Starting phenix.real_space_refine on Fri Nov 17 04:59:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ss4_40743/11_2023/8ss4_40743_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ss4_40743/11_2023/8ss4_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_40743/11_2023/8ss4_40743.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ss4_40743/11_2023/8ss4_40743.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ss4_40743/11_2023/8ss4_40743_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ss4_40743/11_2023/8ss4_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-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 17978 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4662 Classifications: {'peptide': 595} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 577} Chain breaks: 4 Chain: "B" Number of atoms: 3156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3156 Classifications: {'peptide': 404} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 390} Chain breaks: 2 Chain: "C" Number of atoms: 4662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4662 Classifications: {'peptide': 595} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 577} Chain breaks: 4 Chain: "D" Number of atoms: 3156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3156 Classifications: {'peptide': 404} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 390} Chain breaks: 2 Chain: "E" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1166 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain breaks: 1 Chain: "F" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1166 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain breaks: 1 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'SPD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.84, per 1000 atoms: 0.55 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: 6.97 Conformation dependent library (CDL) restraints added in 3.6 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: 3.87 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: 4.94 Time building geometry restraints manager: 7.52 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: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.800 Check model and map are aligned: 0.270 Set scattering table: 0.180 Process input model: 49.170 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.630 ------------------------------------------------------------------------------- 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 *********************** 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 : 2.032 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 398 average time/residue: 0.3353 time to fit residues: 197.3367 Evaluate side-chains 261 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 260 time to evaluate : 1.978 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1625 time to fit residues: 3.0095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7515 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18393 Z= 0.208 Angle : 0.661 11.182 24850 Z= 0.344 Chirality : 0.042 0.184 2794 Planarity : 0.005 0.080 3042 Dihedral : 5.910 46.647 2467 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.51 % Favored : 92.31 % Rotamer: Outliers : 2.27 % Allowed : 10.17 % Favored : 87.56 % 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: -3.60 (0.15), residues: 2238 helix: -1.45 (0.13), residues: 1274 sheet: -3.45 (0.33), residues: 178 loop : -3.59 (0.18), residues: 786 *********************** 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 326 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 282 time to evaluate : 1.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 17 residues processed: 318 average time/residue: 0.2923 time to fit residues: 143.8873 Evaluate side-chains 265 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 248 time to evaluate : 1.972 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1659 time to fit residues: 8.1695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 114 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 170 optimal weight: 0.8980 chunk 139 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 205 optimal weight: 0.0050 chunk 222 optimal weight: 7.9990 chunk 183 optimal weight: 0.7980 chunk 203 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 164 optimal weight: 0.8980 overall best weight: 0.6994 ------------------------------------------------------------------------------- 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** B 435 HIS B 756 GLN ** C 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 756 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: 0.7521 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18393 Z= 0.185 Angle : 0.601 9.214 24850 Z= 0.307 Chirality : 0.040 0.190 2794 Planarity : 0.004 0.063 3042 Dihedral : 5.366 46.366 2467 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.51 % Favored : 92.31 % Rotamer: Outliers : 2.06 % Allowed : 11.87 % Favored : 86.07 % 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: -2.24 (0.17), residues: 2238 helix: -0.18 (0.14), residues: 1280 sheet: -3.09 (0.35), residues: 172 loop : -3.32 (0.19), residues: 786 *********************** 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 314 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 274 time to evaluate : 1.882 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 15 residues processed: 306 average time/residue: 0.2800 time to fit residues: 134.1680 Evaluate side-chains 263 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 248 time to evaluate : 1.915 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1669 time to fit residues: 7.3360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 203 optimal weight: 0.6980 chunk 154 optimal weight: 8.9990 chunk 106 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 98 optimal weight: 7.9990 chunk 138 optimal weight: 6.9990 chunk 206 optimal weight: 10.0000 chunk 218 optimal weight: 8.9990 chunk 107 optimal weight: 1.9990 chunk 195 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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** B 756 GLN C 764 ASN C 872 GLN D 756 GLN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 18393 Z= 0.429 Angle : 0.716 12.277 24850 Z= 0.363 Chirality : 0.045 0.245 2794 Planarity : 0.005 0.067 3042 Dihedral : 5.640 44.849 2467 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.25 % Favored : 90.57 % Rotamer: Outliers : 2.43 % Allowed : 13.83 % Favored : 83.75 % 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: -2.06 (0.17), residues: 2238 helix: 0.00 (0.14), residues: 1284 sheet: -3.08 (0.35), residues: 186 loop : -3.28 (0.20), residues: 768 *********************** 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 304 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 257 time to evaluate : 2.071 Fit side-chains revert: symmetry clash outliers start: 47 outliers final: 22 residues processed: 286 average time/residue: 0.3066 time to fit residues: 137.5065 Evaluate side-chains 255 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 233 time to evaluate : 2.150 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1715 time to fit residues: 10.1952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 181 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 chunk 162 optimal weight: 0.9980 chunk 90 optimal weight: 0.4980 chunk 186 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 0 optimal weight: 0.9990 chunk 111 optimal weight: 0.5980 chunk 196 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 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** B 764 ASN C 764 ASN ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 587 GLN E 107 HIS F 107 HIS ** F 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.3608 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= 0.187 Angle : 0.601 13.109 24850 Z= 0.304 Chirality : 0.040 0.203 2794 Planarity : 0.004 0.059 3042 Dihedral : 5.231 44.084 2467 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.02 % Favored : 92.90 % Rotamer: Outliers : 1.34 % Allowed : 14.09 % Favored : 84.57 % 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: -1.49 (0.18), residues: 2238 helix: 0.52 (0.15), residues: 1280 sheet: -2.99 (0.35), residues: 178 loop : -3.12 (0.20), residues: 780 *********************** 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 289 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 263 time to evaluate : 1.953 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 14 residues processed: 280 average time/residue: 0.2745 time to fit residues: 120.8295 Evaluate side-chains 252 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 238 time to evaluate : 2.169 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 14 outliers final: 1 residues processed: 14 average time/residue: 0.1789 time to fit residues: 7.6732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 73 optimal weight: 0.9990 chunk 196 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 128 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 218 optimal weight: 10.0000 chunk 181 optimal weight: 0.7980 chunk 101 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 114 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 764 ASN D 587 GLN ** F 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18393 Z= 0.197 Angle : 0.591 12.785 24850 Z= 0.300 Chirality : 0.040 0.208 2794 Planarity : 0.004 0.063 3042 Dihedral : 5.075 42.723 2467 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.28 % Favored : 92.63 % Rotamer: Outliers : 1.08 % Allowed : 15.38 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.00 % Twisted Proline : 6.06 % Twisted General : 0.09 % Rama-Z (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: -1.19 (0.18), residues: 2238 helix: 0.78 (0.15), residues: 1278 sheet: -2.92 (0.35), residues: 178 loop : -3.00 (0.20), residues: 782 *********************** 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 274 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 253 time to evaluate : 2.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 9 residues processed: 267 average time/residue: 0.2801 time to fit residues: 118.0246 Evaluate side-chains 252 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 243 time to evaluate : 2.036 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 9 average time/residue: 0.1828 time to fit residues: 5.9263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 124 optimal weight: 5.9990 chunk 159 optimal weight: 0.0980 chunk 123 optimal weight: 3.9990 chunk 184 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 chunk 217 optimal weight: 0.8980 chunk 136 optimal weight: 0.0670 chunk 132 optimal weight: 0.7980 chunk 100 optimal weight: 0.5980 overall best weight: 0.4718 ------------------------------------------------------------------------------- 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 ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.3989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 18393 Z= 0.155 Angle : 0.579 13.799 24850 Z= 0.292 Chirality : 0.040 0.213 2794 Planarity : 0.004 0.062 3042 Dihedral : 4.861 40.676 2467 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 1.03 % Allowed : 15.84 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.18), residues: 2238 helix: 1.11 (0.15), residues: 1264 sheet: -2.69 (0.38), residues: 154 loop : -2.89 (0.20), residues: 820 *********************** 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 293 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 273 time to evaluate : 1.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 7 residues processed: 286 average time/residue: 0.2848 time to fit residues: 128.0233 Evaluate side-chains 265 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 258 time to evaluate : 1.851 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 7 average time/residue: 0.1768 time to fit residues: 4.9996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 130 optimal weight: 0.3980 chunk 65 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 138 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 198 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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** A1000 ASN C 764 ASN D 435 HIS D 764 ASN ** F 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18393 Z= 0.219 Angle : 0.607 13.736 24850 Z= 0.305 Chirality : 0.041 0.220 2794 Planarity : 0.004 0.065 3042 Dihedral : 4.904 40.033 2467 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 0.83 % Allowed : 16.25 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.18), residues: 2238 helix: 1.07 (0.15), residues: 1274 sheet: -2.88 (0.34), residues: 184 loop : -2.79 (0.21), residues: 780 *********************** 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 274 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 258 time to evaluate : 2.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 11 residues processed: 267 average time/residue: 0.2977 time to fit residues: 123.0682 Evaluate side-chains 261 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 250 time to evaluate : 2.085 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 11 outliers final: 1 residues processed: 11 average time/residue: 0.1814 time to fit residues: 6.6246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 208 optimal weight: 0.0370 chunk 190 optimal weight: 0.9980 chunk 202 optimal weight: 6.9990 chunk 122 optimal weight: 0.3980 chunk 88 optimal weight: 3.9990 chunk 159 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 183 optimal weight: 0.4980 chunk 191 optimal weight: 0.6980 chunk 133 optimal weight: 1.9990 chunk 214 optimal weight: 6.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- 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** ** F 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.4257 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= 0.161 Angle : 0.595 14.293 24850 Z= 0.298 Chirality : 0.040 0.227 2794 Planarity : 0.004 0.064 3042 Dihedral : 4.782 37.945 2467 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.34 % Favored : 93.61 % Rotamer: Outliers : 0.46 % Allowed : 16.46 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.18), residues: 2238 helix: 1.29 (0.15), residues: 1264 sheet: -2.54 (0.36), residues: 174 loop : -2.80 (0.20), residues: 800 *********************** 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 275 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 266 time to evaluate : 2.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 270 average time/residue: 0.2998 time to fit residues: 124.9913 Evaluate side-chains 258 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 253 time to evaluate : 2.024 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.2110 time to fit residues: 4.7005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 131 optimal weight: 0.2980 chunk 101 optimal weight: 1.9990 chunk 149 optimal weight: 10.0000 chunk 225 optimal weight: 7.9990 chunk 207 optimal weight: 9.9990 chunk 179 optimal weight: 1.9990 chunk 18 optimal weight: 0.0970 chunk 138 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 142 optimal weight: 10.0000 chunk 190 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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** A1000 ASN ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN D 642 GLN D 756 GLN ** F 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 18393 Z= 0.290 Angle : 0.653 13.727 24850 Z= 0.327 Chirality : 0.043 0.227 2794 Planarity : 0.004 0.065 3042 Dihedral : 4.977 37.476 2467 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.91 % Favored : 92.05 % Rotamer: Outliers : 0.31 % Allowed : 16.82 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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: -0.86 (0.18), residues: 2238 helix: 1.01 (0.15), residues: 1284 sheet: -2.82 (0.35), residues: 184 loop : -2.78 (0.21), residues: 770 ********************** 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 261 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 255 time to evaluate : 1.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 261 average time/residue: 0.3018 time to fit residues: 121.5205 Evaluate side-chains 252 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 248 time to evaluate : 2.108 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.1847 time to fit residues: 4.3224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 54 optimal weight: 0.9990 chunk 165 optimal weight: 0.1980 chunk 26 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 179 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 184 optimal weight: 0.7980 chunk 22 optimal weight: 6.9990 chunk 33 optimal weight: 0.5980 chunk 157 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.208674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.161929 restraints weight = 20044.274| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 3.63 r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.4428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18393 Z= 0.180 Angle : 0.608 14.680 24850 Z= 0.304 Chirality : 0.041 0.227 2794 Planarity : 0.004 0.065 3042 Dihedral : 4.810 36.145 2467 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.57 % Favored : 93.34 % Rotamer: Outliers : 0.36 % Allowed : 17.23 % Favored : 82.40 % 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: -0.58 (0.18), residues: 2238 helix: 1.26 (0.15), residues: 1270 sheet: -2.14 (0.40), residues: 152 loop : -2.79 (0.20), residues: 816 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3611.46 seconds wall clock time: 66 minutes 44.06 seconds (4004.06 seconds total)