Starting phenix.real_space_refine on Sun Sep 13 02:56:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6cij_7480/09_2026/6cij_7480.cif Found real_map, /net/cci-nas-00/data/ceres_data/6cij_7480/09_2026/6cij_7480.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6cij_7480/09_2026/6cij_7480.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6cij_7480/09_2026/6cij_7480.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6cij_7480/09_2026/6cij_7480.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6cij_7480/09_2026/6cij_7480.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6cij_7480/09_2026/6cij_7480.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6cij_7480/09_2026/6cij_7480.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 Zn 2 6.06 5 P 209 5.49 5 S 109 5.16 5 C 12241 2.51 5 N 3602 2.21 5 O 4248 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20413 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4921 Classifications: {'peptide': 614} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 25, 'TRANS': 588} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 4946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 616, 4946 Classifications: {'peptide': 616} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 25, 'TRANS': 590} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 947 Classifications: {'DNA': 46} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 45} Chain: "I" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 323 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Chain: "J" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 387 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "G" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1225 Classifications: {'DNA': 60} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 59} Chain: "N" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 910 Classifications: {'peptide': 133} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 43} Link IDs: {'PTRANS': 8, 'TRANS': 124} Chain breaks: 3 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 167 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 5, 'PHE:plan': 1, 'GLN:plan1': 2, 'GLU:plan': 9, 'TYR:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 88 Chain: "L" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 610 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "D" Number of atoms: 2643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2643 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 19, 'TRANS': 320} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2652 Classifications: {'peptide': 342} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 19, 'TRANS': 322} Chain breaks: 2 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'ASN:plan1': 2} Unresolved non-hydrogen planarities: 6 Chain: "M" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 845 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2590 SG CYS A 727 97.498 23.316 70.665 1.00 75.34 S ATOM 2611 SG CYS A 730 98.266 20.427 68.704 1.00 76.35 S ATOM 7544 SG CYS C 727 62.510 83.572 69.781 1.00 72.00 S ATOM 7565 SG CYS C 730 61.451 86.448 68.000 1.00 75.09 S Time building chain proxies: 3.45, per 1000 atoms: 0.17 Number of scatterers: 20413 At special positions: 0 Unit cell: (160.5, 109.14, 182.97, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 Ca 2 19.99 S 109 16.00 P 209 15.00 O 4248 8.00 N 3602 7.00 C 12241 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.55 Conformation dependent library (CDL) restraints added in 751.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 730 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 937 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 727 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 942 " pdb=" ZN C1101 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 937 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 942 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 727 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 730 " Number of angles added : 4 4042 Ramachandran restraints generated. 2021 Oldfield, 0 Emsley, 2021 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3832 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 24 sheets defined 40.5% alpha, 17.9% beta 93 base pairs and 160 stacking pairs defined. Time for finding SS restraints: 2.54 Creating SS restraints... Processing helix chain 'A' and resid 403 through 423 removed outlier: 5.800A pdb=" N GLU A 410 " --> pdb=" O HIS A 406 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N LEU A 411 " --> pdb=" O ARG A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 442 removed outlier: 3.567A pdb=" N ARG A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 455 Processing helix chain 'A' and resid 463 through 474 Processing helix chain 'A' and resid 477 through 493 Processing helix chain 'A' and resid 499 through 511 removed outlier: 3.571A pdb=" N LEU A 503 " --> pdb=" O PRO A 499 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS A 508 " --> pdb=" O ARG A 504 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N VAL A 509 " --> pdb=" O ASN A 505 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LEU A 510 " --> pdb=" O ALA A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 570 Processing helix chain 'A' and resid 570 through 581 Processing helix chain 'A' and resid 648 through 652 removed outlier: 3.595A pdb=" N CYS A 652 " --> pdb=" O GLU A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 683 Proline residue: A 674 - end of helix Processing helix chain 'A' and resid 708 through 716 Processing helix chain 'A' and resid 733 through 740 Processing helix chain 'A' and resid 749 through 763 removed outlier: 3.738A pdb=" N ASN A 753 " --> pdb=" O SER A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 777 Processing helix chain 'A' and resid 792 through 813 Processing helix chain 'A' and resid 822 through 842 removed outlier: 3.605A pdb=" N ASN A 842 " --> pdb=" O ARG A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 858 Processing helix chain 'A' and resid 859 through 868 Processing helix chain 'A' and resid 873 through 890 removed outlier: 3.536A pdb=" N GLU A 877 " --> pdb=" O GLU A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 894 removed outlier: 3.794A pdb=" N ARG A 894 " --> pdb=" O PRO A 891 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 891 through 894' Processing helix chain 'A' and resid 897 through 902 Processing helix chain 'A' and resid 902 through 908 Processing helix chain 'A' and resid 908 through 924 removed outlier: 3.543A pdb=" N ASN A 912 " --> pdb=" O GLN A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 942 removed outlier: 3.837A pdb=" N HIS A 937 " --> pdb=" O THR A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 951 Processing helix chain 'A' and resid 958 through 975 removed outlier: 3.717A pdb=" N LYS A 966 " --> pdb=" O GLN A 962 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU A 967 " --> pdb=" O SER A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 995 removed outlier: 3.717A pdb=" N ASP A 986 " --> pdb=" O TYR A 982 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR A 995 " --> pdb=" O HIS A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1001 Processing helix chain 'C' and resid 400 through 421 removed outlier: 5.433A pdb=" N GLU C 410 " --> pdb=" O HIS C 406 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N LEU C 411 " --> pdb=" O ARG C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 441 Processing helix chain 'C' and resid 444 through 457 Processing helix chain 'C' and resid 463 through 474 Processing helix chain 'C' and resid 477 through 492 removed outlier: 3.708A pdb=" N LYS C 489 " --> pdb=" O TYR C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 507 removed outlier: 3.639A pdb=" N LEU C 503 " --> pdb=" O PRO C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 510 No H-bonds generated for 'chain 'C' and resid 508 through 510' Processing helix chain 'C' and resid 558 through 570 Processing helix chain 'C' and resid 570 through 581 Processing helix chain 'C' and resid 648 through 652 removed outlier: 3.560A pdb=" N CYS C 651 " --> pdb=" O SER C 648 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 683 Proline residue: C 674 - end of helix Processing helix chain 'C' and resid 708 through 716 Processing helix chain 'C' and resid 735 through 739 Processing helix chain 'C' and resid 749 through 763 Processing helix chain 'C' and resid 768 through 777 Processing helix chain 'C' and resid 792 through 813 removed outlier: 4.013A pdb=" N GLY C 813 " --> pdb=" O GLN C 809 " (cutoff:3.500A) Processing helix chain 'C' and resid 822 through 841 removed outlier: 4.070A pdb=" N ARG C 826 " --> pdb=" O SER C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 858 Processing helix chain 'C' and resid 859 through 867 Processing helix chain 'C' and resid 868 through 870 No H-bonds generated for 'chain 'C' and resid 868 through 870' Processing helix chain 'C' and resid 873 through 895 Proline residue: C 891 - end of helix Processing helix chain 'C' and resid 897 through 902 Processing helix chain 'C' and resid 902 through 908 Processing helix chain 'C' and resid 908 through 923 removed outlier: 3.676A pdb=" N ASN C 912 " --> pdb=" O GLN C 908 " (cutoff:3.500A) Processing helix chain 'C' and resid 933 through 942 removed outlier: 3.647A pdb=" N HIS C 937 " --> pdb=" O THR C 933 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 950 Processing helix chain 'C' and resid 953 through 957 removed outlier: 3.618A pdb=" N ALA C 957 " --> pdb=" O GLY C 954 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 975 removed outlier: 3.722A pdb=" N GLN C 962 " --> pdb=" O SER C 958 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS C 973 " --> pdb=" O ARG C 969 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 996 Processing helix chain 'C' and resid 996 through 1002 removed outlier: 3.588A pdb=" N GLN C1000 " --> pdb=" O SER C 996 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N PHE C1002 " --> pdb=" O TYR C 998 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 30 removed outlier: 3.635A pdb=" N VAL N 20 " --> pdb=" O TYR N 16 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N THR N 22 " --> pdb=" O PHE N 18 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 43 Processing helix chain 'N' and resid 44 through 49 removed outlier: 3.502A pdb=" N ARG N 48 " --> pdb=" O LYS N 44 " (cutoff:3.500A) Processing helix chain 'N' and resid 57 through 66 removed outlier: 4.210A pdb=" N MET N 63 " --> pdb=" O LYS N 59 " (cutoff:3.500A) Processing helix chain 'N' and resid 67 through 72 Processing helix chain 'N' and resid 100 through 117 Proline residue: N 111 - end of helix Processing helix chain 'N' and resid 121 through 134 Processing helix chain 'N' and resid 142 through 158 removed outlier: 4.269A pdb=" N LYS N 147 " --> pdb=" O PRO N 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 172 Processing helix chain 'D' and resid 310 through 314 removed outlier: 3.586A pdb=" N HIS D 313 " --> pdb=" O ASP D 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 15 Processing helix chain 'B' and resid 308 through 313 removed outlier: 3.607A pdb=" N LYS B 312 " --> pdb=" O THR B 308 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N HIS B 313 " --> pdb=" O SER B 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 308 through 313' Processing sheet with id=AA1, first strand: chain 'A' and resid 518 through 519 removed outlier: 3.757A pdb=" N GLU A 518 " --> pdb=" O THR A 688 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR A 688 " --> pdb=" O GLU A 518 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 535 through 536 removed outlier: 6.805A pdb=" N PHE A 622 " --> pdb=" O LEU A 655 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N LEU A 657 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N VAL A 620 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE A 641 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ILE A 631 " --> pdb=" O LYS A 639 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N LYS A 639 " --> pdb=" O ILE A 631 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N HIS A 633 " --> pdb=" O ASN A 637 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ASN A 637 " --> pdb=" O HIS A 633 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 535 through 536 removed outlier: 6.805A pdb=" N PHE A 622 " --> pdb=" O LEU A 655 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N LEU A 657 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N VAL A 620 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP A 600 " --> pdb=" O ARG A 621 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL A 594 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ILE A 629 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N THR A 592 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ILE A 631 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL A 595 " --> pdb=" O ILE A 701 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N THR A 705 " --> pdb=" O GLU A 597 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N CYS A 599 " --> pdb=" O THR A 705 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 690 through 691 Processing sheet with id=AA5, first strand: chain 'C' and resid 518 through 519 removed outlier: 3.519A pdb=" N GLU C 518 " --> pdb=" O THR C 688 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR C 705 " --> pdb=" O GLU C 597 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N CYS C 599 " --> pdb=" O THR C 705 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ILE C 631 " --> pdb=" O PRO C 590 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N THR C 592 " --> pdb=" O ILE C 629 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ILE C 629 " --> pdb=" O THR C 592 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL C 594 " --> pdb=" O MET C 627 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASP C 600 " --> pdb=" O ARG C 621 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N VAL C 620 " --> pdb=" O LEU C 657 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N LEU C 657 " --> pdb=" O VAL C 620 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N PHE C 622 " --> pdb=" O LEU C 655 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 518 through 519 removed outlier: 3.519A pdb=" N GLU C 518 " --> pdb=" O THR C 688 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR C 705 " --> pdb=" O GLU C 597 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N CYS C 599 " --> pdb=" O THR C 705 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ILE C 631 " --> pdb=" O PRO C 590 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N THR C 592 " --> pdb=" O ILE C 629 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ILE C 629 " --> pdb=" O THR C 592 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL C 594 " --> pdb=" O MET C 627 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASP C 600 " --> pdb=" O ARG C 621 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N MET C 627 " --> pdb=" O GLU C 642 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLU C 642 " --> pdb=" O MET C 627 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE C 629 " --> pdb=" O VAL C 640 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 2 through 6 removed outlier: 4.784A pdb=" N PHE D 345 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE D 328 " --> pdb=" O SER D 320 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE D 318 " --> pdb=" O GLY D 330 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 22 through 24 Processing sheet with id=AA9, first strand: chain 'D' and resid 49 through 51 removed outlier: 3.683A pdb=" N ASP D 49 " --> pdb=" O LYS D 56 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 61 through 62 removed outlier: 7.780A pdb=" N ILE D 61 " --> pdb=" O PHE D 122 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 75 through 78 removed outlier: 3.599A pdb=" N HIS D 94 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N CYS D 78 " --> pdb=" O ILE D 92 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 130 through 131 removed outlier: 6.082A pdb=" N VAL D 130 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N SER D 194 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N SER D 141 " --> pdb=" O PHE D 156 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 159 through 161 Processing sheet with id=AB5, first strand: chain 'D' and resid 208 through 210 Processing sheet with id=AB6, first strand: chain 'D' and resid 208 through 210 removed outlier: 4.580A pdb=" N LEU D 233 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG D 235 " --> pdb=" O THR D 250 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR D 250 " --> pdb=" O ARG D 235 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 263 through 267 removed outlier: 4.943A pdb=" N GLN D 265 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL D 272 " --> pdb=" O GLN D 265 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 2 through 5 removed outlier: 3.510A pdb=" N PHE B 318 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 22 through 24 removed outlier: 3.775A pdb=" N VAL B 28 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS B 58 " --> pdb=" O HIS B 47 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ASP B 49 " --> pdb=" O LYS B 56 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS B 56 " --> pdb=" O ASP B 49 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 93 through 94 removed outlier: 4.287A pdb=" N ILE B 107 " --> pdb=" O LYS B 127 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 112 through 115 removed outlier: 6.408A pdb=" N THR B 121 " --> pdb=" O ALA B 113 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 130 through 131 removed outlier: 6.646A pdb=" N VAL B 130 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N SER B 194 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE B 156 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER B 141 " --> pdb=" O PHE B 156 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AC5, first strand: chain 'B' and resid 208 through 211 removed outlier: 3.632A pdb=" N TYR B 234 " --> pdb=" O ILE B 218 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 262 through 267 removed outlier: 3.985A pdb=" N THR B 266 " --> pdb=" O GLU B 270 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N GLU B 270 " --> pdb=" O THR B 266 " (cutoff:3.500A) 723 hydrogen bonds defined for protein. 2022 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 229 hydrogen bonds 450 hydrogen bond angles 0 basepair planarities 93 basepair parallelities 160 stacking parallelities Total time for adding SS restraints: 5.10 Time building geometry restraints manager: 2.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5655 1.34 - 1.46: 4775 1.46 - 1.57: 10285 1.57 - 1.69: 415 1.69 - 1.81: 165 Bond restraints: 21295 Sorted by residual: bond pdb=" C3' DC J 9 " pdb=" C2' DC J 9 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 bond pdb=" C3' DC M 43 " pdb=" C2' DC M 43 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C3' DA F 32 " pdb=" C2' DA F 32 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.00e+01 bond pdb=" C3' DG F 38 " pdb=" C2' DG F 38 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.63e+00 bond pdb=" C3' DA M 33 " pdb=" C2' DA M 33 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.13e+00 ... (remaining 21290 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 28626 1.69 - 3.37: 990 3.37 - 5.06: 66 5.06 - 6.74: 12 6.74 - 8.43: 3 Bond angle restraints: 29697 Sorted by residual: angle pdb=" N GLN A 456 " pdb=" CA GLN A 456 " pdb=" C GLN A 456 " ideal model delta sigma weight residual 112.45 104.02 8.43 1.39e+00 5.18e-01 3.68e+01 angle pdb=" O4' DC G 19 " pdb=" C4' DC G 19 " pdb=" C3' DC G 19 " ideal model delta sigma weight residual 106.00 102.89 3.11 6.00e-01 2.78e+00 2.68e+01 angle pdb=" C GLY A 457 " pdb=" N ARG A 458 " pdb=" CA ARG A 458 " ideal model delta sigma weight residual 122.59 114.89 7.70 1.57e+00 4.06e-01 2.41e+01 angle pdb=" N ARG A 558 " pdb=" CA ARG A 558 " pdb=" C ARG A 558 " ideal model delta sigma weight residual 109.96 101.89 8.07 1.68e+00 3.54e-01 2.31e+01 angle pdb=" N3 DT F 29 " pdb=" C4 DT F 29 " pdb=" O4 DT F 29 " ideal model delta sigma weight residual 119.90 122.75 -2.85 6.00e-01 2.78e+00 2.26e+01 ... (remaining 29692 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.10: 11302 35.10 - 70.20: 914 70.20 - 105.31: 25 105.31 - 140.41: 1 140.41 - 175.51: 2 Dihedral angle restraints: 12244 sinusoidal: 6307 harmonic: 5937 Sorted by residual: dihedral pdb=" CA PHE N 18 " pdb=" C PHE N 18 " pdb=" N PHE N 19 " pdb=" CA PHE N 19 " ideal model delta harmonic sigma weight residual 180.00 154.23 25.77 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CA ALA N 94 " pdb=" C ALA N 94 " pdb=" N PRO N 95 " pdb=" CA PRO N 95 " ideal model delta harmonic sigma weight residual 180.00 155.98 24.02 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" C4' DC J 9 " pdb=" C3' DC J 9 " pdb=" O3' DC J 9 " pdb=" P DT J 10 " ideal model delta sinusoidal sigma weight residual 220.00 44.49 175.51 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 12241 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2478 0.045 - 0.091: 578 0.091 - 0.136: 192 0.136 - 0.181: 7 0.181 - 0.226: 6 Chirality restraints: 3261 Sorted by residual: chirality pdb=" CA ARG A 558 " pdb=" N ARG A 558 " pdb=" C ARG A 558 " pdb=" CB ARG A 558 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA LYS A 890 " pdb=" N LYS A 890 " pdb=" C LYS A 890 " pdb=" CB LYS A 890 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA ASP N 91 " pdb=" N ASP N 91 " pdb=" C ASP N 91 " pdb=" CB ASP N 91 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 3258 not shown) Planarity restraints: 3091 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 558 " 0.013 2.00e-02 2.50e+03 2.60e-02 6.77e+00 pdb=" C ARG C 558 " -0.045 2.00e-02 2.50e+03 pdb=" O ARG C 558 " 0.017 2.00e-02 2.50e+03 pdb=" N TYR C 559 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 520 " -0.037 5.00e-02 4.00e+02 5.56e-02 4.95e+00 pdb=" N PRO A 521 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 521 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 521 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 441 " 0.011 2.00e-02 2.50e+03 2.14e-02 4.60e+00 pdb=" C ALA C 441 " -0.037 2.00e-02 2.50e+03 pdb=" O ALA C 441 " 0.014 2.00e-02 2.50e+03 pdb=" N ARG C 442 " 0.013 2.00e-02 2.50e+03 ... (remaining 3088 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.62: 221 2.62 - 3.19: 17247 3.19 - 3.76: 32894 3.76 - 4.33: 43345 4.33 - 4.90: 67820 Nonbonded interactions: 161527 Sorted by model distance: nonbonded pdb=" OP2 DT G 42 " pdb="CA CA C1102 " model vdw 2.055 2.510 nonbonded pdb=" NH2 ARG D 212 " pdb=" O GLY D 293 " model vdw 2.203 3.120 nonbonded pdb=" OG1 THR D 308 " pdb=" OD1 ASP D 310 " model vdw 2.214 3.040 nonbonded pdb=" N MET B 1 " pdb=" O ARG B 349 " model vdw 2.215 3.120 nonbonded pdb=" OD1 ASP C 569 " pdb=" OG SER C 996 " model vdw 2.228 3.040 ... (remaining 161522 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 395 through 401 or (resid 402 through 403 and (name N or n \ ame CA or name C or name O or name CB )) or resid 404 through 519 or (resid 520 \ and (name N or name CA or name C or name O or name CB )) or resid 521 through 10 \ 06 or (resid 1007 and (name N or name CA or name C or name O or name CB )) or re \ sid 1101 through 1102)) selection = (chain 'C' and ((resid 395 and (name N or name CA or name C or name O or name CB \ )) or resid 396 or (resid 397 and (name N or name CA or name C or name O or nam \ e CB )) or resid 398 through 523 or (resid 524 and (name N or name CA or name C \ or name O or name CB )) or resid 525 through 689 or (resid 690 and (name N or na \ me CA or name C or name O or name CB )) or resid 691 through 1102)) } ncs_group { reference = (chain 'B' and (resid 1 through 335 or resid 341 through 350 or (resid 351 and ( \ name N or name CA or name C or name O or name CB )))) selection = (chain 'D' and (resid 1 through 115 or (resid 116 through 119 and (name N or nam \ e CA or name C or name O or name CB )) or resid 120 through 351)) } 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 group one per residue 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: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 22.350 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 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:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 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 : 0.006 0.481 21303 Z= 0.364 Angle : 0.675 21.934 29701 Z= 0.535 Chirality : 0.044 0.226 3261 Planarity : 0.004 0.056 3091 Dihedral : 19.646 175.510 8412 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.56 % Favored : 96.39 % Rotamer: Outliers : 2.25 % Allowed : 3.41 % Favored : 94.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.66 (0.17), residues: 2021 helix: -0.57 (0.18), residues: 730 sheet: -2.01 (0.27), residues: 346 loop : -2.65 (0.17), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 679 TYR 0.012 0.001 TYR A 805 PHE 0.011 0.001 PHE A 916 TRP 0.011 0.001 TRP A 829 HIS 0.003 0.000 HIS N 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.35 (21295) covalent geometry : angle 0.65881 / 0.53 (29697) hydrogen bonds : bond 0.17919 / 11.92 ( 915) hydrogen bonds : angle 6.79413 / 4.79 ( 2472) metal coordination : bond 0.22026 / 11.48 ( 8) metal coordination : angle 12.51722 / 6.81 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4042 Ramachandran restraints generated. 2021 Oldfield, 0 Emsley, 2021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4042 Ramachandran restraints generated. 2021 Oldfield, 0 Emsley, 2021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 258 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 ARG cc_start: 0.9380 (OUTLIER) cc_final: 0.9107 (ttp80) REVERT: A 504 ARG cc_start: 0.8931 (OUTLIER) cc_final: 0.8677 (ttm170) REVERT: C 780 SER cc_start: 0.9032 (m) cc_final: 0.8500 (p) REVERT: N 27 HIS cc_start: 0.6185 (p-80) cc_final: 0.5516 (m90) REVERT: N 67 ASP cc_start: 0.4382 (t0) cc_final: 0.4178 (t70) REVERT: N 109 TYR cc_start: 0.8054 (m-80) cc_final: 0.7124 (t80) REVERT: D 16 GLN cc_start: 0.8719 (pt0) cc_final: 0.8434 (pt0) REVERT: D 283 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8288 (ttpp) REVERT: B 110 MET cc_start: 0.8877 (mmm) cc_final: 0.8524 (mmp) REVERT: B 214 ASP cc_start: 0.8104 (p0) cc_final: 0.7743 (p0) REVERT: B 283 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8009 (ptmm) outliers start: 39 outliers final: 14 residues processed: 291 average time/residue: 0.1865 time to fit residues: 77.8458 Evaluate side-chains 138 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 ARG Chi-restraints excluded: chain A residue 504 ARG Chi-restraints excluded: chain A residue 558 ARG Chi-restraints excluded: chain A residue 628 ARG Chi-restraints excluded: chain A residue 784 PHE Chi-restraints excluded: chain A residue 827 LYS Chi-restraints excluded: chain A residue 972 ARG Chi-restraints excluded: chain C residue 458 ARG Chi-restraints excluded: chain C residue 641 PHE Chi-restraints excluded: chain C residue 758 GLU Chi-restraints excluded: chain C residue 804 PHE Chi-restraints excluded: chain C residue 823 LYS Chi-restraints excluded: chain C residue 828 ARG Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 235 ARG Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain B residue 283 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 0.0060 chunk 212 optimal weight: 8.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 414 GLN A 473 ASN A 495 GLN A 505 ASN A 850 ASN A 978 GLN A 990 HIS ** A1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 495 GLN C 809 GLN C 860 GLN ** C 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 962 GLN C 978 GLN C 990 HIS C1000 GLN N 135 ASN D 94 HIS ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 HIS B 52 GLN B 222 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.069940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.049717 restraints weight = 82191.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.051074 restraints weight = 38778.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.051930 restraints weight = 23815.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.052445 restraints weight = 17548.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.052680 restraints weight = 14526.687| |-----------------------------------------------------------------------------| r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21303 Z= 0.144 Angle : 0.625 9.284 29701 Z= 0.352 Chirality : 0.042 0.247 3261 Planarity : 0.005 0.051 3091 Dihedral : 23.982 177.398 4605 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.50 % Allowed : 8.37 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.18), residues: 2021 helix: 0.42 (0.19), residues: 739 sheet: -1.30 (0.28), residues: 342 loop : -2.21 (0.18), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 713 TYR 0.014 0.001 TYR C 928 PHE 0.015 0.001 PHE A 622 TRP 0.012 0.001 TRP A 893 HIS 0.006 0.001 HIS A 937 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.14 (21295) covalent geometry : angle 0.62336 / 0.35 (29697) hydrogen bonds : bond 0.05365 / 3.77 ( 915) hydrogen bonds : angle 4.96325 / 3.50 ( 2472) metal coordination : bond 0.01072 / 0.72 ( 8) metal coordination : angle 3.91694 / 2.21 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4042 Ramachandran restraints generated. 2021 Oldfield, 0 Emsley, 2021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4042 Ramachandran restraints generated. 2021 Oldfield, 0 Emsley, 2021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 471 ARG cc_start: 0.9425 (OUTLIER) cc_final: 0.9119 (ttt90) REVERT: C 780 SER cc_start: 0.9103 (m) cc_final: 0.8621 (p) REVERT: C 823 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8684 (mmtp) REVERT: C 828 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.7942 (mpt-90) REVERT: C 883 MET cc_start: 0.8721 (mmm) cc_final: 0.8038 (tpt) REVERT: N 108 GLU cc_start: 0.6562 (mt-10) cc_final: 0.5832 (mt-10) REVERT: N 109 TYR cc_start: 0.8053 (m-80) cc_final: 0.6990 (t80) REVERT: D 61 ILE cc_start: 0.9432 (pt) cc_final: 0.9229 (mp) REVERT: B 214 ASP cc_start: 0.8369 (p0) cc_final: 0.7935 (p0) outliers start: 26 outliers final: 9 residues processed: 158 average time/residue: 0.1529 time to fit residues: 36.9028 Evaluate side-chains 121 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 ARG Chi-restraints excluded: chain A residue 784 PHE Chi-restraints excluded: chain A residue 996 SER Chi-restraints excluded: chain C residue 582 ASP Chi-restraints excluded: chain C residue 758 GLU Chi-restraints excluded: chain C residue 823 LYS Chi-restraints excluded: chain C residue 828 ARG Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain B residue 67 CYS Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain B residue 283 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 6 optimal weight: 5.9990 chunk 215 optimal weight: 0.7980 chunk 152 optimal weight: 1.9990 chunk 170 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 133 optimal weight: 40.0000 chunk 156 optimal weight: 0.9990 chunk 149 optimal weight: 40.0000 chunk 62 optimal weight: 4.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1000 GLN C 406 HIS ** C 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 961 ASN ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.069170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.048536 restraints weight = 82825.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.049911 restraints weight = 38752.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.050801 restraints weight = 23861.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.051337 restraints weight = 17497.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.051673 restraints weight = 14484.257| |-----------------------------------------------------------------------------| r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21303 Z= 0.135 Angle : 0.578 9.720 29701 Z= 0.326 Chirality : 0.041 0.249 3261 Planarity : 0.004 0.046 3091 Dihedral : 24.050 176.665 4569 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.50 % Allowed : 8.95 % Favored : 89.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.19), residues: 2021 helix: 0.86 (0.20), residues: 740 sheet: -1.01 (0.28), residues: 350 loop : -1.96 (0.19), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 713 TYR 0.014 0.001 TYR B 346 PHE 0.020 0.001 PHE N 105 TRP 0.011 0.001 TRP C 893 HIS 0.005 0.001 HIS N 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.13 (21295) covalent geometry : angle 0.57709 / 0.33 (29697) hydrogen bonds : bond 0.04791 / 3.33 ( 915) hydrogen bonds : angle 4.58711 / 3.24 ( 2472) metal coordination : bond 0.00787 / 0.49 ( 8) metal coordination : angle 3.07318 / 1.78 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4042 Ramachandran restraints generated. 2021 Oldfield, 0 Emsley, 2021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4042 Ramachandran restraints generated. 2021 Oldfield, 0 Emsley, 2021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 111 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 471 ARG cc_start: 0.9412 (OUTLIER) cc_final: 0.9022 (ttt90) REVERT: A 929 GLU cc_start: 0.7626 (mm-30) cc_final: 0.7312 (mm-30) REVERT: C 780 SER cc_start: 0.9079 (m) cc_final: 0.8644 (p) REVERT: C 828 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.7927 (mpt-90) REVERT: C 883 MET cc_start: 0.8619 (mmm) cc_final: 0.8175 (tpt) REVERT: N 105 PHE cc_start: 0.7583 (t80) cc_final: 0.7314 (t80) REVERT: D 322 MET cc_start: 0.9239 (mtm) cc_final: 0.8988 (mtm) REVERT: B 162 MET cc_start: 0.9062 (mmm) cc_final: 0.8784 (mmm) REVERT: B 214 ASP cc_start: 0.8485 (p0) cc_final: 0.8071 (p0) outliers start: 26 outliers final: 12 residues processed: 131 average time/residue: 0.1547 time to fit residues: 31.4165 Evaluate side-chains 117 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 471 ARG Chi-restraints excluded: chain A residue 996 SER Chi-restraints excluded: chain C residue 406 HIS Chi-restraints excluded: chain C residue 582 ASP Chi-restraints excluded: chain C residue 828 ARG Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 33 GLN Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain B residue 22 MET Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain B residue 283 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 35 optimal weight: 0.0870 chunk 165 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 199 optimal weight: 5.9990 chunk 95 optimal weight: 7.9990 chunk 133 optimal weight: 40.0000 chunk 17 optimal weight: 6.9990 chunk 110 optimal weight: 0.8980 chunk 210 optimal weight: 3.9990 chunk 131 optimal weight: 20.0000 chunk 36 optimal weight: 0.8980 overall best weight: 1.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.067953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.047271 restraints weight = 82008.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.048578 restraints weight = 39813.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.049412 restraints weight = 24921.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.049923 restraints weight = 18468.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.050248 restraints weight = 15403.699| |-----------------------------------------------------------------------------| r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21303 Z= 0.163 Angle : 0.586 9.566 29701 Z= 0.327 Chirality : 0.041 0.248 3261 Planarity : 0.004 0.042 3091 Dihedral : 24.087 176.451 4560 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.33 % Allowed : 9.30 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.19), residues: 2021 helix: 0.96 (0.20), residues: 753 sheet: -0.83 (0.28), residues: 349 loop : -1.83 (0.19), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 407 TYR 0.011 0.001 TYR A 805 PHE 0.028 0.001 PHE N 105 TRP 0.012 0.001 TRP C 893 HIS 0.022 0.001 HIS C 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.16 (21295) covalent geometry : angle 0.58509 / 0.33 (29697) hydrogen bonds : bond 0.04773 / 3.31 ( 915) hydrogen bonds : angle 4.39980 / 3.11 ( 2472) metal coordination : bond 0.01627 / 1.04 ( 8) metal coordination : angle 2.15424 / 1.22 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4042 Ramachandran restraints generated. 2021 Oldfield, 0 Emsley, 2021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4042 Ramachandran restraints generated. 2021 Oldfield, 0 Emsley, 2021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.699 Fit side-chains revert: symmetry clash REVERT: C 780 SER cc_start: 0.9118 (m) cc_final: 0.8630 (p) REVERT: C 883 MET cc_start: 0.8598 (mmm) cc_final: 0.8144 (tpt) REVERT: D 322 MET cc_start: 0.9336 (mtm) cc_final: 0.9111 (mtm) REVERT: B 214 ASP cc_start: 0.8362 (p0) cc_final: 0.7966 (p0) outliers start: 23 outliers final: 13 residues processed: 119 average time/residue: 0.1572 time to fit residues: 29.4097 Evaluate side-chains 111 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 658 MET Chi-restraints excluded: chain A residue 996 SER Chi-restraints excluded: chain C residue 582 ASP Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 33 GLN Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 178 CYS Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain B residue 22 MET Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain B residue 283 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 172 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 216 optimal weight: 7.9990 chunk 81 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 136 optimal weight: 30.0000 chunk 163 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 61 optimal weight: 0.6980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 860 GLN ** C 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.067066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.046230 restraints weight = 81924.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.047528 restraints weight = 40019.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.048334 restraints weight = 25275.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.048847 restraints weight = 18884.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.049155 restraints weight = 15910.568| |-----------------------------------------------------------------------------| r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21303 Z= 0.165 Angle : 0.590 13.651 29701 Z= 0.328 Chirality : 0.041 0.250 3261 Planarity : 0.004 0.042 3091 Dihedral : 24.169 176.203 4552 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.85 % Allowed : 8.95 % Favored : 89.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.19), residues: 2021 helix: 1.12 (0.20), residues: 753 sheet: -0.65 (0.28), residues: 349 loop : -1.74 (0.19), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 828 TYR 0.012 0.001 TYR C 909 PHE 0.018 0.001 PHE B 189 TRP 0.013 0.001 TRP C 893 HIS 0.009 0.001 HIS C 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.17 (21295) covalent geometry : angle 0.58966 / 0.33 (29697) hydrogen bonds : bond 0.04691 / 3.24 ( 915) hydrogen bonds : angle 4.27607 / 3.03 ( 2472) metal coordination : bond 0.01658 / 1.07 ( 8) metal coordination : angle 2.12235 / 1.18 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4042 Ramachandran restraints generated. 2021 Oldfield, 0 Emsley, 2021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4042 Ramachandran restraints generated. 2021 Oldfield, 0 Emsley, 2021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 103 time to evaluate : 0.491 Fit side-chains revert: symmetry clash REVERT: A 929 GLU cc_start: 0.7543 (mm-30) cc_final: 0.7253 (mm-30) REVERT: C 780 SER cc_start: 0.9064 (m) cc_final: 0.8634 (p) REVERT: C 823 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8517 (mmtp) REVERT: C 849 MET cc_start: 0.7831 (tpp) cc_final: 0.7479 (tpp) REVERT: C 883 MET cc_start: 0.8631 (mmm) cc_final: 0.8257 (tpt) REVERT: B 214 ASP cc_start: 0.8366 (p0) cc_final: 0.7983 (p0) outliers start: 32 outliers final: 17 residues processed: 128 average time/residue: 0.1401 time to fit residues: 28.1627 Evaluate side-chains 117 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 409 ARG Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 996 SER Chi-restraints excluded: chain C residue 823 LYS Chi-restraints excluded: chain C residue 947 ILE Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 132 MET Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 33 GLN Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 178 CYS Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain B residue 22 MET Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain B residue 283 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 196 optimal weight: 0.9980 chunk 199 optimal weight: 10.0000 chunk 106 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 194 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 124 optimal weight: 10.0000 chunk 25 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 744 HIS C 860 GLN ** C 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.067820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.046997 restraints weight = 81159.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.048291 restraints weight = 39518.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.049132 restraints weight = 24867.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.049618 restraints weight = 18560.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.049944 restraints weight = 15558.146| |-----------------------------------------------------------------------------| r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 21303 Z= 0.120 Angle : 0.565 13.405 29701 Z= 0.312 Chirality : 0.040 0.254 3261 Planarity : 0.003 0.042 3091 Dihedral : 24.137 176.571 4552 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.39 % Allowed : 9.87 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.19), residues: 2021 helix: 1.19 (0.20), residues: 755 sheet: -0.54 (0.28), residues: 360 loop : -1.57 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 828 TYR 0.010 0.001 TYR C 909 PHE 0.016 0.001 PHE N 105 TRP 0.013 0.001 TRP C 893 HIS 0.005 0.001 HIS N 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.12 (21295) covalent geometry : angle 0.56450 / 0.31 (29697) hydrogen bonds : bond 0.04297 / 3.02 ( 915) hydrogen bonds : angle 4.14603 / 2.94 ( 2472) metal coordination : bond 0.00792 / 0.51 ( 8) metal coordination : angle 2.22501 / 1.30 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4042 Ramachandran restraints generated. 2021 Oldfield, 0 Emsley, 2021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4042 Ramachandran restraints generated. 2021 Oldfield, 0 Emsley, 2021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.676 Fit side-chains REVERT: C 476 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9159 (mm) REVERT: C 780 SER cc_start: 0.9054 (m) cc_final: 0.8649 (p) REVERT: C 823 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8387 (mmtp) REVERT: C 849 MET cc_start: 0.7740 (tpp) cc_final: 0.7269 (tpp) REVERT: C 883 MET cc_start: 0.8571 (mmm) cc_final: 0.8220 (tpt) REVERT: B 214 ASP cc_start: 0.8342 (p0) cc_final: 0.7974 (p0) outliers start: 24 outliers final: 13 residues processed: 114 average time/residue: 0.1422 time to fit residues: 25.5950 Evaluate side-chains 110 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 996 SER Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 823 LYS Chi-restraints excluded: chain C residue 947 ILE Chi-restraints excluded: chain N residue 132 MET Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 287 CYS Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain B residue 22 MET Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain B residue 283 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 152 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 219 optimal weight: 30.0000 chunk 171 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 173 optimal weight: 0.7980 chunk 186 optimal weight: 4.9990 chunk 189 optimal weight: 4.9990 chunk 169 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 146 optimal weight: 7.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 860 GLN ** C 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.066549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.045614 restraints weight = 82727.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.046895 restraints weight = 40376.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.047717 restraints weight = 25501.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.048232 restraints weight = 18929.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.048543 restraints weight = 15948.954| |-----------------------------------------------------------------------------| r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 21303 Z= 0.179 Angle : 0.595 9.790 29701 Z= 0.327 Chirality : 0.041 0.248 3261 Planarity : 0.004 0.041 3091 Dihedral : 24.243 176.105 4552 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.21 % Allowed : 10.22 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.19), residues: 2021 helix: 1.29 (0.20), residues: 754 sheet: -0.36 (0.28), residues: 340 loop : -1.62 (0.20), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 349 TYR 0.012 0.001 TYR C 909 PHE 0.021 0.001 PHE A 641 TRP 0.013 0.001 TRP C 893 HIS 0.004 0.001 HIS D 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.18 (21295) covalent geometry : angle 0.59477 / 0.33 (29697) hydrogen bonds : bond 0.04603 / 3.21 ( 915) hydrogen bonds : angle 4.20273 / 2.97 ( 2472) metal coordination : bond 0.02050 / 1.29 ( 8) metal coordination : angle 2.21899 / 1.09 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4042 Ramachandran restraints generated. 2021 Oldfield, 0 Emsley, 2021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4042 Ramachandran restraints generated. 2021 Oldfield, 0 Emsley, 2021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 0.702 Fit side-chains REVERT: A 409 ARG cc_start: 0.9150 (OUTLIER) cc_final: 0.8733 (mtm180) REVERT: C 476 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.9185 (mm) REVERT: C 780 SER cc_start: 0.9067 (m) cc_final: 0.8666 (p) REVERT: C 823 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8401 (mmtp) REVERT: C 849 MET cc_start: 0.7939 (tpp) cc_final: 0.7486 (tpp) REVERT: C 883 MET cc_start: 0.8696 (mmm) cc_final: 0.8331 (tpt) REVERT: B 162 MET cc_start: 0.8924 (mmm) cc_final: 0.8708 (mmm) REVERT: B 214 ASP cc_start: 0.8392 (p0) cc_final: 0.8012 (p0) outliers start: 21 outliers final: 16 residues processed: 115 average time/residue: 0.1451 time to fit residues: 26.5947 Evaluate side-chains 117 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 409 ARG Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 996 SER Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 823 LYS Chi-restraints excluded: chain C residue 947 ILE Chi-restraints excluded: chain N residue 132 MET Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 33 GLN Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 178 CYS Chi-restraints excluded: chain D residue 287 CYS Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain B residue 22 MET Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain B residue 283 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 63 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 176 optimal weight: 5.9990 chunk 164 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 157 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 173 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.065887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.044887 restraints weight = 82287.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.046149 restraints weight = 40664.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.046959 restraints weight = 25733.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.047453 restraints weight = 19259.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.047667 restraints weight = 16217.072| |-----------------------------------------------------------------------------| r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 21303 Z= 0.188 Angle : 0.612 15.434 29701 Z= 0.334 Chirality : 0.042 0.254 3261 Planarity : 0.004 0.045 3091 Dihedral : 24.339 175.723 4552 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.56 % Allowed : 10.28 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.19), residues: 2021 helix: 1.25 (0.20), residues: 755 sheet: -0.33 (0.28), residues: 339 loop : -1.61 (0.20), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 442 TYR 0.017 0.001 TYR D 161 PHE 0.018 0.002 PHE A 641 TRP 0.013 0.001 TRP C 893 HIS 0.005 0.001 HIS A 836 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.19 (21295) covalent geometry : angle 0.61158 / 0.33 (29697) hydrogen bonds : bond 0.04733 / 3.30 ( 915) hydrogen bonds : angle 4.23298 / 3.01 ( 2472) metal coordination : bond 0.02035 / 1.27 ( 8) metal coordination : angle 2.50766 / 1.30 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4042 Ramachandran restraints generated. 2021 Oldfield, 0 Emsley, 2021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4042 Ramachandran restraints generated. 2021 Oldfield, 0 Emsley, 2021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 0.459 Fit side-chains REVERT: A 409 ARG cc_start: 0.9166 (OUTLIER) cc_final: 0.8764 (mtm180) REVERT: C 445 HIS cc_start: 0.8175 (m-70) cc_final: 0.7940 (m-70) REVERT: C 780 SER cc_start: 0.9056 (m) cc_final: 0.8624 (p) REVERT: C 823 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8393 (mmtp) REVERT: C 849 MET cc_start: 0.7984 (tpp) cc_final: 0.7522 (tpp) REVERT: C 883 MET cc_start: 0.8742 (mmm) cc_final: 0.8367 (tpt) REVERT: C 936 PHE cc_start: 0.9231 (OUTLIER) cc_final: 0.8998 (m-10) REVERT: N 131 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8212 (tp30) REVERT: B 214 ASP cc_start: 0.8389 (p0) cc_final: 0.7951 (p0) outliers start: 27 outliers final: 19 residues processed: 116 average time/residue: 0.1418 time to fit residues: 26.3000 Evaluate side-chains 117 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 409 ARG Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 658 MET Chi-restraints excluded: chain A residue 996 SER Chi-restraints excluded: chain C residue 501 HIS Chi-restraints excluded: chain C residue 823 LYS Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain C residue 947 ILE Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 41 PHE Chi-restraints excluded: chain N residue 132 MET Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 33 GLN Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 178 CYS Chi-restraints excluded: chain D residue 287 CYS Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain B residue 22 MET Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain B residue 283 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 220 optimal weight: 40.0000 chunk 205 optimal weight: 4.9990 chunk 189 optimal weight: 0.0070 chunk 127 optimal weight: 40.0000 chunk 178 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 215 optimal weight: 5.9990 chunk 198 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 overall best weight: 1.1604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 962 GLN ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.066882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.045949 restraints weight = 81416.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.047239 restraints weight = 39782.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.048069 restraints weight = 25128.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.048578 restraints weight = 18780.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.048873 restraints weight = 15722.102| |-----------------------------------------------------------------------------| r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 21303 Z= 0.125 Angle : 0.578 14.162 29701 Z= 0.316 Chirality : 0.040 0.273 3261 Planarity : 0.004 0.042 3091 Dihedral : 24.294 176.207 4552 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.15 % Allowed : 10.62 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.19), residues: 2021 helix: 1.32 (0.20), residues: 755 sheet: -0.08 (0.29), residues: 327 loop : -1.48 (0.20), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 442 TYR 0.013 0.001 TYR C 909 PHE 0.019 0.001 PHE A 641 TRP 0.013 0.001 TRP C 893 HIS 0.004 0.001 HIS N 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.12 (21295) covalent geometry : angle 0.57785 / 0.32 (29697) hydrogen bonds : bond 0.04340 / 3.08 ( 915) hydrogen bonds : angle 4.11331 / 2.91 ( 2472) metal coordination : bond 0.01050 / 0.68 ( 8) metal coordination : angle 2.08813 / 1.20 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4042 Ramachandran restraints generated. 2021 Oldfield, 0 Emsley, 2021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4042 Ramachandran restraints generated. 2021 Oldfield, 0 Emsley, 2021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.519 Fit side-chains REVERT: A 409 ARG cc_start: 0.9154 (OUTLIER) cc_final: 0.8740 (mtm180) REVERT: C 445 HIS cc_start: 0.8121 (m-70) cc_final: 0.7906 (m-70) REVERT: C 780 SER cc_start: 0.9014 (m) cc_final: 0.8585 (p) REVERT: C 823 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8334 (mmtp) REVERT: C 883 MET cc_start: 0.8661 (mmm) cc_final: 0.8262 (tpt) REVERT: N 131 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8212 (tp30) REVERT: B 214 ASP cc_start: 0.8285 (p0) cc_final: 0.7985 (p0) outliers start: 20 outliers final: 13 residues processed: 107 average time/residue: 0.1423 time to fit residues: 23.8922 Evaluate side-chains 110 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 409 ARG Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 996 SER Chi-restraints excluded: chain C residue 501 HIS Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 823 LYS Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 132 MET Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain B residue 283 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 220 optimal weight: 40.0000 chunk 192 optimal weight: 2.9990 chunk 212 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 177 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 chunk 221 optimal weight: 30.0000 chunk 40 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 443 ASN ** C 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.065836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.044767 restraints weight = 81625.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.046039 restraints weight = 40046.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.046847 restraints weight = 25387.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.047337 restraints weight = 19096.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.047553 restraints weight = 16078.327| |-----------------------------------------------------------------------------| r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21303 Z= 0.188 Angle : 0.621 14.831 29701 Z= 0.335 Chirality : 0.041 0.279 3261 Planarity : 0.004 0.045 3091 Dihedral : 24.392 175.590 4552 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.21 % Allowed : 10.80 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.19), residues: 2021 helix: 1.35 (0.20), residues: 754 sheet: -0.18 (0.29), residues: 337 loop : -1.48 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 442 TYR 0.014 0.001 TYR C 909 PHE 0.021 0.001 PHE A 641 TRP 0.012 0.001 TRP C 893 HIS 0.004 0.001 HIS A 836 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.19 (21295) covalent geometry : angle 0.62021 / 0.33 (29697) hydrogen bonds : bond 0.04715 / 3.30 ( 915) hydrogen bonds : angle 4.20387 / 2.98 ( 2472) metal coordination : bond 0.02163 / 1.35 ( 8) metal coordination : angle 2.58511 / 1.24 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4042 Ramachandran restraints generated. 2021 Oldfield, 0 Emsley, 2021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4042 Ramachandran restraints generated. 2021 Oldfield, 0 Emsley, 2021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.719 Fit side-chains REVERT: A 409 ARG cc_start: 0.9167 (OUTLIER) cc_final: 0.8762 (mtm180) REVERT: C 780 SER cc_start: 0.9049 (m) cc_final: 0.8653 (p) REVERT: C 823 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8385 (mmtp) REVERT: C 883 MET cc_start: 0.8790 (mmm) cc_final: 0.8375 (tpt) REVERT: C 936 PHE cc_start: 0.9236 (OUTLIER) cc_final: 0.8987 (m-10) REVERT: N 131 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8259 (tp30) REVERT: B 214 ASP cc_start: 0.8342 (p0) cc_final: 0.7979 (p0) outliers start: 21 outliers final: 15 residues processed: 110 average time/residue: 0.1438 time to fit residues: 25.1538 Evaluate side-chains 113 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 409 ARG Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 996 SER Chi-restraints excluded: chain C residue 501 HIS Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 823 LYS Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain C residue 947 ILE Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 132 MET Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 33 GLN Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 178 CYS Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain B residue 283 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 180 optimal weight: 3.9990 chunk 162 optimal weight: 7.9990 chunk 210 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 85 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 51 optimal weight: 0.4980 chunk 166 optimal weight: 0.4980 chunk 19 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.066824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.045618 restraints weight = 81673.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.046907 restraints weight = 39857.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.047727 restraints weight = 25207.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.048236 restraints weight = 18892.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.048487 restraints weight = 15901.832| |-----------------------------------------------------------------------------| r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21303 Z= 0.132 Angle : 0.596 13.609 29701 Z= 0.322 Chirality : 0.041 0.282 3261 Planarity : 0.004 0.043 3091 Dihedral : 24.371 175.708 4552 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.04 % Allowed : 10.80 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.19), residues: 2021 helix: 1.37 (0.20), residues: 754 sheet: -0.08 (0.29), residues: 334 loop : -1.41 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 442 TYR 0.013 0.001 TYR C 909 PHE 0.027 0.001 PHE A 418 TRP 0.013 0.001 TRP C 893 HIS 0.004 0.001 HIS N 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.13 (21295) covalent geometry : angle 0.59503 / 0.32 (29697) hydrogen bonds : bond 0.04415 / 3.13 ( 915) hydrogen bonds : angle 4.12384 / 2.93 ( 2472) metal coordination : bond 0.01173 / 0.76 ( 8) metal coordination : angle 2.17061 / 1.22 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3155.34 seconds wall clock time: 55 minutes 27.22 seconds (3327.22 seconds total)