVERT: C 467 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8598 (pp) REVERT: C 592 SER cc_start: 0.9000 (t) cc_final: 0.8762 (p) REVERT: C 641 LYS cc_start: 0.7251 (OUTLIER) cc_final: 0.6580 (mmtp) REVERT: C 642 GLN cc_start: 0.6522 (OUTLIER) cc_final: 0.5459 (mp-120) REVERT: C 729 SER cc_start: 0.9029 (t) cc_final: 0.8797 (p) REVERT: C 734 ILE cc_start: 0.9038 (OUTLIER) cc_final: 0.8543 (mm) REVERT: C 1029 MET cc_start: 0.6122 (mmt) cc_final: 0.4903 (mmt) REVERT: D 393 LYS cc_start: 0.6958 (ttpt) cc_final: 0.6352 (ttpt) REVERT: D 661 ARG cc_start: 0.7772 (ptp-110) cc_final: 0.7407 (ptm160) REVERT: D 719 ASP cc_start: 0.7962 (t0) cc_final: 0.7598 (t0) REVERT: F 27 HIS cc_start: 0.7384 (OUTLIER) cc_final: 0.6710 (p-80) REVERT: F 83 LEU cc_start: 0.7448 (tp) cc_final: 0.7153 (tp) REVERT: F 128 LEU cc_start: 0.4898 (tp) cc_final: 0.4409 (mt) outliers start: 71 outliers final: 47 residues processed: 323 average time/residue: 0.3177 time to fit residues: 162.5786 Evaluate side-chains 322 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 265 time to evaluate : 2.158 ------------------------------------------------------------------------------- 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 503 MET Chi-restraints excluded: chain A residue 540 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 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 A residue 1023 MET Chi-restraints excluded: chain B residue 397 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 416 GLU 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 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 C residue 1023 MET Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 683 VAL 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 212 optimal weight: 3.9990 chunk 213 optimal weight: 0.9980 chunk 165 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 66 optimal weight: 0.5980 chunk 225 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 85 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 chunk 200 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 508 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.208789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.166026 restraints weight = 20057.295| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 3.33 r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.4324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18399 Z= 0.127 Angle : 0.594 10.214 24862 Z= 0.304 Chirality : 0.041 0.175 2794 Planarity : 0.004 0.064 3042 Dihedral : 5.006 53.705 2468 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.24 % Favored : 92.67 % Rotamer: Outliers : 2.94 % Allowed : 15.89 % Favored : 81.17 % 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: -0.34 (0.18), residues: 2238 helix: 1.48 (0.15), residues: 1288 sheet: -2.15 (0.41), residues: 138 loop : -2.82 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 88 HIS 0.010 0.001 HIS E 27 PHE 0.018 0.001 PHE E 78 TYR 0.022 0.001 TYR F 100 ARG 0.003 0.000 ARG C 545 Details of bonding type rmsd hydrogen bonds : bond 0.03386 ( 890) hydrogen bonds : angle 3.64116 ( 2604) SS BOND : bond 0.00749 ( 6) SS BOND : angle 0.74826 ( 12) covalent geometry : bond 0.00293 (18393) covalent geometry : angle 0.59385 (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 340 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 283 time to evaluate : 2.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7905 (tttm) REVERT: A 467 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7948 (pt) REVERT: A 651 ASP cc_start: 0.6230 (p0) cc_final: 0.6006 (p0) REVERT: A 734 ILE cc_start: 0.8485 (OUTLIER) cc_final: 0.8013 (mm) REVERT: A 863 TYR cc_start: 0.6744 (m-10) cc_final: 0.6130 (m-80) REVERT: A 1029 MET cc_start: 0.6933 (mtm) cc_final: 0.6457 (mtp) REVERT: B 393 LYS cc_start: 0.6848 (ttpt) cc_final: 0.6629 (ttmt) REVERT: B 719 ASP cc_start: 0.7375 (t0) cc_final: 0.7072 (t0) REVERT: C 434 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7938 (tttm) REVERT: C 467 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7954 (pt) REVERT: C 642 GLN cc_start: 0.6615 (OUTLIER) cc_final: 0.5920 (mp10) REVERT: C 729 SER cc_start: 0.8621 (t) cc_final: 0.8387 (p) REVERT: C 734 ILE cc_start: 0.8510 (OUTLIER) cc_final: 0.8042 (mm) REVERT: C 1029 MET cc_start: 0.4956 (mmt) cc_final: 0.4409 (mmt) REVERT: D 393 LYS cc_start: 0.6723 (ttpt) cc_final: 0.6495 (ttmt) REVERT: D 661 ARG cc_start: 0.7745 (ptp-110) cc_final: 0.7464 (ptm160) REVERT: D 719 ASP cc_start: 0.7454 (t0) cc_final: 0.7139 (t0) REVERT: F 27 HIS cc_start: 0.6948 (OUTLIER) cc_final: 0.6420 (p-80) REVERT: F 83 LEU cc_start: 0.7896 (tp) cc_final: 0.7529 (tp) outliers start: 57 outliers final: 40 residues processed: 318 average time/residue: 0.2972 time to fit residues: 148.4139 Evaluate side-chains 318 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 270 time to evaluate : 1.762 ------------------------------------------------------------------------------- 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 503 MET Chi-restraints excluded: chain A residue 542 LEU 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 744 THR Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 1023 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 416 GLU 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 642 GLN Chi-restraints excluded: chain C residue 718 CYS Chi-restraints excluded: chain C residue 734 ILE 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 C residue 1023 MET Chi-restraints excluded: chain D residue 408 MET 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 14 LEU 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: 10.0000 chunk 98 optimal weight: 4.9990 chunk 143 optimal weight: 5.9990 chunk 153 optimal weight: 0.5980 chunk 167 optimal weight: 0.3980 chunk 170 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 185 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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 = 0.4254 r_free = 0.4254 target = 0.201284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.150919 restraints weight = 19640.051| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 4.61 r_work: 0.3281 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 18399 Z= 0.232 Angle : 0.678 12.553 24862 Z= 0.347 Chirality : 0.045 0.221 2794 Planarity : 0.004 0.064 3042 Dihedral : 5.271 54.916 2468 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.22 % Favored : 91.69 % Rotamer: Outliers : 2.99 % Allowed : 16.10 % Favored : 80.91 % 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: -0.63 (0.18), residues: 2238 helix: 1.22 (0.15), residues: 1294 sheet: -2.41 (0.37), residues: 164 loop : -2.90 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 88 HIS 0.010 0.002 HIS E 27 PHE 0.023 0.002 PHE F 78 TYR 0.024 0.002 TYR B 647 ARG 0.004 0.000 ARG D 628 Details of bonding type rmsd hydrogen bonds : bond 0.03941 ( 890) hydrogen bonds : angle 3.86780 ( 2604) SS BOND : bond 0.00653 ( 6) SS BOND : angle 0.80921 ( 12) covalent geometry : bond 0.00575 (18393) covalent geometry : angle 0.67766 (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 326 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 268 time to evaluate : 1.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8283 (tttm) REVERT: A 651 ASP cc_start: 0.7059 (p0) cc_final: 0.6809 (p0) REVERT: A 734 ILE cc_start: 0.9051 (OUTLIER) cc_final: 0.8543 (mm) REVERT: A 807 MET cc_start: 0.8419 (mtm) cc_final: 0.8033 (mtm) REVERT: A 863 TYR cc_start: 0.5810 (m-10) cc_final: 0.5015 (m-80) REVERT: A 1029 MET cc_start: 0.7037 (mtm) cc_final: 0.6613 (mtp) REVERT: B 393 LYS cc_start: 0.7016 (ttpt) cc_final: 0.6725 (ttmt) REVERT: B 719 ASP cc_start: 0.7843 (t0) cc_final: 0.7390 (t0) REVERT: C 434 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8289 (tttm) REVERT: C 467 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8581 (pp) REVERT: C 592 SER cc_start: 0.8974 (t) cc_final: 0.8745 (p) REVERT: C 641 LYS cc_start: 0.7382 (OUTLIER) cc_final: 0.6753 (mmtp) REVERT: C 642 GLN cc_start: 0.6489 (OUTLIER) cc_final: 0.5406 (mp-120) REVERT: C 729 SER cc_start: 0.9028 (t) cc_final: 0.8795 (p) REVERT: C 734 ILE cc_start: 0.9042 (OUTLIER) cc_final: 0.8547 (mm) REVERT: C 1029 MET cc_start: 0.5782 (mmt) cc_final: 0.5223 (mmt) REVERT: D 393 LYS cc_start: 0.7021 (ttpt) cc_final: 0.6372 (ttpt) REVERT: D 719 ASP cc_start: 0.7863 (t0) cc_final: 0.7483 (t0) REVERT: E 128 LEU cc_start: 0.3150 (mt) cc_final: 0.2693 (pt) REVERT: E 147 PHE cc_start: 0.7486 (m-80) cc_final: 0.7239 (m-80) REVERT: F 27 HIS cc_start: 0.7290 (OUTLIER) cc_final: 0.6642 (p-80) outliers start: 58 outliers final: 46 residues processed: 303 average time/residue: 0.2855 time to fit residues: 134.9201 Evaluate side-chains 313 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 259 time to evaluate : 1.918 ------------------------------------------------------------------------------- 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 503 MET Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 631 SER 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 795 VAL Chi-restraints excluded: chain A residue 1023 MET Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 411 ASN Chi-restraints excluded: chain B residue 647 TYR Chi-restraints excluded: chain B residue 792 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 416 GLU 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 795 VAL Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 1013 SER Chi-restraints excluded: chain C residue 1015 LEU Chi-restraints excluded: chain C residue 1023 MET 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 14 LEU 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: 0.9980 chunk 68 optimal weight: 0.9980 chunk 138 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 119 optimal weight: 0.5980 chunk 65 optimal weight: 0.0970 chunk 203 optimal weight: 0.7980 chunk 135 optimal weight: 3.9990 chunk 187 optimal weight: 3.9990 chunk 181 optimal weight: 1.9990 chunk 171 optimal weight: 0.6980 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 = 0.4318 r_free = 0.4318 target = 0.211281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.166446 restraints weight = 20160.557| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 3.46 r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.4454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18399 Z= 0.124 Angle : 0.608 12.338 24862 Z= 0.310 Chirality : 0.041 0.182 2794 Planarity : 0.004 0.062 3042 Dihedral : 5.034 53.985 2468 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.88 % Favored : 92.94 % Rotamer: Outliers : 2.68 % Allowed : 16.87 % Favored : 80.44 % 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: -0.31 (0.18), residues: 2238 helix: 1.49 (0.15), residues: 1290 sheet: -2.21 (0.41), residues: 138 loop : -2.80 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 88 HIS 0.011 0.001 HIS E 27 PHE 0.020 0.001 PHE F 78 TYR 0.023 0.001 TYR B 647 ARG 0.004 0.000 ARG B 545 Details of bonding type rmsd hydrogen bonds : bond 0.03373 ( 890) hydrogen bonds : angle 3.64040 ( 2604) SS BOND : bond 0.00496 ( 6) SS BOND : angle 0.75564 ( 12) covalent geometry : bond 0.00285 (18393) covalent geometry : angle 0.60773 (24850) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8741.36 seconds wall clock time: 156 minutes 57.33 seconds (9417.33 seconds total)