Starting phenix.real_space_refine on Sat Jun 29 09:55:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ss4_40743/06_2024/8ss4_40743_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ss4_40743/06_2024/8ss4_40743.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ss4_40743/06_2024/8ss4_40743.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ss4_40743/06_2024/8ss4_40743.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ss4_40743/06_2024/8ss4_40743_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ss4_40743/06_2024/8ss4_40743_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.091 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 130 5.16 5 C 11763 2.51 5 N 2877 2.21 5 O 3208 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 545": "NH1" <-> "NH2" Residue "A ARG 599": "NH1" <-> "NH2" Residue "A ARG 675": "NH1" <-> "NH2" Residue "A ARG 819": "NH1" <-> "NH2" Residue "A ARG 952": "NH1" <-> "NH2" Residue "A ARG 955": "NH1" <-> "NH2" Residue "A ARG 991": "NH1" <-> "NH2" Residue "A ARG 1031": "NH1" <-> "NH2" Residue "B ARG 594": "NH1" <-> "NH2" Residue "B ARG 628": "NH1" <-> "NH2" Residue "B ARG 660": "NH1" <-> "NH2" Residue "B ARG 819": "NH1" <-> "NH2" Residue "C PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 545": "NH1" <-> "NH2" Residue "C ARG 599": "NH1" <-> "NH2" Residue "C ARG 675": "NH1" <-> "NH2" Residue "C ARG 819": "NH1" <-> "NH2" Residue "C ARG 952": "NH1" <-> "NH2" Residue "C ARG 955": "NH1" <-> "NH2" Residue "C ARG 991": "NH1" <-> "NH2" Residue "C ARG 1031": "NH1" <-> "NH2" Residue "D ARG 594": "NH1" <-> "NH2" Residue "D ARG 628": "NH1" <-> "NH2" Residue "D ARG 660": "NH1" <-> "NH2" Residue "D ARG 819": "NH1" <-> "NH2" Residue "E ARG 59": "NH1" <-> "NH2" Residue "E ARG 65": "NH1" <-> "NH2" Residue "E ARG 108": "NH1" <-> "NH2" Residue "F ARG 59": "NH1" <-> "NH2" Residue "F ARG 65": "NH1" <-> "NH2" Residue "F ARG 108": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 17978 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4662 Classifications: {'peptide': 595} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 577} Chain breaks: 4 Chain: "B" Number of atoms: 3156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3156 Classifications: {'peptide': 404} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 390} Chain breaks: 2 Chain: "C" Number of atoms: 4662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4662 Classifications: {'peptide': 595} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 577} Chain breaks: 4 Chain: "D" Number of atoms: 3156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3156 Classifications: {'peptide': 404} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 390} Chain breaks: 2 Chain: "E" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1166 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain breaks: 1 Chain: "F" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1166 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain breaks: 1 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'SPD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.09, per 1000 atoms: 0.56 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 - 3.50 Amino acid : False - 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: 6.34 Conformation dependent library (CDL) restraints added in 3.3 seconds 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4204 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 82 helices and 16 sheets defined 51.4% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.17 Creating SS restraints... Processing helix chain 'A' and resid 418 through 420 No H-bonds generated for 'chain 'A' and resid 418 through 420' Processing helix chain 'A' and resid 424 through 436 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 462 through 468 removed outlier: 3.877A pdb=" N LEU A 467 " --> pdb=" O MET A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 486 No H-bonds generated for 'chain 'A' and resid 483 through 486' Processing helix chain 'A' and resid 516 through 519 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 516 through 519' Processing helix chain 'A' and resid 523 through 542 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 573 through 584 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) Processing helix chain 'A' and resid 596 through 628 removed outlier: 3.529A pdb=" N ILE A 600 " --> pdb=" O LEU A 596 " (cutoff:3.500A) 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 636 through 641 removed outlier: 3.683A pdb=" N LYS A 641 " --> pdb=" O GLU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 661 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 665 through 675 Processing helix chain 'A' and resid 686 through 694 Processing helix chain 'A' and resid 709 through 713 Processing helix chain 'A' and resid 744 through 756 removed outlier: 3.799A pdb=" N GLU A 755 " --> pdb=" O LEU A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 767 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 794 through 821 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 855 Processing helix chain 'A' and resid 894 through 896 No H-bonds generated for 'chain 'A' and resid 894 through 896' Processing helix chain 'A' and resid 927 through 951 Proline residue: A 930 - end of helix removed outlier: 3.616A pdb=" N VAL A 934 " --> pdb=" O PHE A 931 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N PHE A 938 " --> pdb=" O SER A 935 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N MET A 939 " --> pdb=" O LEU A 936 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE A 941 " --> pdb=" O PHE A 938 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU A 945 " --> pdb=" O GLY A 942 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER A 946 " --> pdb=" O PHE A 943 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ILE A 948 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE A 951 " --> pdb=" O ILE A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 989 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 1005 through 1034 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 424 through 435 Processing helix chain 'B' and resid 463 through 468 Processing helix chain 'B' and resid 483 through 486 No H-bonds generated for 'chain 'B' and resid 483 through 486' Processing helix chain 'B' and resid 516 through 518 No H-bonds generated for 'chain 'B' and resid 516 through 518' Processing helix chain 'B' and resid 523 through 545 removed outlier: 3.527A pdb=" N MET B 527 " --> pdb=" O TYR B 523 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA B 532 " --> pdb=" O CYS B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 582 Processing helix chain 'B' and resid 596 through 625 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 636 through 641 removed outlier: 3.745A pdb=" N LYS B 641 " --> pdb=" O GLU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 660 removed outlier: 3.788A pdb=" N PHE B 659 " --> pdb=" O THR B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 676 removed outlier: 3.505A pdb=" N SER B 676 " --> pdb=" O THR B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 695 Processing helix chain 'B' and resid 706 through 714 removed outlier: 3.530A pdb=" N GLU B 710 " --> pdb=" O SER B 706 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLN B 714 " --> pdb=" O GLU B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 743 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 758 through 766 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 791 through 819 removed outlier: 4.744A pdb=" N GLY B 794 " --> pdb=" O ASN B 791 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N VAL B 795 " --> pdb=" O VAL B 792 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE B 798 " --> pdb=" O VAL B 795 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU B 799 " --> pdb=" O PHE B 796 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL B 800 " --> pdb=" O TYR B 797 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY B 801 " --> pdb=" O ILE B 798 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY B 804 " --> pdb=" O GLY B 801 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU B 805 " --> pdb=" O GLY B 802 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET B 807 " --> pdb=" O GLY B 804 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU B 808 " --> pdb=" O LEU B 805 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU B 813 " --> pdb=" O ALA B 810 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N PHE B 814 " --> pdb=" O LEU B 811 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR B 816 " --> pdb=" O GLU B 813 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N SER B 818 " --> pdb=" O CYS B 815 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG B 819 " --> pdb=" O TYR B 816 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 420 No H-bonds generated for 'chain 'C' and resid 418 through 420' Processing helix chain 'C' and resid 424 through 436 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 462 through 468 removed outlier: 3.878A pdb=" N LEU C 467 " --> pdb=" O MET C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 486 No H-bonds generated for 'chain 'C' and resid 483 through 486' Processing helix chain 'C' and resid 516 through 519 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 516 through 519' Processing helix chain 'C' and resid 523 through 542 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 573 through 584 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) Processing helix chain 'C' and resid 596 through 628 removed outlier: 3.529A pdb=" N ILE C 600 " --> pdb=" O LEU C 596 " (cutoff:3.500A) 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 636 through 641 removed outlier: 3.683A pdb=" N LYS C 641 " --> pdb=" O GLU C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 654 through 661 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 665 through 675 Processing helix chain 'C' and resid 686 through 694 Processing helix chain 'C' and resid 709 through 713 Processing helix chain 'C' and resid 744 through 756 removed outlier: 3.799A pdb=" N GLU C 755 " --> pdb=" O LEU C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 767 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 794 through 821 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 855 Processing helix chain 'C' and resid 894 through 896 No H-bonds generated for 'chain 'C' and resid 894 through 896' Processing helix chain 'C' and resid 927 through 951 Proline residue: C 930 - end of helix removed outlier: 3.616A pdb=" N VAL C 934 " --> pdb=" O PHE C 931 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N PHE C 938 " --> pdb=" O SER C 935 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N MET C 939 " --> pdb=" O LEU C 936 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE C 941 " --> pdb=" O PHE C 938 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU C 945 " --> pdb=" O GLY C 942 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER C 946 " --> pdb=" O PHE C 943 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ILE C 948 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE C 951 " --> pdb=" O ILE C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 956 through 989 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 1005 through 1034 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 424 through 435 Processing helix chain 'D' and resid 463 through 468 Processing helix chain 'D' and resid 483 through 486 No H-bonds generated for 'chain 'D' and resid 483 through 486' Processing helix chain 'D' and resid 516 through 518 No H-bonds generated for 'chain 'D' and resid 516 through 518' Processing helix chain 'D' and resid 523 through 545 removed outlier: 3.527A pdb=" N MET D 527 " --> pdb=" O TYR D 523 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA D 532 " --> pdb=" O CYS D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 582 Processing helix chain 'D' and resid 596 through 625 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 636 through 641 removed outlier: 3.745A pdb=" N LYS D 641 " --> pdb=" O GLU D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 654 through 660 removed outlier: 3.789A pdb=" N PHE D 659 " --> pdb=" O THR D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 667 through 676 removed outlier: 3.505A pdb=" N SER D 676 " --> pdb=" O THR D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 686 through 695 Processing helix chain 'D' and resid 706 through 714 removed outlier: 3.531A pdb=" N GLU D 710 " --> pdb=" O SER D 706 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN D 714 " --> pdb=" O GLU D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 743 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 758 through 766 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 791 through 819 removed outlier: 4.744A pdb=" N GLY D 794 " --> pdb=" O ASN D 791 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N VAL D 795 " --> pdb=" O VAL D 792 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE D 798 " --> pdb=" O VAL D 795 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU D 799 " --> pdb=" O PHE D 796 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL D 800 " --> pdb=" O TYR D 797 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY D 801 " --> pdb=" O ILE D 798 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY D 804 " --> pdb=" O GLY D 801 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU D 805 " --> pdb=" O GLY D 802 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET D 807 " --> pdb=" O GLY D 804 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU D 808 " --> pdb=" O LEU D 805 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU D 813 " --> pdb=" O ALA D 810 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N PHE D 814 " --> pdb=" O LEU D 811 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR D 816 " --> pdb=" O GLU D 813 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER D 818 " --> pdb=" O CYS D 815 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ARG D 819 " --> pdb=" O TYR D 816 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 35 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 67 removed outlier: 3.624A pdb=" N LYS E 66 " --> pdb=" O CYS E 62 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LEU E 67 " --> pdb=" O LEU E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 84 removed outlier: 3.587A pdb=" N LEU E 80 " --> pdb=" O GLY E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 105 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) Processing helix chain 'E' and resid 132 through 158 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 5 through 35 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 67 removed outlier: 4.455A pdb=" N LEU F 67 " --> pdb=" O LEU F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 84 Processing helix chain 'F' and resid 88 through 105 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) Processing helix chain 'F' and resid 132 through 158 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= A, first strand: chain 'A' and resid 396 through 399 removed outlier: 6.253A pdb=" N LYS A 441 " --> pdb=" O VAL A 397 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N THR A 399 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N THR A 443 " --> pdb=" O THR A 399 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 703 through 705 removed outlier: 3.852A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 646 through 648 removed outlier: 4.025A pdb=" N GLY A 648 " --> pdb=" O ALA A 701 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 862 through 864 Processing sheet with id= E, first strand: chain 'A' and resid 867 through 869 Processing sheet with id= F, first strand: chain 'B' and resid 395 through 397 Processing sheet with id= G, first strand: chain 'B' and resid 496 through 498 removed outlier: 4.449A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 720 through 723 removed outlier: 4.009A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 8.777A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 396 through 399 removed outlier: 6.253A pdb=" N LYS C 441 " --> pdb=" O VAL C 397 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N THR C 399 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N THR C 443 " --> pdb=" O THR C 399 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'C' and resid 703 through 705 removed outlier: 3.852A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 646 through 648 removed outlier: 4.025A pdb=" N GLY C 648 " --> pdb=" O ALA C 701 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 862 through 864 Processing sheet with id= M, first strand: chain 'C' and resid 867 through 869 Processing sheet with id= N, first strand: chain 'D' and resid 395 through 397 Processing sheet with id= O, first strand: chain 'D' and resid 496 through 498 removed outlier: 4.450A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 720 through 723 removed outlier: 4.009A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 8.778A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) 729 hydrogen bonds defined for protein. 2049 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: 4.90 Time building geometry restraints manager: 6.98 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: 98.04 - 105.33: 314 105.33 - 112.62: 9170 112.62 - 119.91: 6749 119.91 - 127.21: 8398 127.21 - 134.50: 219 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: 3873 2.77 - 3.30: 16313 3.30 - 3.84: 28299 3.84 - 4.37: 34434 4.37 - 4.90: 59200 Nonbonded interactions: 142119 Sorted by model distance: nonbonded pdb=" O LEU B 639 " pdb=" OH TYR B 647 " model vdw 2.238 2.440 nonbonded pdb=" O LEU D 639 " pdb=" OH TYR D 647 " model vdw 2.239 2.440 nonbonded pdb=" O ALA C 959 " pdb=" OG SER C 962 " model vdw 2.274 2.440 nonbonded pdb=" O ALA A 959 " pdb=" OG SER A 962 " model vdw 2.274 2.440 nonbonded pdb=" OE1 GLU B 402 " pdb=" OH TYR B 450 " model vdw 2.283 2.440 ... (remaining 142114 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 7.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 5.890 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 46.210 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.060 ------------------------------------------------------------------------------- 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 18393 Z= 0.594 Angle : 1.233 13.714 24850 Z= 0.719 Chirality : 0.060 0.380 2794 Planarity : 0.007 0.084 3042 Dihedral : 10.768 70.869 6587 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.49 % Favored : 91.15 % Rotamer: Outliers : 0.36 % Allowed : 5.68 % Favored : 93.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.00 % Twisted Proline : 6.06 % Twisted General : 0.50 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.98 (0.12), residues: 2238 helix: -3.73 (0.08), residues: 1282 sheet: -3.97 (0.29), residues: 196 loop : -3.99 (0.17), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP A 861 HIS 0.014 0.002 HIS F 107 PHE 0.034 0.003 PHE B 667 TYR 0.031 0.003 TYR D 702 ARG 0.015 0.001 ARG D 628 *********************** 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 fitting. rotamer outliers: 7 poor density : 391 time to evaluate : 1.869 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: 0.3082 time to fit residues: 181.0391 Evaluate side-chains 272 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 271 time to evaluate : 1.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 69 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 190 optimal weight: 0.7980 chunk 171 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 177 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 107 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 chunk 205 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS A 575 ASN A 747 ASN ** A 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 ASN B 412 HIS C 412 HIS C 575 ASN C 586 GLN C 587 GLN C 747 ASN ** C 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** F 124 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18393 Z= 0.206 Angle : 0.662 11.544 24850 Z= 0.346 Chirality : 0.042 0.188 2794 Planarity : 0.005 0.080 3042 Dihedral : 6.076 54.851 2468 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.51 % Favored : 92.31 % Rotamer: Outliers : 2.22 % Allowed : 9.91 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.58 (0.15), residues: 2238 helix: -1.43 (0.13), residues: 1276 sheet: -3.47 (0.33), residues: 178 loop : -3.59 (0.18), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 766 HIS 0.005 0.001 HIS E 27 PHE 0.031 0.002 PHE E 31 TYR 0.017 0.001 TYR B 702 ARG 0.004 0.000 ARG A 888 *********************** 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 333 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 290 time to evaluate : 2.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 MET cc_start: 0.6916 (tmm) cc_final: 0.6594 (tmm) REVERT: A 431 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7583 (mm-30) REVERT: A 467 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8030 (pt) REVERT: A 637 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7837 (mt-10) REVERT: A 644 GLU cc_start: 0.7540 (pt0) cc_final: 0.7308 (pt0) REVERT: A 669 LYS cc_start: 0.7224 (mtmt) cc_final: 0.6760 (tttt) REVERT: A 907 MET cc_start: 0.4981 (ttt) cc_final: 0.4277 (mpp) REVERT: A 1002 LYS cc_start: 0.6628 (ttmp) cc_final: 0.6188 (mmtt) REVERT: B 393 LYS cc_start: 0.6948 (ttpt) cc_final: 0.6332 (tptp) REVERT: B 708 MET cc_start: 0.7514 (tpt) cc_final: 0.7186 (mmp) REVERT: B 719 ASP cc_start: 0.7265 (t0) cc_final: 0.7057 (t0) REVERT: C 431 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7429 (mm-30) REVERT: C 467 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8231 (pt) REVERT: C 637 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7653 (mt-10) REVERT: C 651 ASP cc_start: 0.7364 (t70) cc_final: 0.7122 (t70) REVERT: C 729 SER cc_start: 0.8834 (t) cc_final: 0.8546 (p) REVERT: C 863 TYR cc_start: 0.5692 (m-10) cc_final: 0.5114 (m-80) REVERT: D 393 LYS cc_start: 0.6811 (ttpt) cc_final: 0.6026 (tptp) REVERT: D 661 ARG cc_start: 0.7959 (ptp-110) cc_final: 0.7698 (ptm160) REVERT: D 708 MET cc_start: 0.7870 (tpt) cc_final: 0.7636 (tpt) REVERT: D 719 ASP cc_start: 0.7457 (t0) cc_final: 0.7147 (t0) REVERT: E 23 PHE cc_start: 0.6023 (m-80) cc_final: 0.5702 (m-10) REVERT: F 139 LEU cc_start: 0.6414 (tp) cc_final: 0.5242 (pp) outliers start: 43 outliers final: 16 residues processed: 323 average time/residue: 0.2854 time to fit residues: 142.1782 Evaluate side-chains 274 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 256 time to evaluate : 1.975 ------------------------------------------------------------------------------- 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 411 ASN Chi-restraints excluded: chain A residue 467 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 411 ASN Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain D residue 590 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 114 optimal weight: 4.9990 chunk 63 optimal weight: 0.5980 chunk 170 optimal weight: 0.9990 chunk 139 optimal weight: 10.0000 chunk 56 optimal weight: 0.9990 chunk 205 optimal weight: 1.9990 chunk 222 optimal weight: 0.3980 chunk 183 optimal weight: 7.9990 chunk 203 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 164 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 642 GLN ** A 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 HIS C 586 GLN ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18393 Z= 0.202 Angle : 0.600 9.015 24850 Z= 0.309 Chirality : 0.040 0.188 2794 Planarity : 0.004 0.063 3042 Dihedral : 5.542 54.173 2468 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.64 % Favored : 92.18 % Rotamer: Outliers : 3.15 % Allowed : 11.20 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.00 % Twisted Proline : 6.06 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.17), residues: 2238 helix: -0.23 (0.14), residues: 1282 sheet: -3.21 (0.35), residues: 176 loop : -3.37 (0.19), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 766 HIS 0.006 0.001 HIS E 27 PHE 0.024 0.001 PHE E 141 TYR 0.024 0.001 TYR F 100 ARG 0.005 0.000 ARG D 628 *********************** 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 343 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 282 time to evaluate : 1.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 MET cc_start: 0.6885 (tmm) cc_final: 0.6618 (tmm) REVERT: A 431 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7612 (mm-30) REVERT: A 467 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.7819 (pt) REVERT: A 669 LYS cc_start: 0.7143 (mtmt) cc_final: 0.6716 (tttt) REVERT: A 907 MET cc_start: 0.4933 (ttt) cc_final: 0.4224 (mpp) REVERT: A 921 VAL cc_start: 0.5959 (OUTLIER) cc_final: 0.5754 (t) REVERT: A 1002 LYS cc_start: 0.6506 (ttmp) cc_final: 0.6164 (mmtt) REVERT: A 1029 MET cc_start: 0.7501 (mmm) cc_final: 0.6945 (mtp) REVERT: B 393 LYS cc_start: 0.6960 (ttpt) cc_final: 0.6146 (tptp) REVERT: B 708 MET cc_start: 0.7630 (tpt) cc_final: 0.7373 (tpt) REVERT: B 719 ASP cc_start: 0.7304 (t0) cc_final: 0.7103 (t0) REVERT: C 431 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7473 (mm-30) REVERT: C 467 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8076 (pt) REVERT: C 630 VAL cc_start: 0.8582 (p) cc_final: 0.8282 (m) REVERT: C 651 ASP cc_start: 0.7383 (t70) cc_final: 0.6971 (t70) REVERT: C 729 SER cc_start: 0.8839 (t) cc_final: 0.8534 (p) REVERT: C 863 TYR cc_start: 0.5718 (m-10) cc_final: 0.5098 (m-80) REVERT: D 393 LYS cc_start: 0.6902 (ttpt) cc_final: 0.6230 (tptp) REVERT: D 545 ARG cc_start: 0.7435 (ttm-80) cc_final: 0.7115 (tpp80) REVERT: D 661 ARG cc_start: 0.7967 (ptp-110) cc_final: 0.7725 (ptm160) REVERT: D 719 ASP cc_start: 0.7420 (t0) cc_final: 0.7042 (t0) outliers start: 61 outliers final: 30 residues processed: 326 average time/residue: 0.2509 time to fit residues: 128.7203 Evaluate side-chains 287 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 254 time to evaluate : 1.880 ------------------------------------------------------------------------------- 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 527 MET Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 716 LYS Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 921 VAL Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 411 ASN Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 649 THR 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 411 ASN Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 596 LEU Chi-restraints excluded: chain C residue 719 ASP 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 490 ASP Chi-restraints excluded: chain D residue 590 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 90 THR Chi-restraints excluded: chain F residue 4 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 203 optimal weight: 3.9990 chunk 154 optimal weight: 9.9990 chunk 106 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 98 optimal weight: 9.9990 chunk 138 optimal weight: 9.9990 chunk 206 optimal weight: 7.9990 chunk 218 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 195 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 642 GLN ** A 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 HIS B 756 GLN B 764 ASN C 764 ASN C 872 GLN D 764 ASN ** E 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.070 18393 Z= 0.526 Angle : 0.766 12.623 24850 Z= 0.392 Chirality : 0.048 0.311 2794 Planarity : 0.005 0.067 3042 Dihedral : 6.007 54.924 2468 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.41 % Favored : 89.41 % Rotamer: Outliers : 3.61 % Allowed : 12.64 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.00 % Twisted Proline : 6.06 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.17), residues: 2238 helix: -0.24 (0.14), residues: 1278 sheet: -3.18 (0.34), residues: 188 loop : -3.38 (0.20), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 136 HIS 0.010 0.003 HIS E 27 PHE 0.027 0.002 PHE C 495 TYR 0.024 0.002 TYR C 533 ARG 0.009 0.001 ARG C 545 *********************** 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 336 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 266 time to evaluate : 2.001 Fit side-chains REVERT: A 414 MET cc_start: 0.7095 (tmm) cc_final: 0.6852 (tmm) REVERT: A 431 GLU cc_start: 0.8396 (mm-30) cc_final: 0.8004 (mm-30) REVERT: A 592 SER cc_start: 0.9033 (t) cc_final: 0.8756 (p) REVERT: A 641 LYS cc_start: 0.7364 (OUTLIER) cc_final: 0.6845 (mmtp) REVERT: A 669 LYS cc_start: 0.7188 (mtmt) cc_final: 0.6778 (tttt) REVERT: A 719 ASP cc_start: 0.6322 (t70) cc_final: 0.6067 (t0) REVERT: A 863 TYR cc_start: 0.5701 (m-10) cc_final: 0.5070 (m-80) REVERT: A 891 PHE cc_start: 0.6821 (m-80) cc_final: 0.6606 (m-80) REVERT: A 907 MET cc_start: 0.5125 (ttt) cc_final: 0.4270 (mpp) REVERT: A 1029 MET cc_start: 0.7530 (mmm) cc_final: 0.6505 (mmm) REVERT: B 708 MET cc_start: 0.7702 (tpt) cc_final: 0.7478 (tpt) REVERT: B 719 ASP cc_start: 0.7670 (t0) cc_final: 0.7447 (t0) REVERT: C 431 GLU cc_start: 0.8332 (mm-30) cc_final: 0.7980 (mm-30) REVERT: C 641 LYS cc_start: 0.7190 (OUTLIER) cc_final: 0.6671 (mmtp) REVERT: C 642 GLN cc_start: 0.6012 (OUTLIER) cc_final: 0.5180 (mp10) REVERT: C 651 ASP cc_start: 0.7623 (t70) cc_final: 0.7243 (t70) REVERT: C 669 LYS cc_start: 0.7328 (mtmt) cc_final: 0.6972 (mtpt) REVERT: C 704 LEU cc_start: 0.8839 (tp) cc_final: 0.8615 (tp) REVERT: C 729 SER cc_start: 0.8965 (t) cc_final: 0.8644 (p) REVERT: C 863 TYR cc_start: 0.5938 (m-10) cc_final: 0.5186 (m-80) REVERT: C 988 MET cc_start: 0.7810 (mmp) cc_final: 0.7329 (mmm) REVERT: C 1029 MET cc_start: 0.5864 (mmt) cc_final: 0.5360 (mmt) REVERT: D 678 GLU cc_start: 0.6813 (mm-30) cc_final: 0.6515 (mm-30) REVERT: D 708 MET cc_start: 0.7734 (tpt) cc_final: 0.7488 (tpt) REVERT: D 719 ASP cc_start: 0.7482 (t0) cc_final: 0.7148 (t0) outliers start: 70 outliers final: 42 residues processed: 314 average time/residue: 0.2749 time to fit residues: 133.0274 Evaluate side-chains 294 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 249 time to evaluate : 2.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 596 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 644 GLU Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 411 ASN Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 706 SER Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 596 LEU Chi-restraints excluded: chain C residue 641 LYS Chi-restraints excluded: chain C residue 642 GLN Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 718 CYS Chi-restraints excluded: chain C residue 719 ASP Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain D residue 411 ASN Chi-restraints excluded: chain D residue 490 ASP Chi-restraints excluded: chain D residue 590 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 120 VAL Chi-restraints excluded: chain E residue 153 MET Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 90 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 181 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 162 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 186 optimal weight: 1.9990 chunk 151 optimal weight: 0.9990 chunk 0 optimal weight: 0.5980 chunk 111 optimal weight: 0.9980 chunk 196 optimal weight: 0.4980 chunk 55 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 HIS ** F 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18393 Z= 0.186 Angle : 0.591 9.385 24850 Z= 0.303 Chirality : 0.040 0.200 2794 Planarity : 0.004 0.060 3042 Dihedral : 5.438 52.439 2468 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.06 % Favored : 92.76 % Rotamer: Outliers : 2.84 % Allowed : 14.14 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.00 % Twisted Proline : 6.06 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.18), residues: 2238 helix: 0.39 (0.15), residues: 1276 sheet: -2.96 (0.36), residues: 166 loop : -3.25 (0.19), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 136 HIS 0.009 0.001 HIS E 27 PHE 0.020 0.001 PHE E 141 TYR 0.025 0.001 TYR F 100 ARG 0.005 0.000 ARG D 628 *********************** 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 323 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 268 time to evaluate : 2.065 Fit side-chains REVERT: A 431 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7859 (mm-30) REVERT: A 467 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8091 (pt) REVERT: A 592 SER cc_start: 0.8984 (t) cc_final: 0.8701 (p) REVERT: A 669 LYS cc_start: 0.7111 (mtmt) cc_final: 0.6737 (tttt) REVERT: A 716 LYS cc_start: 0.7908 (OUTLIER) cc_final: 0.7419 (mmmt) REVERT: A 863 TYR cc_start: 0.5752 (m-10) cc_final: 0.5126 (m-80) REVERT: A 907 MET cc_start: 0.5139 (ttt) cc_final: 0.4344 (mpp) REVERT: A 1026 TYR cc_start: 0.7387 (OUTLIER) cc_final: 0.7033 (m-10) REVERT: A 1029 MET cc_start: 0.7244 (OUTLIER) cc_final: 0.5977 (mmm) REVERT: B 708 MET cc_start: 0.7671 (tpt) cc_final: 0.7452 (tpt) REVERT: B 719 ASP cc_start: 0.7385 (t0) cc_final: 0.7056 (t0) REVERT: C 431 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7823 (mm-30) REVERT: C 467 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8222 (pt) REVERT: C 545 ARG cc_start: 0.7269 (mmm160) cc_final: 0.6509 (ttt-90) REVERT: C 651 ASP cc_start: 0.7647 (t70) cc_final: 0.7252 (t70) REVERT: C 669 LYS cc_start: 0.7256 (mtmt) cc_final: 0.6848 (tttt) REVERT: C 729 SER cc_start: 0.8907 (t) cc_final: 0.8581 (p) REVERT: C 863 TYR cc_start: 0.5720 (m-10) cc_final: 0.4969 (m-80) REVERT: C 988 MET cc_start: 0.7822 (mmp) cc_final: 0.7344 (mmm) REVERT: C 1029 MET cc_start: 0.5756 (mmt) cc_final: 0.4839 (mmt) REVERT: D 393 LYS cc_start: 0.7863 (mmmt) cc_final: 0.7585 (tptp) REVERT: D 545 ARG cc_start: 0.7641 (ttm-80) cc_final: 0.7377 (tpp80) REVERT: D 708 MET cc_start: 0.7774 (tpt) cc_final: 0.7526 (tpt) REVERT: D 719 ASP cc_start: 0.7518 (t0) cc_final: 0.7121 (t0) outliers start: 55 outliers final: 30 residues processed: 307 average time/residue: 0.2798 time to fit residues: 133.9616 Evaluate side-chains 286 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 251 time to evaluate : 1.787 ------------------------------------------------------------------------------- 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 467 LEU Chi-restraints excluded: chain A residue 527 MET Chi-restraints excluded: chain A residue 596 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 744 THR Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1026 TYR Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain B residue 411 ASN Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 706 SER Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 596 LEU Chi-restraints excluded: chain C residue 719 ASP Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 411 ASN Chi-restraints excluded: chain D residue 490 ASP Chi-restraints excluded: chain D residue 590 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 120 VAL Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 120 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 73 optimal weight: 0.7980 chunk 196 optimal weight: 1.9990 chunk 43 optimal weight: 9.9990 chunk 128 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 218 optimal weight: 9.9990 chunk 181 optimal weight: 2.9990 chunk 101 optimal weight: 0.0060 chunk 18 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 114 optimal weight: 0.0980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 HIS ** F 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18393 Z= 0.162 Angle : 0.565 9.425 24850 Z= 0.288 Chirality : 0.040 0.213 2794 Planarity : 0.004 0.064 3042 Dihedral : 5.076 43.928 2468 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.15 % Favored : 92.72 % Rotamer: Outliers : 3.04 % Allowed : 14.55 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.00 % Twisted Proline : 6.06 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.18), residues: 2238 helix: 0.83 (0.15), residues: 1278 sheet: -2.81 (0.38), residues: 154 loop : -3.00 (0.20), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 578 HIS 0.010 0.001 HIS E 27 PHE 0.019 0.001 PHE C 960 TYR 0.029 0.001 TYR E 100 ARG 0.007 0.000 ARG C1031 *********************** 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 343 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 284 time to evaluate : 1.741 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 431 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7840 (mm-30) REVERT: A 467 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.7862 (pt) REVERT: A 592 SER cc_start: 0.8865 (t) cc_final: 0.8603 (p) REVERT: A 641 LYS cc_start: 0.7391 (OUTLIER) cc_final: 0.6980 (mmtp) REVERT: A 669 LYS cc_start: 0.7070 (mtmt) cc_final: 0.6721 (tttt) REVERT: A 716 LYS cc_start: 0.7845 (OUTLIER) cc_final: 0.7437 (mmmt) REVERT: A 734 ILE cc_start: 0.8629 (OUTLIER) cc_final: 0.8147 (mm) REVERT: A 863 TYR cc_start: 0.5751 (m-10) cc_final: 0.5092 (m-80) REVERT: A 880 MET cc_start: 0.7266 (tmm) cc_final: 0.6724 (tmm) REVERT: A 907 MET cc_start: 0.4992 (ttt) cc_final: 0.4249 (mpp) REVERT: A 1026 TYR cc_start: 0.7279 (OUTLIER) cc_final: 0.7002 (m-10) REVERT: A 1029 MET cc_start: 0.6912 (OUTLIER) cc_final: 0.5634 (mmm) REVERT: B 527 MET cc_start: 0.6898 (mmt) cc_final: 0.6646 (mmt) REVERT: B 719 ASP cc_start: 0.7258 (t0) cc_final: 0.6960 (t0) REVERT: C 431 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7727 (mm-30) REVERT: C 467 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.7996 (pt) REVERT: C 545 ARG cc_start: 0.7410 (mmm160) cc_final: 0.6849 (ttt-90) REVERT: C 651 ASP cc_start: 0.7582 (t70) cc_final: 0.7173 (t70) REVERT: C 669 LYS cc_start: 0.7181 (mtmt) cc_final: 0.6782 (tttt) REVERT: C 734 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8252 (mm) REVERT: C 813 GLU cc_start: 0.6697 (OUTLIER) cc_final: 0.6485 (mt-10) REVERT: C 863 TYR cc_start: 0.5826 (m-10) cc_final: 0.4980 (m-80) REVERT: C 880 MET cc_start: 0.7356 (tmm) cc_final: 0.6837 (tmm) REVERT: C 901 PHE cc_start: 0.5961 (m-80) cc_final: 0.5324 (m-80) REVERT: C 988 MET cc_start: 0.7725 (mmp) cc_final: 0.7330 (mmm) REVERT: C 1029 MET cc_start: 0.5714 (mmt) cc_final: 0.4830 (mmt) REVERT: D 393 LYS cc_start: 0.7898 (mmmt) cc_final: 0.7294 (ttmt) REVERT: D 678 GLU cc_start: 0.6416 (mm-30) cc_final: 0.6102 (mm-30) REVERT: D 719 ASP cc_start: 0.7290 (t0) cc_final: 0.6955 (t0) REVERT: F 27 HIS cc_start: 0.6618 (OUTLIER) cc_final: 0.6299 (p-80) REVERT: F 83 LEU cc_start: 0.7025 (tt) cc_final: 0.6764 (tp) outliers start: 59 outliers final: 35 residues processed: 325 average time/residue: 0.2679 time to fit residues: 136.0229 Evaluate side-chains 317 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 272 time to evaluate : 1.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 596 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 716 LYS Chi-restraints excluded: chain A residue 718 CYS Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1023 MET Chi-restraints excluded: chain A residue 1026 TYR Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 411 ASN Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 706 SER Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 416 GLU Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 596 LEU Chi-restraints excluded: chain C residue 718 CYS Chi-restraints excluded: chain C residue 719 ASP Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 813 GLU Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 411 ASN Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain F residue 93 LEU 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 210 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 159 optimal weight: 0.3980 chunk 123 optimal weight: 2.9990 chunk 184 optimal weight: 0.9990 chunk 122 optimal weight: 4.9990 chunk 217 optimal weight: 0.6980 chunk 136 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 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 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18393 Z= 0.221 Angle : 0.589 9.627 24850 Z= 0.299 Chirality : 0.041 0.224 2794 Planarity : 0.004 0.058 3042 Dihedral : 5.042 41.314 2468 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.24 % Favored : 92.67 % Rotamer: Outliers : 3.46 % Allowed : 14.40 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.00 % Twisted Proline : 6.06 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.18), residues: 2238 helix: 0.86 (0.15), residues: 1280 sheet: -2.69 (0.38), residues: 154 loop : -2.93 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 88 HIS 0.010 0.001 HIS E 27 PHE 0.019 0.001 PHE C 960 TYR 0.021 0.001 TYR F 100 ARG 0.007 0.000 ARG B 545 *********************** 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 335 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 268 time to evaluate : 1.669 Fit side-chains revert: symmetry clash REVERT: A 431 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7852 (mm-30) REVERT: A 467 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.7983 (pt) REVERT: A 592 SER cc_start: 0.8870 (t) cc_final: 0.8654 (p) REVERT: A 641 LYS cc_start: 0.7428 (OUTLIER) cc_final: 0.7044 (mmtp) REVERT: A 669 LYS cc_start: 0.7074 (mtmt) cc_final: 0.6725 (tttt) REVERT: A 716 LYS cc_start: 0.7852 (OUTLIER) cc_final: 0.7428 (mmmt) REVERT: A 734 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8227 (mm) REVERT: A 863 TYR cc_start: 0.6058 (m-10) cc_final: 0.5298 (m-80) REVERT: A 880 MET cc_start: 0.7262 (tmm) cc_final: 0.6717 (tmm) REVERT: A 1026 TYR cc_start: 0.7307 (OUTLIER) cc_final: 0.7020 (m-10) REVERT: A 1029 MET cc_start: 0.6874 (mmm) cc_final: 0.5586 (mmm) REVERT: B 527 MET cc_start: 0.7007 (mmt) cc_final: 0.6756 (mmt) REVERT: B 719 ASP cc_start: 0.7388 (t0) cc_final: 0.7054 (t0) REVERT: C 431 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7821 (mm-30) REVERT: C 467 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8194 (pp) REVERT: C 545 ARG cc_start: 0.7481 (mmm160) cc_final: 0.7151 (tpt90) REVERT: C 651 ASP cc_start: 0.7534 (t70) cc_final: 0.7170 (t70) REVERT: C 669 LYS cc_start: 0.7190 (mtmt) cc_final: 0.6790 (tttt) REVERT: C 734 ILE cc_start: 0.8783 (OUTLIER) cc_final: 0.8292 (mm) REVERT: C 813 GLU cc_start: 0.6722 (OUTLIER) cc_final: 0.6503 (mt-10) REVERT: C 863 TYR cc_start: 0.5755 (m-10) cc_final: 0.4970 (m-80) REVERT: C 880 MET cc_start: 0.7393 (tmm) cc_final: 0.6866 (tmm) REVERT: C 901 PHE cc_start: 0.5952 (m-80) cc_final: 0.5318 (m-80) REVERT: C 988 MET cc_start: 0.7807 (mmp) cc_final: 0.7300 (mmm) REVERT: C 1029 MET cc_start: 0.5799 (mmt) cc_final: 0.5141 (mmt) REVERT: D 393 LYS cc_start: 0.7847 (mmmt) cc_final: 0.7174 (tptt) REVERT: D 678 GLU cc_start: 0.6442 (mm-30) cc_final: 0.6189 (mm-30) REVERT: D 719 ASP cc_start: 0.7465 (t0) cc_final: 0.7071 (t0) REVERT: F 27 HIS cc_start: 0.6823 (OUTLIER) cc_final: 0.6438 (p-80) REVERT: F 83 LEU cc_start: 0.7196 (tt) cc_final: 0.6861 (tp) REVERT: F 139 LEU cc_start: 0.6923 (tp) cc_final: 0.6668 (tp) outliers start: 67 outliers final: 48 residues processed: 311 average time/residue: 0.2693 time to fit residues: 131.0611 Evaluate side-chains 322 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 265 time to evaluate : 1.947 ------------------------------------------------------------------------------- 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 411 ASN Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 596 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 644 GLU Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 716 LYS Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 1026 TYR Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 411 ASN Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 647 TYR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 706 SER 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 411 ASN Chi-restraints excluded: chain C residue 416 GLU 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 683 VAL Chi-restraints excluded: chain C residue 718 CYS Chi-restraints excluded: chain C residue 719 ASP Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 813 GLU Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 411 ASN Chi-restraints excluded: chain D residue 490 ASP Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 683 VAL Chi-restraints excluded: chain D residue 706 SER Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 69 VAL 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 F residue 27 HIS Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 120 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 134 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 130 optimal weight: 0.0980 chunk 65 optimal weight: 0.8980 chunk 42 optimal weight: 9.9990 chunk 138 optimal weight: 5.9990 chunk 148 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 171 optimal weight: 1.9990 chunk 198 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 435 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18393 Z= 0.180 Angle : 0.570 9.717 24850 Z= 0.289 Chirality : 0.040 0.224 2794 Planarity : 0.004 0.065 3042 Dihedral : 4.882 40.099 2468 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.15 % Favored : 92.76 % Rotamer: Outliers : 3.20 % Allowed : 15.02 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.18), residues: 2238 helix: 1.09 (0.15), residues: 1268 sheet: -2.62 (0.38), residues: 154 loop : -2.89 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 88 HIS 0.010 0.001 HIS E 27 PHE 0.019 0.001 PHE F 141 TYR 0.024 0.001 TYR D 647 ARG 0.005 0.000 ARG C1031 *********************** 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 336 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 274 time to evaluate : 2.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 431 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7823 (mm-30) REVERT: A 467 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7814 (pt) REVERT: A 505 LYS cc_start: 0.8563 (tttm) cc_final: 0.8350 (tptp) REVERT: A 545 ARG cc_start: 0.7672 (ttm-80) cc_final: 0.7393 (tmm-80) REVERT: A 592 SER cc_start: 0.8850 (t) cc_final: 0.8643 (p) REVERT: A 669 LYS cc_start: 0.7066 (mtmt) cc_final: 0.6703 (tttt) REVERT: A 734 ILE cc_start: 0.8675 (OUTLIER) cc_final: 0.8179 (mm) REVERT: A 863 TYR cc_start: 0.6009 (m-10) cc_final: 0.5179 (m-80) REVERT: A 880 MET cc_start: 0.7256 (tmm) cc_final: 0.6736 (tmm) REVERT: A 1026 TYR cc_start: 0.7215 (OUTLIER) cc_final: 0.6977 (m-10) REVERT: B 719 ASP cc_start: 0.7300 (t0) cc_final: 0.7003 (t0) REVERT: C 467 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8113 (pt) REVERT: C 545 ARG cc_start: 0.7610 (mmm160) cc_final: 0.7284 (tpt90) REVERT: C 642 GLN cc_start: 0.5967 (OUTLIER) cc_final: 0.4811 (mp-120) REVERT: C 651 ASP cc_start: 0.7506 (t70) cc_final: 0.7139 (t70) REVERT: C 669 LYS cc_start: 0.7150 (mtmt) cc_final: 0.6781 (tttt) REVERT: C 716 LYS cc_start: 0.7659 (OUTLIER) cc_final: 0.7426 (tptt) REVERT: C 734 ILE cc_start: 0.8724 (OUTLIER) cc_final: 0.8257 (mm) REVERT: C 863 TYR cc_start: 0.5717 (m-10) cc_final: 0.4937 (m-80) REVERT: C 880 MET cc_start: 0.7392 (tmm) cc_final: 0.6869 (tmm) REVERT: C 901 PHE cc_start: 0.6013 (m-80) cc_final: 0.5399 (m-80) REVERT: C 988 MET cc_start: 0.7587 (mmp) cc_final: 0.7190 (mmm) REVERT: C 1029 MET cc_start: 0.5524 (mmt) cc_final: 0.4918 (mmt) REVERT: D 393 LYS cc_start: 0.7923 (mmmt) cc_final: 0.7626 (tptp) REVERT: D 678 GLU cc_start: 0.6424 (mm-30) cc_final: 0.6194 (mm-30) REVERT: D 719 ASP cc_start: 0.7423 (t0) cc_final: 0.7024 (t0) REVERT: F 27 HIS cc_start: 0.6839 (OUTLIER) cc_final: 0.6469 (p-80) REVERT: F 83 LEU cc_start: 0.7266 (tt) cc_final: 0.6912 (tp) REVERT: F 139 LEU cc_start: 0.6906 (tp) cc_final: 0.6504 (tp) outliers start: 62 outliers final: 41 residues processed: 316 average time/residue: 0.2664 time to fit residues: 131.6948 Evaluate side-chains 313 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 264 time to evaluate : 1.859 ------------------------------------------------------------------------------- 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 411 ASN Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 1026 TYR Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 411 ASN Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 706 SER 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 411 ASN Chi-restraints excluded: chain C residue 416 GLU 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 716 LYS Chi-restraints excluded: chain C residue 718 CYS Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain D residue 406 VAL 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 706 SER Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 120 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 208 optimal weight: 3.9990 chunk 190 optimal weight: 2.9990 chunk 202 optimal weight: 6.9990 chunk 122 optimal weight: 7.9990 chunk 88 optimal weight: 0.8980 chunk 159 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 183 optimal weight: 0.2980 chunk 191 optimal weight: 0.6980 chunk 133 optimal weight: 0.7980 chunk 214 optimal weight: 7.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 587 GLN D 642 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18393 Z= 0.182 Angle : 0.574 12.356 24850 Z= 0.292 Chirality : 0.040 0.229 2794 Planarity : 0.004 0.065 3042 Dihedral : 4.821 38.276 2468 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.88 % Favored : 93.03 % Rotamer: Outliers : 2.79 % Allowed : 15.38 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.18), residues: 2238 helix: 1.19 (0.15), residues: 1272 sheet: -2.55 (0.39), residues: 154 loop : -2.83 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 88 HIS 0.010 0.001 HIS E 27 PHE 0.019 0.001 PHE F 141 TYR 0.020 0.001 TYR F 100 ARG 0.007 0.000 ARG B 545 *********************** 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 315 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 261 time to evaluate : 1.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 431 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7859 (mm-30) REVERT: A 467 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7811 (pt) REVERT: A 505 LYS cc_start: 0.8487 (tttm) cc_final: 0.8279 (tptp) REVERT: A 545 ARG cc_start: 0.7714 (ttm-80) cc_final: 0.7324 (tmm-80) REVERT: A 669 LYS cc_start: 0.7055 (mtmt) cc_final: 0.6708 (tttt) REVERT: A 734 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8172 (mm) REVERT: B 719 ASP cc_start: 0.7286 (t0) cc_final: 0.6979 (t0) REVERT: C 467 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8128 (pt) REVERT: C 545 ARG cc_start: 0.7545 (mmm160) cc_final: 0.7249 (tpt90) REVERT: C 585 MET cc_start: 0.8503 (mmt) cc_final: 0.8250 (mmm) REVERT: C 642 GLN cc_start: 0.5903 (OUTLIER) cc_final: 0.4713 (mp-120) REVERT: C 651 ASP cc_start: 0.7500 (t70) cc_final: 0.7142 (t70) REVERT: C 669 LYS cc_start: 0.7153 (mtmt) cc_final: 0.6778 (tttt) REVERT: C 734 ILE cc_start: 0.8722 (OUTLIER) cc_final: 0.8243 (mm) REVERT: C 863 TYR cc_start: 0.6004 (m-10) cc_final: 0.5298 (m-80) REVERT: C 901 PHE cc_start: 0.5958 (m-80) cc_final: 0.5398 (m-80) REVERT: C 988 MET cc_start: 0.7577 (mmp) cc_final: 0.7174 (mmm) REVERT: C 1029 MET cc_start: 0.5490 (mmt) cc_final: 0.4891 (mmt) REVERT: D 678 GLU cc_start: 0.6469 (mm-30) cc_final: 0.6254 (mm-30) REVERT: D 719 ASP cc_start: 0.7428 (t0) cc_final: 0.7063 (t0) REVERT: F 27 HIS cc_start: 0.6960 (OUTLIER) cc_final: 0.6595 (p-80) outliers start: 54 outliers final: 42 residues processed: 299 average time/residue: 0.2891 time to fit residues: 137.0024 Evaluate side-chains 306 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 258 time to evaluate : 1.872 ------------------------------------------------------------------------------- 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 467 LEU Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 773 CYS 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 649 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 706 SER Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 416 GLU Chi-restraints excluded: chain C residue 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 683 VAL Chi-restraints excluded: chain C residue 718 CYS Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 921 VAL Chi-restraints excluded: chain C residue 979 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 706 SER Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain F residue 80 LEU 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 131 optimal weight: 0.0980 chunk 101 optimal weight: 0.3980 chunk 149 optimal weight: 10.0000 chunk 225 optimal weight: 7.9990 chunk 207 optimal weight: 10.0000 chunk 179 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 138 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 142 optimal weight: 9.9990 chunk 190 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 392 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.4252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18393 Z= 0.227 Angle : 0.603 12.162 24850 Z= 0.305 Chirality : 0.041 0.228 2794 Planarity : 0.004 0.066 3042 Dihedral : 4.866 37.379 2468 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.06 % Favored : 92.81 % Rotamer: Outliers : 2.58 % Allowed : 16.00 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.18), residues: 2238 helix: 1.15 (0.15), residues: 1272 sheet: -2.58 (0.36), residues: 174 loop : -2.83 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 88 HIS 0.010 0.001 HIS E 27 PHE 0.019 0.001 PHE F 141 TYR 0.020 0.001 TYR F 100 ARG 0.005 0.000 ARG C1031 ********************** 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 320 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 270 time to evaluate : 2.168 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 431 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7854 (mm-30) REVERT: A 467 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.7955 (pt) REVERT: A 545 ARG cc_start: 0.7786 (ttm-80) cc_final: 0.7374 (tmm-80) REVERT: A 669 LYS cc_start: 0.7079 (mtmt) cc_final: 0.6723 (tttt) REVERT: A 734 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8222 (mm) REVERT: A 863 TYR cc_start: 0.5887 (m-10) cc_final: 0.5125 (m-80) REVERT: A 1029 MET cc_start: 0.6720 (mmm) cc_final: 0.6072 (mtm) REVERT: B 719 ASP cc_start: 0.7349 (t0) cc_final: 0.7033 (t0) REVERT: C 467 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8203 (pp) REVERT: C 542 LEU cc_start: 0.8634 (tp) cc_final: 0.8403 (tp) REVERT: C 545 ARG cc_start: 0.7559 (mmm160) cc_final: 0.7232 (tpt90) REVERT: C 585 MET cc_start: 0.8592 (mmt) cc_final: 0.8312 (mmm) REVERT: C 642 GLN cc_start: 0.5866 (OUTLIER) cc_final: 0.4675 (mp-120) REVERT: C 651 ASP cc_start: 0.7473 (t70) cc_final: 0.7148 (t70) REVERT: C 669 LYS cc_start: 0.7178 (mtmt) cc_final: 0.6799 (tttt) REVERT: C 734 ILE cc_start: 0.8794 (OUTLIER) cc_final: 0.8295 (mm) REVERT: C 863 TYR cc_start: 0.5925 (m-10) cc_final: 0.5233 (m-80) REVERT: C 880 MET cc_start: 0.7361 (tmm) cc_final: 0.7059 (tmm) REVERT: C 901 PHE cc_start: 0.5925 (m-80) cc_final: 0.5363 (m-80) REVERT: C 988 MET cc_start: 0.7609 (mmp) cc_final: 0.7204 (mmm) REVERT: C 1029 MET cc_start: 0.5585 (mmt) cc_final: 0.5128 (mmt) REVERT: D 393 LYS cc_start: 0.8135 (mmmt) cc_final: 0.7577 (tptp) REVERT: D 678 GLU cc_start: 0.6517 (mm-30) cc_final: 0.6312 (mm-30) REVERT: D 719 ASP cc_start: 0.7461 (t0) cc_final: 0.7086 (t0) REVERT: F 27 HIS cc_start: 0.7160 (OUTLIER) cc_final: 0.6752 (p-80) outliers start: 50 outliers final: 42 residues processed: 304 average time/residue: 0.2611 time to fit residues: 124.9698 Evaluate side-chains 315 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 267 time to evaluate : 1.891 ------------------------------------------------------------------------------- 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 467 LEU Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 734 ILE 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 649 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 668 ASP Chi-restraints excluded: chain B residue 706 SER Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 416 GLU Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 596 LEU Chi-restraints excluded: chain C residue 642 GLN Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 718 CYS Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 921 VAL Chi-restraints excluded: chain C residue 979 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 683 VAL Chi-restraints excluded: chain D residue 706 SER Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain F residue 80 LEU 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 ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 64, in __init__ weight = self.w, xray_structure = self.xray_structure) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.0833 > 50: distance: 179 - 180: 5.460 distance: 179 - 182: 4.558 distance: 182 - 183: 4.857 distance: 183 - 184: 5.150 distance: 859 - 2466: 3.153 distance: 872 - 2452: 3.023 distance: 1243 - 1244: 5.025 distance: 1244 - 1245: 5.793 distance: 1246 - 1247: 7.112 distance: 1247 - 1248: 5.017 distance: 1721 - 1726: 3.348 distance: 2403 - 2412: 3.641 distance: 2592 - 2593: 4.358 distance: 2593 - 2596: 5.174 distance: 2596 - 2597: 4.068 distance: 2911 - 2912: 5.119 distance: 2912 - 2913: 4.567 distance: 2912 - 2915: 4.291 distance: 3019 - 3020: 8.007 distance: 3172 - 3200: 3.013 distance: 3401 - 3474: 3.016 distance: 3578 - 3579: 3.314 distance: 3647 - 3656: 3.248 distance: 3656 - 3657: 3.690 distance: 3657 - 3658: 5.365 distance: 3767 - 3768: 4.181 distance: 3768 - 3769: 4.127 distance: 3769 - 3770: 14.020 distance: 3836 - 3854: 3.079 distance: 3865 - 3892: 3.055 distance: 3929 - 3948: 3.030 distance: 4074 - 4100: 3.089 distance: 4120 - 4123: 3.254 distance: 4180 - 4212: 3.286 distance: 4257 - 4260: 4.120 distance: 4260 - 4261: 3.969 distance: 4261 - 4262: 3.470 distance: 4262 - 4263: 4.996 distance: 4262 - 4264: 4.146 distance: 4380 - 4381: 3.312 distance: 4382 - 4384: 3.099 distance: 4545 - 4570: 3.261 distance: 4848 - 4849: 3.716 distance: 4849 - 4850: 3.486 distance: 4849 - 4852: 5.579 distance: 4852 - 4853: 3.344 distance: 5073 - 5074: 3.115 distance: 5074 - 5075: 3.476 distance: 5221 - 5222: 3.283 distance: 5518 - 5519: 3.155 distance: 5569 - 5570: 3.179 distance: 5618 - 5619: 3.505 distance: 5619 - 5622: 3.227 distance: 5623 - 5624: 3.994 distance: 5625 - 5627: 3.109 distance: 5866 - 5867: 4.638 distance: 5868 - 5869: 3.336 distance: 5869 - 5870: 4.359 distance: 6386 - 6389: 4.168 distance: 6389 - 6390: 3.991 distance: 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