Starting phenix.real_space_refine on Sat Oct 11 21:27:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ss4_40743/10_2025/8ss4_40743.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ss4_40743/10_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 { model { file = "/net/cci-nas-00/data/ceres_data/8ss4_40743/10_2025/8ss4_40743.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ss4_40743/10_2025/8ss4_40743.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ss4_40743/10_2025/8ss4_40743.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ss4_40743/10_2025/8ss4_40743.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 4.25, per 1000 atoms: 0.24 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: 1.41 Conformation dependent library (CDL) restraints added in 804.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.62 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: 3.11 Time building geometry restraints manager: 1.87 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: 2.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.890 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.130 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.015 0.001 ARG D 628 TYR 0.031 0.003 TYR D 702 PHE 0.034 0.003 PHE B 667 TRP 0.023 0.003 TRP A 861 HIS 0.014 0.002 HIS F 107 Details of bonding type rmsd covalent geometry : bond 0.00934 (18393) covalent geometry : angle 1.23269 (24850) SS BOND : bond 0.01272 ( 6) SS BOND : angle 1.30098 ( 12) hydrogen bonds : bond 0.30924 ( 890) hydrogen bonds : angle 10.40833 ( 2604) *********************** 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 : 0.668 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: 0.1523 time to fit residues: 89.6936 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 : 0.863 ------------------------------------------------------------------------------- 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 216 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.1980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.6980 chunk 200 optimal weight: 2.9990 chunk 212 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 = 0.4162 r_free = 0.4162 target = 0.195982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.133656 restraints weight = 20313.012| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.72 r_work: 0.3246 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 18399 Z= 0.152 Angle : 0.681 10.662 24862 Z= 0.359 Chirality : 0.043 0.186 2794 Planarity : 0.005 0.078 3042 Dihedral : 6.070 56.147 2468 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.28 % Favored : 92.54 % Rotamer: Outliers : 2.43 % Allowed : 9.65 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.28 (0.15), residues: 2238 helix: -1.13 (0.13), residues: 1280 sheet: -3.51 (0.33), residues: 172 loop : -3.55 (0.19), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 628 TYR 0.019 0.001 TYR B 702 PHE 0.030 0.002 PHE E 31 TRP 0.012 0.001 TRP C 766 HIS 0.007 0.001 HIS E 27 Details of bonding type rmsd covalent geometry : bond 0.00339 (18393) covalent geometry : angle 0.68095 (24850) SS BOND : bond 0.00680 ( 6) SS BOND : angle 1.35986 ( 12) hydrogen bonds : bond 0.04996 ( 890) hydrogen bonds : angle 4.55576 ( 2604) *********************** 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 348 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 301 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 MET cc_start: 0.7395 (tmm) cc_final: 0.7091 (tmm) REVERT: A 431 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8168 (mm-30) REVERT: A 467 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.7949 (pt) REVERT: A 637 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8102 (mt-10) REVERT: A 669 LYS cc_start: 0.7443 (mtmt) cc_final: 0.6862 (tttt) REVERT: A 688 GLU cc_start: 0.7873 (tt0) cc_final: 0.7315 (pt0) REVERT: A 716 LYS cc_start: 0.8218 (ttpt) cc_final: 0.7790 (tmtt) REVERT: A 907 MET cc_start: 0.4939 (ttt) cc_final: 0.4165 (mpp) REVERT: A 1002 LYS cc_start: 0.6373 (ttmp) cc_final: 0.5935 (mmtt) REVERT: B 393 LYS cc_start: 0.6914 (ttpt) cc_final: 0.5742 (tptp) REVERT: B 397 VAL cc_start: 0.8105 (OUTLIER) cc_final: 0.7890 (m) REVERT: B 695 LYS cc_start: 0.7566 (mtpm) cc_final: 0.7268 (mtmt) REVERT: B 708 MET cc_start: 0.8208 (tpt) cc_final: 0.7838 (mmt) REVERT: B 713 GLU cc_start: 0.8943 (tt0) cc_final: 0.8728 (tt0) REVERT: B 719 ASP cc_start: 0.7692 (t0) cc_final: 0.7476 (t0) REVERT: C 467 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8388 (pt) REVERT: C 637 GLU cc_start: 0.8317 (mt-10) cc_final: 0.8031 (mt-10) REVERT: C 688 GLU cc_start: 0.8282 (tt0) cc_final: 0.7735 (pt0) REVERT: C 729 SER cc_start: 0.9122 (t) cc_final: 0.8873 (p) REVERT: C 789 LEU cc_start: 0.8833 (mt) cc_final: 0.8612 (mt) REVERT: C 863 TYR cc_start: 0.5375 (m-10) cc_final: 0.4828 (m-80) REVERT: D 393 LYS cc_start: 0.6796 (ttpt) cc_final: 0.5660 (tptp) REVERT: D 397 VAL cc_start: 0.7971 (OUTLIER) cc_final: 0.7729 (m) REVERT: D 527 MET cc_start: 0.8251 (mmt) cc_final: 0.7920 (mmt) REVERT: D 545 ARG cc_start: 0.7867 (ttm-80) cc_final: 0.7424 (tpp80) REVERT: D 661 ARG cc_start: 0.7638 (ptp-110) cc_final: 0.7375 (ptm160) REVERT: D 719 ASP cc_start: 0.7715 (t0) cc_final: 0.7429 (t0) outliers start: 47 outliers final: 15 residues processed: 340 average time/residue: 0.1293 time to fit residues: 68.5114 Evaluate side-chains 284 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 265 time to evaluate : 0.630 ------------------------------------------------------------------------------- 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 467 LEU Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 596 LEU Chi-restraints excluded: chain C residue 744 THR 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 188 optimal weight: 0.7980 chunk 204 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 52 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 212 optimal weight: 0.6980 chunk 84 optimal weight: 6.9990 chunk 185 optimal weight: 4.9990 chunk 198 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 213 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.206278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.156782 restraints weight = 19848.999| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 4.64 r_work: 0.3339 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18399 Z= 0.141 Angle : 0.619 10.257 24862 Z= 0.321 Chirality : 0.041 0.193 2794 Planarity : 0.004 0.060 3042 Dihedral : 5.534 52.304 2468 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.69 % Favored : 92.14 % Rotamer: Outliers : 2.79 % Allowed : 10.73 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.88 (0.17), residues: 2238 helix: 0.26 (0.14), residues: 1286 sheet: -3.32 (0.33), residues: 178 loop : -3.35 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 628 TYR 0.027 0.001 TYR F 100 PHE 0.023 0.002 PHE E 141 TRP 0.009 0.001 TRP C 766 HIS 0.007 0.001 HIS E 27 Details of bonding type rmsd covalent geometry : bond 0.00325 (18393) covalent geometry : angle 0.61892 (24850) SS BOND : bond 0.00623 ( 6) SS BOND : angle 1.33455 ( 12) hydrogen bonds : bond 0.04020 ( 890) hydrogen bonds : angle 4.01977 ( 2604) *********************** 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 351 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 297 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 414 MET cc_start: 0.7301 (tmm) cc_final: 0.7059 (tmm) REVERT: A 467 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8270 (pt) REVERT: A 669 LYS cc_start: 0.7516 (mtmt) cc_final: 0.7043 (tttt) REVERT: A 716 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7750 (tmtt) REVERT: A 863 TYR cc_start: 0.5635 (m-10) cc_final: 0.5154 (m-80) REVERT: A 907 MET cc_start: 0.4911 (ttt) cc_final: 0.4135 (mpp) REVERT: A 1002 LYS cc_start: 0.6411 (ttmp) cc_final: 0.6148 (mmtt) REVERT: A 1029 MET cc_start: 0.7481 (OUTLIER) cc_final: 0.6891 (mtp) REVERT: B 393 LYS cc_start: 0.6764 (ttpt) cc_final: 0.6011 (tptp) REVERT: B 397 VAL cc_start: 0.8223 (OUTLIER) cc_final: 0.7970 (m) REVERT: B 695 LYS cc_start: 0.7677 (mtpm) cc_final: 0.7411 (mtmt) REVERT: B 719 ASP cc_start: 0.7744 (t0) cc_final: 0.7433 (t0) REVERT: C 434 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8204 (tttm) REVERT: C 467 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8363 (pt) REVERT: C 545 ARG cc_start: 0.7807 (mmm160) cc_final: 0.7033 (ttt-90) REVERT: C 630 VAL cc_start: 0.8598 (p) cc_final: 0.8221 (m) REVERT: C 729 SER cc_start: 0.8944 (t) cc_final: 0.8696 (p) REVERT: C 863 TYR cc_start: 0.5655 (m-10) cc_final: 0.5016 (m-80) REVERT: D 393 LYS cc_start: 0.6814 (ttpt) cc_final: 0.6001 (tptp) REVERT: D 397 VAL cc_start: 0.8032 (OUTLIER) cc_final: 0.7743 (m) REVERT: D 508 GLN cc_start: 0.7364 (mp10) cc_final: 0.6462 (mp10) REVERT: D 527 MET cc_start: 0.8333 (mmt) cc_final: 0.7933 (mmt) REVERT: D 545 ARG cc_start: 0.7862 (ttm-80) cc_final: 0.7441 (tpp80) REVERT: D 627 GLU cc_start: 0.8512 (tt0) cc_final: 0.8101 (tp30) REVERT: D 661 ARG cc_start: 0.7760 (ptp-110) cc_final: 0.7382 (ptm160) REVERT: D 719 ASP cc_start: 0.7813 (t0) cc_final: 0.7473 (t0) REVERT: F 5 PHE cc_start: 0.7107 (t80) cc_final: 0.6846 (t80) REVERT: F 23 PHE cc_start: 0.6524 (m-80) cc_final: 0.6033 (m-10) outliers start: 54 outliers final: 24 residues processed: 338 average time/residue: 0.1257 time to fit residues: 66.3473 Evaluate side-chains 285 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 254 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 716 LYS Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 411 ASN Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 434 LYS Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 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 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 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 120 VAL Chi-restraints excluded: chain E residue 127 ILE 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 89 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 79 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 119 optimal weight: 0.5980 chunk 55 optimal weight: 8.9990 chunk 120 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 12 optimal weight: 0.3980 chunk 86 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 435 HIS C 872 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.207292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.158343 restraints weight = 19828.478| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 4.58 r_work: 0.3361 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18399 Z= 0.128 Angle : 0.590 9.560 24862 Z= 0.304 Chirality : 0.041 0.189 2794 Planarity : 0.004 0.067 3042 Dihedral : 5.266 47.595 2468 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.88 % Favored : 92.94 % Rotamer: Outliers : 2.89 % Allowed : 12.18 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.18), residues: 2238 helix: 0.88 (0.14), residues: 1304 sheet: -2.47 (0.40), residues: 138 loop : -3.17 (0.20), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1031 TYR 0.028 0.001 TYR F 100 PHE 0.027 0.001 PHE F 78 TRP 0.007 0.001 TRP C 766 HIS 0.009 0.001 HIS E 27 Details of bonding type rmsd covalent geometry : bond 0.00293 (18393) covalent geometry : angle 0.58975 (24850) SS BOND : bond 0.00457 ( 6) SS BOND : angle 1.02871 ( 12) hydrogen bonds : bond 0.03584 ( 890) hydrogen bonds : angle 3.80606 ( 2604) *********************** 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 341 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 285 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8146 (tttm) REVERT: A 467 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8246 (pt) REVERT: A 592 SER cc_start: 0.8902 (t) cc_final: 0.8554 (p) REVERT: A 669 LYS cc_start: 0.7446 (mtmt) cc_final: 0.7008 (tttt) REVERT: A 682 PHE cc_start: 0.8482 (m-10) cc_final: 0.8239 (m-80) REVERT: A 716 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7778 (tmtt) REVERT: A 863 TYR cc_start: 0.5446 (m-10) cc_final: 0.4920 (m-80) REVERT: A 907 MET cc_start: 0.4777 (ttt) cc_final: 0.4075 (mpp) REVERT: A 1002 LYS cc_start: 0.6493 (ttmp) cc_final: 0.6236 (mmtt) REVERT: A 1029 MET cc_start: 0.7195 (mmm) cc_final: 0.6779 (mtp) REVERT: B 393 LYS cc_start: 0.6941 (ttpt) cc_final: 0.6137 (tptp) REVERT: B 397 VAL cc_start: 0.8132 (OUTLIER) cc_final: 0.7898 (m) REVERT: B 719 ASP cc_start: 0.7647 (t0) cc_final: 0.7352 (t0) REVERT: C 467 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8288 (pt) REVERT: C 688 GLU cc_start: 0.7956 (tt0) cc_final: 0.7414 (pt0) REVERT: C 901 PHE cc_start: 0.6046 (m-80) cc_final: 0.5397 (m-80) REVERT: C 1029 MET cc_start: 0.5868 (mmt) cc_final: 0.4912 (mmt) REVERT: D 393 LYS cc_start: 0.6922 (ttpt) cc_final: 0.5953 (tptp) REVERT: D 527 MET cc_start: 0.8289 (mmt) cc_final: 0.7894 (mmt) REVERT: D 545 ARG cc_start: 0.7843 (ttm-80) cc_final: 0.7444 (tpp80) REVERT: D 661 ARG cc_start: 0.7757 (ptp-110) cc_final: 0.7395 (ptm160) REVERT: D 719 ASP cc_start: 0.7792 (t0) cc_final: 0.7452 (t0) REVERT: E 100 TYR cc_start: 0.7445 (t80) cc_final: 0.7144 (t80) outliers start: 56 outliers final: 30 residues processed: 329 average time/residue: 0.1315 time to fit residues: 67.1620 Evaluate side-chains 305 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 270 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 716 LYS Chi-restraints excluded: chain A residue 718 CYS 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 411 ASN 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 467 LEU Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 596 LEU 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 1026 TYR Chi-restraints excluded: chain D residue 490 ASP Chi-restraints excluded: chain D residue 519 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 F residue 4 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 152 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 215 optimal weight: 20.0000 chunk 173 optimal weight: 5.9990 chunk 224 optimal weight: 9.9990 chunk 166 optimal weight: 0.6980 chunk 185 optimal weight: 5.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.200935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.151043 restraints weight = 19746.684| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 4.65 r_work: 0.3263 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.3583 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= 0.248 Angle : 0.693 10.803 24862 Z= 0.354 Chirality : 0.045 0.239 2794 Planarity : 0.005 0.058 3042 Dihedral : 5.535 51.363 2468 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.62 % Favored : 91.20 % Rotamer: Outliers : 3.10 % Allowed : 13.36 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.00 % Twisted Proline : 6.06 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.23 (0.18), residues: 2238 helix: 0.77 (0.14), residues: 1304 sheet: -2.96 (0.34), residues: 186 loop : -3.17 (0.20), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 545 TYR 0.023 0.002 TYR F 100 PHE 0.024 0.002 PHE C 495 TRP 0.010 0.001 TRP C 861 HIS 0.011 0.002 HIS E 27 Details of bonding type rmsd covalent geometry : bond 0.00617 (18393) covalent geometry : angle 0.69253 (24850) SS BOND : bond 0.00602 ( 6) SS BOND : angle 0.99321 ( 12) hydrogen bonds : bond 0.04174 ( 890) hydrogen bonds : angle 4.03943 ( 2604) *********************** 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 338 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 278 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8145 (tttm) REVERT: A 467 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8486 (pt) REVERT: A 592 SER cc_start: 0.9031 (t) cc_final: 0.8725 (p) REVERT: A 641 LYS cc_start: 0.7458 (OUTLIER) cc_final: 0.6934 (mmtp) REVERT: A 669 LYS cc_start: 0.7486 (mtmt) cc_final: 0.7073 (tttt) REVERT: A 716 LYS cc_start: 0.8112 (OUTLIER) cc_final: 0.7767 (tmtt) REVERT: A 734 ILE cc_start: 0.9069 (OUTLIER) cc_final: 0.8562 (mm) REVERT: A 807 MET cc_start: 0.8382 (mtm) cc_final: 0.8095 (mtm) REVERT: A 863 TYR cc_start: 0.5500 (m-10) cc_final: 0.4880 (m-80) REVERT: A 907 MET cc_start: 0.5011 (ttt) cc_final: 0.4261 (mpp) REVERT: A 1002 LYS cc_start: 0.6418 (ttmp) cc_final: 0.6155 (mmtt) REVERT: A 1029 MET cc_start: 0.7189 (mmm) cc_final: 0.6669 (mtp) REVERT: B 393 LYS cc_start: 0.7047 (ttpt) cc_final: 0.6258 (tptp) REVERT: B 719 ASP cc_start: 0.7875 (t0) cc_final: 0.7459 (t0) REVERT: C 467 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8642 (pp) REVERT: C 642 GLN cc_start: 0.6565 (OUTLIER) cc_final: 0.5576 (mp10) REVERT: C 669 LYS cc_start: 0.7488 (mtmt) cc_final: 0.7013 (tttt) REVERT: C 734 ILE cc_start: 0.9064 (OUTLIER) cc_final: 0.8574 (mm) REVERT: C 880 MET cc_start: 0.7197 (tmm) cc_final: 0.6728 (tmm) REVERT: C 901 PHE cc_start: 0.6116 (m-80) cc_final: 0.5457 (m-80) REVERT: C 1029 MET cc_start: 0.5926 (mmt) cc_final: 0.5378 (mmt) REVERT: D 393 LYS cc_start: 0.6974 (ttpt) cc_final: 0.6074 (tptp) REVERT: D 527 MET cc_start: 0.8459 (mmt) cc_final: 0.8107 (mmt) REVERT: D 545 ARG cc_start: 0.7874 (ttm-80) cc_final: 0.7480 (tpp80) REVERT: D 661 ARG cc_start: 0.7813 (ptp-110) cc_final: 0.7430 (ptm160) REVERT: D 719 ASP cc_start: 0.7935 (t0) cc_final: 0.7571 (t0) REVERT: E 64 LEU cc_start: 0.7620 (tt) cc_final: 0.6979 (mt) REVERT: E 100 TYR cc_start: 0.7481 (t80) cc_final: 0.7250 (t80) outliers start: 60 outliers final: 37 residues processed: 319 average time/residue: 0.1316 time to fit residues: 64.8526 Evaluate side-chains 314 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 269 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 542 LEU 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 734 ILE Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 411 ASN Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 647 TYR Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 399 THR 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 642 GLN Chi-restraints excluded: chain C residue 718 CYS Chi-restraints excluded: chain C residue 734 ILE 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 C residue 1013 SER 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 69 VAL Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 90 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 109 optimal weight: 0.3980 chunk 221 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 190 optimal weight: 0.5980 chunk 48 optimal weight: 20.0000 chunk 142 optimal weight: 5.9990 chunk 135 optimal weight: 0.8980 chunk 152 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.208407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.155154 restraints weight = 19988.581| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 4.36 r_work: 0.3296 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18399 Z= 0.126 Angle : 0.593 13.973 24862 Z= 0.304 Chirality : 0.041 0.184 2794 Planarity : 0.004 0.061 3042 Dihedral : 5.178 43.662 2468 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.84 % Favored : 93.03 % Rotamer: Outliers : 2.73 % Allowed : 14.50 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.18), residues: 2238 helix: 1.18 (0.15), residues: 1298 sheet: -2.31 (0.41), residues: 138 loop : -2.99 (0.20), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 628 TYR 0.024 0.001 TYR F 100 PHE 0.018 0.001 PHE C 960 TRP 0.008 0.001 TRP A 766 HIS 0.010 0.001 HIS E 27 Details of bonding type rmsd covalent geometry : bond 0.00290 (18393) covalent geometry : angle 0.59276 (24850) SS BOND : bond 0.00444 ( 6) SS BOND : angle 0.87515 ( 12) hydrogen bonds : bond 0.03477 ( 890) hydrogen bonds : angle 3.74820 ( 2604) *********************** 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 337 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 284 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.8207 (tttm) REVERT: A 467 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8104 (pt) REVERT: A 592 SER cc_start: 0.8956 (t) cc_final: 0.8695 (p) REVERT: A 641 LYS cc_start: 0.7398 (OUTLIER) cc_final: 0.6877 (mmtp) REVERT: A 669 LYS cc_start: 0.7443 (mtmt) cc_final: 0.7025 (tttt) REVERT: A 715 ARG cc_start: 0.7092 (OUTLIER) cc_final: 0.6691 (mmp-170) REVERT: A 716 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7934 (tmtt) REVERT: A 863 TYR cc_start: 0.5692 (m-10) cc_final: 0.5055 (m-80) REVERT: A 1029 MET cc_start: 0.7032 (OUTLIER) cc_final: 0.6636 (mtm) REVERT: B 393 LYS cc_start: 0.6935 (ttpt) cc_final: 0.6029 (tptp) REVERT: B 678 GLU cc_start: 0.6389 (mm-30) cc_final: 0.6177 (mm-30) REVERT: B 719 ASP cc_start: 0.7870 (t0) cc_final: 0.7479 (t0) REVERT: C 467 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8333 (pt) REVERT: C 642 GLN cc_start: 0.6582 (OUTLIER) cc_final: 0.5876 (mp10) REVERT: C 669 LYS cc_start: 0.7462 (mtmt) cc_final: 0.7028 (tttt) REVERT: C 880 MET cc_start: 0.7318 (tmm) cc_final: 0.6888 (tmm) REVERT: C 901 PHE cc_start: 0.6037 (m-80) cc_final: 0.5425 (m-80) REVERT: C 1029 MET cc_start: 0.5929 (mmt) cc_final: 0.5400 (mmt) REVERT: D 393 LYS cc_start: 0.6943 (ttpt) cc_final: 0.5997 (tptp) REVERT: D 527 MET cc_start: 0.8369 (mmt) cc_final: 0.8067 (mmt) REVERT: D 545 ARG cc_start: 0.7771 (ttm-80) cc_final: 0.7397 (tpp80) REVERT: D 661 ARG cc_start: 0.7676 (ptp-110) cc_final: 0.7323 (ptm160) REVERT: D 719 ASP cc_start: 0.7824 (t0) cc_final: 0.7473 (t0) REVERT: E 100 TYR cc_start: 0.7365 (t80) cc_final: 0.7113 (t80) REVERT: F 143 LEU cc_start: 0.7991 (mm) cc_final: 0.7779 (mm) outliers start: 53 outliers final: 34 residues processed: 317 average time/residue: 0.1316 time to fit residues: 64.8889 Evaluate side-chains 316 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 274 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 641 LYS Chi-restraints excluded: chain A residue 715 ARG Chi-restraints excluded: chain A residue 716 LYS Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 411 ASN Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 647 TYR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 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 683 VAL Chi-restraints excluded: chain C residue 718 CYS Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 1013 SER Chi-restraints excluded: chain D residue 411 ASN Chi-restraints excluded: chain D residue 490 ASP Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 4 THR 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 32 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 154 optimal weight: 7.9990 chunk 79 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 161 optimal weight: 2.9990 chunk 153 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 152 optimal weight: 1.9990 chunk 145 optimal weight: 10.0000 chunk 85 optimal weight: 0.0980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 GLN A 642 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.204426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.155077 restraints weight = 19781.942| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 4.49 r_work: 0.3338 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18399 Z= 0.148 Angle : 0.604 13.267 24862 Z= 0.309 Chirality : 0.041 0.182 2794 Planarity : 0.004 0.062 3042 Dihedral : 5.156 51.174 2468 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.73 % Favored : 92.18 % Rotamer: Outliers : 3.30 % Allowed : 14.09 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.18), residues: 2238 helix: 1.26 (0.15), residues: 1298 sheet: -2.24 (0.41), residues: 138 loop : -2.93 (0.20), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 628 TYR 0.022 0.001 TYR F 100 PHE 0.032 0.001 PHE F 78 TRP 0.007 0.001 TRP E 88 HIS 0.011 0.001 HIS E 27 Details of bonding type rmsd covalent geometry : bond 0.00354 (18393) covalent geometry : angle 0.60367 (24850) SS BOND : bond 0.00352 ( 6) SS BOND : angle 0.84057 ( 12) hydrogen bonds : bond 0.03527 ( 890) hydrogen bonds : angle 3.73198 ( 2604) *********************** 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 356 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 292 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8302 (tttm) REVERT: A 467 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8169 (pt) REVERT: A 592 SER cc_start: 0.8915 (t) cc_final: 0.8677 (p) REVERT: A 641 LYS cc_start: 0.7501 (OUTLIER) cc_final: 0.6957 (mmtp) REVERT: A 669 LYS cc_start: 0.7391 (mtmt) cc_final: 0.6987 (tttt) REVERT: A 715 ARG cc_start: 0.7131 (OUTLIER) cc_final: 0.6738 (mmp-170) REVERT: A 734 ILE cc_start: 0.8989 (OUTLIER) cc_final: 0.8500 (mm) REVERT: A 807 MET cc_start: 0.8431 (mtm) cc_final: 0.8023 (mtm) REVERT: A 863 TYR cc_start: 0.5800 (m-10) cc_final: 0.5130 (m-80) REVERT: A 1016 LEU cc_start: 0.8480 (mp) cc_final: 0.8264 (mp) REVERT: A 1029 MET cc_start: 0.6920 (OUTLIER) cc_final: 0.6636 (mtm) REVERT: B 393 LYS cc_start: 0.6894 (ttpt) cc_final: 0.6624 (ttmt) REVERT: B 678 GLU cc_start: 0.6399 (mm-30) cc_final: 0.6172 (mm-30) REVERT: B 719 ASP cc_start: 0.7790 (t0) cc_final: 0.7422 (t0) REVERT: C 467 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8412 (pp) REVERT: C 642 GLN cc_start: 0.6620 (OUTLIER) cc_final: 0.5586 (mp-120) REVERT: C 669 LYS cc_start: 0.7416 (mtmt) cc_final: 0.6974 (tttt) REVERT: C 734 ILE cc_start: 0.8973 (OUTLIER) cc_final: 0.8502 (mm) REVERT: C 880 MET cc_start: 0.7184 (tmm) cc_final: 0.6750 (tmm) REVERT: C 901 PHE cc_start: 0.6040 (m-80) cc_final: 0.5437 (m-80) REVERT: C 1029 MET cc_start: 0.5752 (mmt) cc_final: 0.5166 (mmt) REVERT: D 393 LYS cc_start: 0.6901 (ttpt) cc_final: 0.5999 (tptp) REVERT: D 527 MET cc_start: 0.8291 (mmt) cc_final: 0.7917 (mmt) REVERT: D 545 ARG cc_start: 0.7804 (ttm-80) cc_final: 0.7477 (tpp80) REVERT: D 661 ARG cc_start: 0.7733 (ptp-110) cc_final: 0.7378 (ptm160) REVERT: D 719 ASP cc_start: 0.7830 (t0) cc_final: 0.7482 (t0) REVERT: E 100 TYR cc_start: 0.7376 (t80) cc_final: 0.7147 (t80) REVERT: E 128 LEU cc_start: 0.4759 (tp) cc_final: 0.4086 (pp) REVERT: F 27 HIS cc_start: 0.7415 (OUTLIER) cc_final: 0.6465 (p-80) REVERT: F 143 LEU cc_start: 0.8055 (mm) cc_final: 0.7822 (mm) outliers start: 64 outliers final: 42 residues processed: 332 average time/residue: 0.1315 time to fit residues: 68.2793 Evaluate side-chains 329 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 277 time to evaluate : 0.702 ------------------------------------------------------------------------------- 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 503 MET Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 641 LYS Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 715 ARG Chi-restraints excluded: chain A residue 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 A residue 1029 MET Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 411 ASN Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 647 TYR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 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 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 D residue 411 ASN Chi-restraints excluded: chain D residue 490 ASP Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 792 VAL Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 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 80 LEU 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 49 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 136 optimal weight: 0.5980 chunk 71 optimal weight: 0.3980 chunk 139 optimal weight: 9.9990 chunk 84 optimal weight: 4.9990 chunk 48 optimal weight: 8.9990 chunk 190 optimal weight: 1.9990 chunk 185 optimal weight: 0.8980 chunk 144 optimal weight: 10.0000 chunk 56 optimal weight: 9.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.4285 r_free = 0.4285 target = 0.204914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.156023 restraints weight = 19668.549| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 4.25 r_work: 0.3341 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.4131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18399 Z= 0.140 Angle : 0.598 13.597 24862 Z= 0.305 Chirality : 0.041 0.178 2794 Planarity : 0.004 0.066 3042 Dihedral : 5.052 50.548 2468 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.97 % Favored : 92.94 % Rotamer: Outliers : 3.41 % Allowed : 14.55 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.18), residues: 2238 helix: 1.38 (0.15), residues: 1294 sheet: -2.20 (0.41), residues: 138 loop : -2.88 (0.20), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 545 TYR 0.022 0.001 TYR F 100 PHE 0.023 0.001 PHE F 141 TRP 0.009 0.001 TRP E 88 HIS 0.011 0.001 HIS E 27 Details of bonding type rmsd covalent geometry : bond 0.00333 (18393) covalent geometry : angle 0.59746 (24850) SS BOND : bond 0.00330 ( 6) SS BOND : angle 0.74973 ( 12) hydrogen bonds : bond 0.03413 ( 890) hydrogen bonds : angle 3.65219 ( 2604) *********************** 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 349 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 283 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8264 (tttm) REVERT: A 467 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8077 (pt) REVERT: A 545 ARG cc_start: 0.7593 (ttm-80) cc_final: 0.7375 (tmm-80) REVERT: A 592 SER cc_start: 0.8898 (t) cc_final: 0.8654 (p) REVERT: A 641 LYS cc_start: 0.7560 (OUTLIER) cc_final: 0.6986 (mmtp) REVERT: A 669 LYS cc_start: 0.7354 (mtmt) cc_final: 0.6976 (tttt) REVERT: A 715 ARG cc_start: 0.7207 (OUTLIER) cc_final: 0.6912 (mmp-170) REVERT: A 716 LYS cc_start: 0.7706 (OUTLIER) cc_final: 0.7228 (tptt) REVERT: A 734 ILE cc_start: 0.8963 (OUTLIER) cc_final: 0.8493 (mm) REVERT: A 807 MET cc_start: 0.8379 (mtm) cc_final: 0.8065 (mtm) REVERT: A 863 TYR cc_start: 0.5745 (m-10) cc_final: 0.4975 (m-80) REVERT: A 1016 LEU cc_start: 0.8475 (mp) cc_final: 0.8275 (mp) REVERT: B 393 LYS cc_start: 0.6900 (ttpt) cc_final: 0.6647 (ttmt) REVERT: B 678 GLU cc_start: 0.6332 (mm-30) cc_final: 0.6097 (mm-30) REVERT: B 719 ASP cc_start: 0.7773 (t0) cc_final: 0.7411 (t0) REVERT: C 467 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8314 (pt) REVERT: C 642 GLN cc_start: 0.6560 (OUTLIER) cc_final: 0.5805 (mp10) REVERT: C 669 LYS cc_start: 0.7438 (mtmt) cc_final: 0.7002 (tttt) REVERT: C 734 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8486 (mm) REVERT: C 880 MET cc_start: 0.7120 (tmm) cc_final: 0.6683 (tmm) REVERT: C 901 PHE cc_start: 0.6233 (m-80) cc_final: 0.5621 (m-80) REVERT: C 1029 MET cc_start: 0.5666 (mmt) cc_final: 0.5202 (mmt) REVERT: D 393 LYS cc_start: 0.6866 (ttpt) cc_final: 0.5922 (tptp) REVERT: D 527 MET cc_start: 0.8265 (mmt) cc_final: 0.7889 (mmt) REVERT: D 545 ARG cc_start: 0.7764 (ttm-80) cc_final: 0.7473 (tpp80) REVERT: D 629 MET cc_start: 0.7806 (tpp) cc_final: 0.7283 (mmm) REVERT: D 661 ARG cc_start: 0.7676 (ptp-110) cc_final: 0.7320 (ptm160) REVERT: D 719 ASP cc_start: 0.7943 (t0) cc_final: 0.7556 (t0) REVERT: E 100 TYR cc_start: 0.7338 (t80) cc_final: 0.7103 (t80) REVERT: E 128 LEU cc_start: 0.4788 (tp) cc_final: 0.4115 (pp) REVERT: F 27 HIS cc_start: 0.7149 (OUTLIER) cc_final: 0.6515 (p-80) REVERT: F 143 LEU cc_start: 0.8104 (mm) cc_final: 0.7876 (mm) outliers start: 66 outliers final: 47 residues processed: 324 average time/residue: 0.1323 time to fit residues: 67.1070 Evaluate side-chains 330 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 273 time to evaluate : 0.733 ------------------------------------------------------------------------------- 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 629 MET Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 641 LYS Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 715 ARG Chi-restraints excluded: chain A residue 716 LYS Chi-restraints excluded: chain A residue 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 490 ASP Chi-restraints excluded: chain B residue 647 TYR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 514 VAL 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 708 MET 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 D residue 411 ASN Chi-restraints excluded: chain D residue 490 ASP Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 792 VAL Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 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 80 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 168 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 202 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 221 optimal weight: 10.0000 chunk 78 optimal weight: 0.7980 chunk 174 optimal weight: 0.9990 chunk 138 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 171 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.4313 r_free = 0.4313 target = 0.210796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.166611 restraints weight = 20236.695| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 3.56 r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.4224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18399 Z= 0.134 Angle : 0.594 13.829 24862 Z= 0.303 Chirality : 0.041 0.176 2794 Planarity : 0.004 0.063 3042 Dihedral : 5.005 53.114 2468 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.46 % Favored : 92.45 % Rotamer: Outliers : 3.30 % Allowed : 14.71 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.18), residues: 2238 helix: 1.46 (0.15), residues: 1294 sheet: -2.11 (0.41), residues: 138 loop : -2.84 (0.20), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 628 TYR 0.022 0.001 TYR F 100 PHE 0.029 0.001 PHE F 78 TRP 0.009 0.001 TRP E 88 HIS 0.011 0.001 HIS E 27 Details of bonding type rmsd covalent geometry : bond 0.00316 (18393) covalent geometry : angle 0.59444 (24850) SS BOND : bond 0.00284 ( 6) SS BOND : angle 0.67044 ( 12) hydrogen bonds : bond 0.03367 ( 890) hydrogen bonds : angle 3.61732 ( 2604) *********************** 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 343 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 279 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7908 (tttm) REVERT: A 467 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7787 (pt) REVERT: A 641 LYS cc_start: 0.7554 (OUTLIER) cc_final: 0.7017 (mmtp) REVERT: A 715 ARG cc_start: 0.6886 (OUTLIER) cc_final: 0.6578 (mmp-170) REVERT: A 734 ILE cc_start: 0.8508 (OUTLIER) cc_final: 0.8017 (mm) REVERT: A 863 TYR cc_start: 0.6776 (m-10) cc_final: 0.6146 (m-80) REVERT: B 393 LYS cc_start: 0.6880 (ttpt) cc_final: 0.6647 (ttmt) REVERT: B 719 ASP cc_start: 0.7385 (t0) cc_final: 0.7115 (t0) REVERT: C 467 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8083 (pt) REVERT: C 638 ASP cc_start: 0.7830 (m-30) cc_final: 0.6820 (m-30) REVERT: C 642 GLN cc_start: 0.6627 (OUTLIER) cc_final: 0.5880 (mp10) REVERT: C 734 ILE cc_start: 0.8480 (OUTLIER) cc_final: 0.7986 (mm) REVERT: C 880 MET cc_start: 0.7702 (tmm) cc_final: 0.7490 (tmm) REVERT: C 1029 MET cc_start: 0.5022 (mmt) cc_final: 0.4367 (mmt) REVERT: D 393 LYS cc_start: 0.6764 (ttpt) cc_final: 0.6384 (tptp) REVERT: D 527 MET cc_start: 0.6970 (mmt) cc_final: 0.6662 (mmt) REVERT: D 642 GLN cc_start: 0.6996 (mt0) cc_final: 0.6787 (pt0) REVERT: D 661 ARG cc_start: 0.7699 (ptp-110) cc_final: 0.7418 (ptm160) REVERT: D 719 ASP cc_start: 0.7551 (t0) cc_final: 0.7264 (t0) REVERT: F 27 HIS cc_start: 0.6958 (OUTLIER) cc_final: 0.6420 (p-80) outliers start: 64 outliers final: 47 residues processed: 318 average time/residue: 0.1347 time to fit residues: 66.4415 Evaluate side-chains 324 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 268 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 641 LYS Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 715 ARG Chi-restraints excluded: chain A residue 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 490 ASP Chi-restraints excluded: chain B residue 650 LEU 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 426 VAL Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 514 VAL 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 708 MET 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 D residue 411 ASN Chi-restraints excluded: chain D residue 490 ASP Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 792 VAL Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 80 LEU 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 183 optimal weight: 3.9990 chunk 162 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 111 optimal weight: 0.6980 chunk 173 optimal weight: 4.9990 chunk 130 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 181 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 642 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.209485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.164686 restraints weight = 20203.042| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 3.52 r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.4312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 18399 Z= 0.164 Angle : 0.630 13.767 24862 Z= 0.321 Chirality : 0.042 0.177 2794 Planarity : 0.004 0.067 3042 Dihedral : 5.071 53.145 2468 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.64 % Favored : 92.27 % Rotamer: Outliers : 3.30 % Allowed : 15.12 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.18), residues: 2238 helix: 1.43 (0.15), residues: 1286 sheet: -2.14 (0.41), residues: 138 loop : -2.83 (0.20), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 545 TYR 0.021 0.001 TYR F 100 PHE 0.022 0.001 PHE F 141 TRP 0.011 0.001 TRP E 88 HIS 0.011 0.001 HIS E 27 Details of bonding type rmsd covalent geometry : bond 0.00400 (18393) covalent geometry : angle 0.62977 (24850) SS BOND : bond 0.00331 ( 6) SS BOND : angle 0.63946 ( 12) hydrogen bonds : bond 0.03556 ( 890) hydrogen bonds : angle 3.69874 ( 2604) ********************** 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 343 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 279 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 434 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.7993 (tttm) REVERT: A 467 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8016 (pt) REVERT: A 641 LYS cc_start: 0.7646 (OUTLIER) cc_final: 0.7232 (mmtp) REVERT: A 715 ARG cc_start: 0.7040 (OUTLIER) cc_final: 0.6661 (mmp-170) REVERT: A 734 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.7966 (mm) REVERT: A 807 MET cc_start: 0.8178 (mtm) cc_final: 0.7866 (mtm) REVERT: A 863 TYR cc_start: 0.6842 (m-10) cc_final: 0.6271 (m-80) REVERT: B 393 LYS cc_start: 0.6924 (ttpt) cc_final: 0.6674 (ttmt) REVERT: B 719 ASP cc_start: 0.7417 (t0) cc_final: 0.7160 (t0) REVERT: C 467 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8189 (pp) REVERT: C 642 GLN cc_start: 0.6550 (OUTLIER) cc_final: 0.5724 (mp10) REVERT: C 734 ILE cc_start: 0.8493 (OUTLIER) cc_final: 0.7982 (mm) REVERT: C 1029 MET cc_start: 0.5345 (mmt) cc_final: 0.4667 (mmt) REVERT: D 393 LYS cc_start: 0.6711 (ttpt) cc_final: 0.6468 (ttmt) REVERT: D 527 MET cc_start: 0.7178 (mmt) cc_final: 0.6855 (mmt) REVERT: D 661 ARG cc_start: 0.7746 (ptp-110) cc_final: 0.7479 (ptm160) REVERT: D 719 ASP cc_start: 0.7595 (t0) cc_final: 0.7300 (t0) REVERT: F 27 HIS cc_start: 0.7140 (OUTLIER) cc_final: 0.6641 (p-80) REVERT: F 83 LEU cc_start: 0.7983 (tp) cc_final: 0.7579 (tp) REVERT: F 116 MET cc_start: 0.5455 (tpt) cc_final: 0.4388 (tpt) outliers start: 64 outliers final: 47 residues processed: 316 average time/residue: 0.1220 time to fit residues: 60.2651 Evaluate side-chains 320 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 264 time to evaluate : 0.598 ------------------------------------------------------------------------------- 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 629 MET Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 641 LYS Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 715 ARG Chi-restraints excluded: chain A residue 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 490 ASP Chi-restraints excluded: chain B residue 650 LEU 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 467 LEU Chi-restraints excluded: chain C residue 514 VAL 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 708 MET 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 D residue 411 ASN Chi-restraints excluded: chain D residue 490 ASP Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 792 VAL Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 80 LEU 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 144 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 201 optimal weight: 10.0000 chunk 116 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 158 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 114 optimal weight: 0.0040 chunk 145 optimal weight: 4.9990 chunk 195 optimal weight: 0.8980 overall best weight: 0.7592 ------------------------------------------------------------------------------- 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 = 0.4293 r_free = 0.4293 target = 0.205884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.159293 restraints weight = 19705.824| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 3.48 r_work: 0.3331 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.4426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18399 Z= 0.129 Angle : 0.605 13.980 24862 Z= 0.307 Chirality : 0.041 0.175 2794 Planarity : 0.004 0.063 3042 Dihedral : 4.964 53.454 2468 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.93 % Favored : 92.94 % Rotamer: Outliers : 2.79 % Allowed : 15.43 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.18), residues: 2238 helix: 1.55 (0.15), residues: 1286 sheet: -2.18 (0.38), residues: 158 loop : -2.75 (0.20), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 545 TYR 0.022 0.001 TYR F 100 PHE 0.020 0.001 PHE F 141 TRP 0.011 0.001 TRP E 88 HIS 0.011 0.001 HIS E 27 Details of bonding type rmsd covalent geometry : bond 0.00302 (18393) covalent geometry : angle 0.60496 (24850) SS BOND : bond 0.00250 ( 6) SS BOND : angle 0.68153 ( 12) hydrogen bonds : bond 0.03353 ( 890) hydrogen bonds : angle 3.60641 ( 2604) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4447.31 seconds wall clock time: 76 minutes 58.25 seconds (4618.25 seconds total)