Starting phenix.real_space_refine on Wed Nov 19 03:32:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6cij_7480/11_2025/6cij_7480.cif Found real_map, /net/cci-nas-00/data/ceres_data/6cij_7480/11_2025/6cij_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6cij_7480/11_2025/6cij_7480.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6cij_7480/11_2025/6cij_7480.map" model { file = "/net/cci-nas-00/data/ceres_data/6cij_7480/11_2025/6cij_7480.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6cij_7480/11_2025/6cij_7480.cif" } 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-2.0-5881/lib/python3.9/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: 4.66, per 1000 atoms: 0.23 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: 1.87 Conformation dependent library (CDL) restraints added in 729.2 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: 2.86 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: 5.07 Time building geometry restraints manager: 2.41 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' DT J 3 " pdb=" O3' DT J 3 " ideal model delta sigma weight residual 1.422 1.462 -0.040 3.00e-02 1.11e+03 1.81e+00 bond pdb=" C LYS A 890 " pdb=" O LYS A 890 " ideal model delta sigma weight residual 1.244 1.231 0.012 1.00e-02 1.00e+04 1.55e+00 bond pdb=" C3' DC J 9 " pdb=" O3' DC J 9 " ideal model delta sigma weight residual 1.422 1.457 -0.035 3.00e-02 1.11e+03 1.38e+00 bond pdb=" CA LYS A 890 " pdb=" C LYS A 890 " ideal model delta sigma weight residual 1.520 1.535 -0.014 1.23e-02 6.61e+03 1.36e+00 bond pdb=" C3' DA F 32 " pdb=" O3' DA F 32 " ideal model delta sigma weight residual 1.422 1.456 -0.034 3.00e-02 1.11e+03 1.27e+00 ... (remaining 21290 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 29013 1.69 - 3.37: 608 3.37 - 5.06: 61 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=" 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=" N LYS A 890 " pdb=" CA LYS A 890 " pdb=" C LYS A 890 " ideal model delta sigma weight residual 112.75 118.40 -5.65 1.36e+00 5.41e-01 1.73e+01 angle pdb=" N TRP B 172 " pdb=" CA TRP B 172 " pdb=" C TRP B 172 " ideal model delta sigma weight residual 111.71 116.26 -4.55 1.15e+00 7.56e-01 1.57e+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: 2685 0.045 - 0.091: 422 0.091 - 0.136: 142 0.136 - 0.181: 6 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: 1.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 25.020 Find NCS groups from input model: 0.300 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: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 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 : 0.005 0.481 21303 Z= 0.181 Angle : 0.596 21.934 29701 Z= 0.366 Chirality : 0.039 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 covalent geometry : bond 0.00259 (21295) covalent geometry : angle 0.57823 (29697) hydrogen bonds : bond 0.17919 ( 915) hydrogen bonds : angle 6.79413 ( 2472) metal coordination : bond 0.22026 ( 8) metal coordination : angle 12.51722 ( 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 : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 ARG cc_start: 0.9380 (OUTLIER) cc_final: 0.9117 (ttp80) REVERT: A 504 ARG cc_start: 0.8931 (OUTLIER) cc_final: 0.8671 (ttm170) REVERT: C 780 SER cc_start: 0.9032 (m) cc_final: 0.8501 (p) REVERT: N 27 HIS cc_start: 0.6185 (p-80) cc_final: 0.5518 (m90) REVERT: N 67 ASP cc_start: 0.4382 (t0) cc_final: 0.4177 (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: 0.8525 (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: 0.8008 (ptmm) outliers start: 39 outliers final: 14 residues processed: 291 average time/residue: 0.2071 time to fit residues: 85.3390 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 : 0.741 ------------------------------------------------------------------------------- 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: 2.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 0.0060 chunk 212 optimal weight: 8.9990 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN A 473 ASN A 495 GLN A 505 ASN A 850 ASN A 978 GLN A 990 HIS 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 47 HIS D 94 HIS ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 HIS B 222 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.069486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.049065 restraints weight = 81889.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.050425 restraints weight = 38717.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.051291 restraints weight = 23846.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.051823 restraints weight = 17509.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.052061 restraints weight = 14516.837| |-----------------------------------------------------------------------------| r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1677 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= 0.141 Angle : 0.595 9.648 29701 Z= 0.325 Chirality : 0.039 0.199 3261 Planarity : 0.004 0.049 3091 Dihedral : 23.815 175.381 4605 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.50 % Allowed : 8.26 % Favored : 90.24 % 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: -1.47 (0.18), residues: 2021 helix: 0.54 (0.19), residues: 738 sheet: -1.17 (0.28), residues: 337 loop : -2.18 (0.18), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 713 TYR 0.013 0.001 TYR N 109 PHE 0.012 0.001 PHE A 743 TRP 0.012 0.001 TRP A 893 HIS 0.005 0.001 HIS N 27 Details of bonding type rmsd covalent geometry : bond 0.00304 (21295) covalent geometry : angle 0.59392 (29697) hydrogen bonds : bond 0.04779 ( 915) hydrogen bonds : angle 4.82312 ( 2472) metal coordination : bond 0.00955 ( 8) metal coordination : angle 3.30718 ( 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 159 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 471 ARG cc_start: 0.9397 (OUTLIER) cc_final: 0.8973 (ttt90) REVERT: A 883 MET cc_start: 0.8607 (tpt) cc_final: 0.8227 (tpt) REVERT: A 929 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7384 (mm-30) REVERT: C 578 MET cc_start: 0.8339 (mtp) cc_final: 0.7943 (mtm) REVERT: C 780 SER cc_start: 0.9110 (m) cc_final: 0.8635 (p) REVERT: C 823 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8681 (mmtp) REVERT: C 828 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.7917 (mpt-90) REVERT: C 883 MET cc_start: 0.8593 (mmm) cc_final: 0.8045 (tpt) REVERT: N 109 TYR cc_start: 0.8150 (m-80) cc_final: 0.7064 (t80) REVERT: D 61 ILE cc_start: 0.9432 (pt) cc_final: 0.9231 (mp) REVERT: B 214 ASP cc_start: 0.8448 (p0) cc_final: 0.7992 (p0) outliers start: 26 outliers final: 5 residues processed: 156 average time/residue: 0.1736 time to fit residues: 40.7052 Evaluate side-chains 113 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 ARG Chi-restraints excluded: chain C residue 582 ASP 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 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: 6.9990 chunk 215 optimal weight: 0.6980 chunk 152 optimal weight: 1.9990 chunk 170 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 133 optimal weight: 10.0000 chunk 156 optimal weight: 20.0000 chunk 149 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1000 GLN C 406 HIS C 473 ASN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 860 GLN ** C 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 961 ASN ** N 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.065457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.044529 restraints weight = 82933.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.045776 restraints weight = 40884.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.046578 restraints weight = 26039.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.047071 restraints weight = 19579.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.047316 restraints weight = 16450.208| |-----------------------------------------------------------------------------| r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 21303 Z= 0.267 Angle : 0.661 9.936 29701 Z= 0.358 Chirality : 0.042 0.196 3261 Planarity : 0.005 0.050 3091 Dihedral : 24.061 173.534 4564 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.56 % Allowed : 8.55 % Favored : 89.90 % 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: -1.13 (0.19), residues: 2021 helix: 0.82 (0.19), residues: 752 sheet: -1.03 (0.29), residues: 330 loop : -2.00 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 349 TYR 0.029 0.002 TYR B 346 PHE 0.017 0.002 PHE A 418 TRP 0.014 0.002 TRP C 893 HIS 0.023 0.002 HIS N 27 Details of bonding type rmsd covalent geometry : bond 0.00598 (21295) covalent geometry : angle 0.66039 (29697) hydrogen bonds : bond 0.05486 ( 915) hydrogen bonds : angle 4.62735 ( 2472) metal coordination : bond 0.02737 ( 8) metal coordination : angle 2.94994 ( 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 126 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 99 time to evaluate : 0.768 Fit side-chains revert: symmetry clash REVERT: A 929 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7462 (mm-30) REVERT: C 578 MET cc_start: 0.8383 (mtp) cc_final: 0.8061 (mtm) REVERT: C 883 MET cc_start: 0.8710 (mmm) cc_final: 0.8209 (tpt) REVERT: N 105 PHE cc_start: 0.7772 (t80) cc_final: 0.7048 (t80) REVERT: N 109 TYR cc_start: 0.8205 (m-80) cc_final: 0.7965 (m-80) REVERT: B 110 MET cc_start: 0.9053 (mmm) cc_final: 0.8832 (mmm) REVERT: B 162 MET cc_start: 0.9011 (mmm) cc_final: 0.8736 (mmm) REVERT: B 212 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7948 (tpt-90) REVERT: B 214 ASP cc_start: 0.8382 (p0) cc_final: 0.7998 (p0) outliers start: 27 outliers final: 16 residues processed: 124 average time/residue: 0.1608 time to fit residues: 31.1784 Evaluate side-chains 110 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 866 VAL 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 947 ILE 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 188 GLU Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 287 CYS Chi-restraints excluded: chain B residue 22 MET Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain B residue 260 SER 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: 10.0000 chunk 165 optimal weight: 6.9990 chunk 54 optimal weight: 0.7980 chunk 199 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 133 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 210 optimal weight: 0.9980 chunk 131 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 406 HIS C 473 ASN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 860 GLN ** C 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3374 r_free = 0.3374 target = 0.067063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.046132 restraints weight = 81899.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.047426 restraints weight = 39850.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.048255 restraints weight = 25173.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.048745 restraints weight = 18798.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.049074 restraints weight = 15738.981| |-----------------------------------------------------------------------------| r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21303 Z= 0.130 Angle : 0.557 12.781 29701 Z= 0.304 Chirality : 0.038 0.133 3261 Planarity : 0.004 0.041 3091 Dihedral : 23.932 174.548 4552 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.39 % Allowed : 8.66 % Favored : 89.95 % 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: -0.76 (0.19), residues: 2021 helix: 1.09 (0.20), residues: 750 sheet: -0.85 (0.28), residues: 352 loop : -1.74 (0.20), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 828 TYR 0.011 0.001 TYR A 485 PHE 0.013 0.001 PHE N 41 TRP 0.013 0.001 TRP C 893 HIS 0.009 0.001 HIS C 406 Details of bonding type rmsd covalent geometry : bond 0.00281 (21295) covalent geometry : angle 0.55663 (29697) hydrogen bonds : bond 0.04208 ( 915) hydrogen bonds : angle 4.30707 ( 2472) metal coordination : bond 0.00859 ( 8) metal coordination : angle 2.44946 ( 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 127 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 0.725 Fit side-chains revert: symmetry clash REVERT: C 476 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9248 (mm) REVERT: C 578 MET cc_start: 0.8306 (mtp) cc_final: 0.8000 (mtm) REVERT: C 780 SER cc_start: 0.9066 (m) cc_final: 0.8638 (p) REVERT: C 883 MET cc_start: 0.8559 (mmm) cc_final: 0.8205 (tpt) REVERT: N 105 PHE cc_start: 0.7661 (t80) cc_final: 0.7161 (t80) REVERT: N 109 TYR cc_start: 0.8153 (m-80) cc_final: 0.7907 (m-80) REVERT: D 41 CYS cc_start: 0.8323 (OUTLIER) cc_final: 0.7845 (p) REVERT: B 110 MET cc_start: 0.9098 (mmm) cc_final: 0.8855 (mmm) REVERT: B 214 ASP cc_start: 0.8331 (p0) cc_final: 0.7948 (p0) outliers start: 24 outliers final: 13 residues processed: 123 average time/residue: 0.1578 time to fit residues: 30.9398 Evaluate side-chains 116 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 996 SER Chi-restraints excluded: chain C residue 406 HIS Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 582 ASP Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 178 CYS Chi-restraints excluded: chain B residue 22 MET Chi-restraints excluded: chain B residue 143 ASP 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: 9.9990 chunk 40 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 216 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 136 optimal weight: 10.0000 chunk 163 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 61 optimal weight: 0.0370 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 744 HIS C 860 GLN ** C 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 HIS ** 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 = 0.3388 r_free = 0.3388 target = 0.067563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.046734 restraints weight = 81436.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.048032 restraints weight = 39542.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.048879 restraints weight = 24909.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.049383 restraints weight = 18540.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.049690 restraints weight = 15481.740| |-----------------------------------------------------------------------------| r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21303 Z= 0.119 Angle : 0.545 12.835 29701 Z= 0.296 Chirality : 0.038 0.132 3261 Planarity : 0.004 0.043 3091 Dihedral : 23.871 174.498 4552 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.56 % Allowed : 9.24 % 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: -0.55 (0.19), residues: 2021 helix: 1.18 (0.20), residues: 755 sheet: -0.61 (0.28), residues: 347 loop : -1.61 (0.20), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 828 TYR 0.013 0.001 TYR C 909 PHE 0.013 0.001 PHE A 497 TRP 0.013 0.001 TRP C 893 HIS 0.008 0.001 HIS C 406 Details of bonding type rmsd covalent geometry : bond 0.00257 (21295) covalent geometry : angle 0.54458 (29697) hydrogen bonds : bond 0.03930 ( 915) hydrogen bonds : angle 4.13847 ( 2472) metal coordination : bond 0.00694 ( 8) metal coordination : angle 1.84625 ( 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 128 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 858 MET cc_start: 0.8587 (mmp) cc_final: 0.8344 (mmp) REVERT: A 929 GLU cc_start: 0.7481 (mm-30) cc_final: 0.7138 (mm-30) REVERT: C 476 LEU cc_start: 0.9434 (OUTLIER) cc_final: 0.9202 (mm) REVERT: C 780 SER cc_start: 0.9076 (m) cc_final: 0.8662 (p) REVERT: C 883 MET cc_start: 0.8522 (mmm) cc_final: 0.8193 (tpt) REVERT: C 936 PHE cc_start: 0.9052 (OUTLIER) cc_final: 0.8848 (m-80) REVERT: N 105 PHE cc_start: 0.7640 (t80) cc_final: 0.7120 (t80) REVERT: N 109 TYR cc_start: 0.8134 (m-80) cc_final: 0.7879 (m-80) REVERT: D 41 CYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7797 (p) REVERT: B 110 MET cc_start: 0.9107 (mmm) cc_final: 0.8848 (mmm) REVERT: B 189 PHE cc_start: 0.7309 (m-80) cc_final: 0.7109 (m-80) REVERT: B 214 ASP cc_start: 0.8318 (p0) cc_final: 0.7949 (p0) outliers start: 27 outliers final: 15 residues processed: 120 average time/residue: 0.1528 time to fit residues: 29.3110 Evaluate side-chains 116 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.763 ------------------------------------------------------------------------------- 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 507 GLU Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 41 CYS 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 B residue 22 MET Chi-restraints excluded: chain B residue 143 ASP 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: 0.3980 chunk 199 optimal weight: 10.0000 chunk 106 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 194 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 962 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 860 GLN ** C 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 HIS ** 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 = 0.3396 r_free = 0.3396 target = 0.067898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.047141 restraints weight = 81027.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.048434 restraints weight = 39420.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.049284 restraints weight = 24748.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.049789 restraints weight = 18475.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.050053 restraints weight = 15431.591| |-----------------------------------------------------------------------------| r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21303 Z= 0.118 Angle : 0.542 12.551 29701 Z= 0.291 Chirality : 0.037 0.133 3261 Planarity : 0.003 0.044 3091 Dihedral : 23.843 174.431 4552 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.56 % Allowed : 9.58 % Favored : 88.86 % 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: -0.34 (0.19), residues: 2021 helix: 1.29 (0.20), residues: 757 sheet: -0.34 (0.28), residues: 339 loop : -1.50 (0.20), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 442 TYR 0.011 0.001 TYR C 909 PHE 0.015 0.001 PHE A 641 TRP 0.012 0.001 TRP C 893 HIS 0.006 0.001 HIS N 27 Details of bonding type rmsd covalent geometry : bond 0.00256 (21295) covalent geometry : angle 0.54140 (29697) hydrogen bonds : bond 0.03738 ( 915) hydrogen bonds : angle 4.01650 ( 2472) metal coordination : bond 0.00708 ( 8) metal coordination : angle 1.70916 ( 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 130 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 103 time to evaluate : 0.698 Fit side-chains revert: symmetry clash REVERT: A 409 ARG cc_start: 0.9146 (OUTLIER) cc_final: 0.8734 (mtm180) REVERT: A 858 MET cc_start: 0.8634 (mmp) cc_final: 0.8401 (mmp) REVERT: C 476 LEU cc_start: 0.9445 (OUTLIER) cc_final: 0.9218 (mm) REVERT: C 780 SER cc_start: 0.9088 (m) cc_final: 0.8705 (p) REVERT: C 883 MET cc_start: 0.8519 (mmm) cc_final: 0.8246 (tpt) REVERT: N 105 PHE cc_start: 0.7697 (t80) cc_final: 0.7193 (t80) REVERT: D 41 CYS cc_start: 0.8297 (OUTLIER) cc_final: 0.7797 (p) REVERT: B 110 MET cc_start: 0.9166 (mmm) cc_final: 0.8945 (mmm) REVERT: B 189 PHE cc_start: 0.7283 (m-80) cc_final: 0.7064 (m-10) REVERT: B 214 ASP cc_start: 0.8309 (p0) cc_final: 0.7935 (p0) outliers start: 27 outliers final: 11 residues processed: 121 average time/residue: 0.1504 time to fit residues: 29.1479 Evaluate side-chains 111 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.769 ------------------------------------------------------------------------------- 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 996 SER Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 501 HIS Chi-restraints excluded: chain C residue 507 GLU Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 41 CYS 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 B residue 143 ASP Chi-restraints excluded: chain B residue 212 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 152 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 219 optimal weight: 8.9990 chunk 171 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 173 optimal weight: 0.9980 chunk 186 optimal weight: 0.9980 chunk 189 optimal weight: 5.9990 chunk 169 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 146 optimal weight: 7.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 962 GLN C 406 HIS C 443 ASN C 456 GLN C 860 GLN ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.066751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.045787 restraints weight = 82725.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.047091 restraints weight = 40419.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.047926 restraints weight = 25474.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.048425 restraints weight = 19047.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.048672 restraints weight = 15976.549| |-----------------------------------------------------------------------------| r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21303 Z= 0.157 Angle : 0.561 9.528 29701 Z= 0.303 Chirality : 0.038 0.143 3261 Planarity : 0.004 0.043 3091 Dihedral : 23.912 173.867 4548 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.33 % Allowed : 9.53 % Favored : 89.15 % 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: 756 sheet: -0.34 (0.28), residues: 348 loop : -1.43 (0.20), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 442 TYR 0.012 0.001 TYR C 909 PHE 0.022 0.001 PHE A 418 TRP 0.012 0.001 TRP C 893 HIS 0.007 0.001 HIS N 27 Details of bonding type rmsd covalent geometry : bond 0.00350 (21295) covalent geometry : angle 0.56059 (29697) hydrogen bonds : bond 0.04072 ( 915) hydrogen bonds : angle 4.01179 ( 2472) metal coordination : bond 0.01576 ( 8) metal coordination : angle 1.55721 ( 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 123 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 0.661 Fit side-chains revert: symmetry clash REVERT: A 409 ARG cc_start: 0.9163 (OUTLIER) cc_final: 0.8761 (mtm180) REVERT: A 858 MET cc_start: 0.8748 (mmp) cc_final: 0.8545 (mmp) REVERT: A 929 GLU cc_start: 0.7592 (mm-30) cc_final: 0.7295 (mm-30) REVERT: C 476 LEU cc_start: 0.9444 (OUTLIER) cc_final: 0.9224 (mm) REVERT: C 780 SER cc_start: 0.9067 (m) cc_final: 0.8688 (p) REVERT: C 849 MET cc_start: 0.8080 (tpt) cc_final: 0.7832 (tpt) REVERT: C 883 MET cc_start: 0.8665 (mmm) cc_final: 0.8362 (tpt) REVERT: N 131 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7947 (tp30) REVERT: D 41 CYS cc_start: 0.8392 (OUTLIER) cc_final: 0.7852 (p) REVERT: B 110 MET cc_start: 0.9202 (mmm) cc_final: 0.8886 (mmm) REVERT: B 189 PHE cc_start: 0.7317 (m-80) cc_final: 0.7048 (m-10) REVERT: B 214 ASP cc_start: 0.8341 (p0) cc_final: 0.7967 (p0) outliers start: 23 outliers final: 13 residues processed: 117 average time/residue: 0.1546 time to fit residues: 28.8558 Evaluate side-chains 114 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.850 ------------------------------------------------------------------------------- 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 406 HIS Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 501 HIS Chi-restraints excluded: chain C residue 507 GLU Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 41 CYS 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 B residue 143 ASP Chi-restraints excluded: chain B residue 212 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 63 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 176 optimal weight: 4.9990 chunk 164 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 157 optimal weight: 0.9990 chunk 197 optimal weight: 0.8980 chunk 47 optimal weight: 0.0770 chunk 8 optimal weight: 0.9980 chunk 173 optimal weight: 10.0000 overall best weight: 1.3942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 406 HIS D 232 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.066982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.046050 restraints weight = 81951.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.047341 restraints weight = 40169.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.048171 restraints weight = 25333.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.048677 restraints weight = 18902.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.048928 restraints weight = 15860.390| |-----------------------------------------------------------------------------| r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21303 Z= 0.139 Angle : 0.565 14.384 29701 Z= 0.303 Chirality : 0.038 0.153 3261 Planarity : 0.003 0.048 3091 Dihedral : 23.902 173.861 4548 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.27 % Allowed : 9.99 % 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: -0.21 (0.19), residues: 2021 helix: 1.36 (0.20), residues: 755 sheet: -0.30 (0.28), residues: 344 loop : -1.37 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 442 TYR 0.012 0.001 TYR C 909 PHE 0.031 0.001 PHE N 105 TRP 0.012 0.001 TRP C 893 HIS 0.006 0.001 HIS N 27 Details of bonding type rmsd covalent geometry : bond 0.00308 (21295) covalent geometry : angle 0.56506 (29697) hydrogen bonds : bond 0.03937 ( 915) hydrogen bonds : angle 4.00731 ( 2472) metal coordination : bond 0.01158 ( 8) metal coordination : angle 1.70036 ( 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 122 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.689 Fit side-chains revert: symmetry clash REVERT: A 409 ARG cc_start: 0.9158 (OUTLIER) cc_final: 0.8760 (mtm180) REVERT: C 476 LEU cc_start: 0.9462 (OUTLIER) cc_final: 0.9250 (mm) REVERT: C 780 SER cc_start: 0.9063 (m) cc_final: 0.8679 (p) REVERT: C 849 MET cc_start: 0.8094 (tpt) cc_final: 0.7837 (tpt) REVERT: C 883 MET cc_start: 0.8687 (mmm) cc_final: 0.8370 (tpt) REVERT: N 131 GLU cc_start: 0.8292 (mm-30) cc_final: 0.7797 (tp30) REVERT: D 41 CYS cc_start: 0.8389 (OUTLIER) cc_final: 0.7849 (p) REVERT: B 110 MET cc_start: 0.9173 (mmm) cc_final: 0.8886 (mmm) REVERT: B 189 PHE cc_start: 0.7382 (m-80) cc_final: 0.7073 (m-10) REVERT: B 214 ASP cc_start: 0.8313 (p0) cc_final: 0.7949 (p0) outliers start: 22 outliers final: 14 residues processed: 114 average time/residue: 0.1508 time to fit residues: 27.5953 Evaluate side-chains 113 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.627 ------------------------------------------------------------------------------- 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 996 SER Chi-restraints excluded: chain C residue 406 HIS Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 501 HIS Chi-restraints excluded: chain C residue 507 GLU Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 41 CYS 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 322 MET Chi-restraints excluded: chain B residue 143 ASP 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: 10.0000 chunk 205 optimal weight: 4.9990 chunk 189 optimal weight: 1.9990 chunk 127 optimal weight: 10.0000 chunk 178 optimal weight: 7.9990 chunk 97 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 198 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 406 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.067002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.045798 restraints weight = 80986.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.047052 restraints weight = 40461.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.047858 restraints weight = 25936.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.048342 restraints weight = 19597.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.048552 restraints weight = 16593.066| |-----------------------------------------------------------------------------| r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21303 Z= 0.147 Angle : 0.563 10.522 29701 Z= 0.303 Chirality : 0.038 0.162 3261 Planarity : 0.003 0.044 3091 Dihedral : 23.916 173.758 4548 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.21 % Allowed : 10.28 % Favored : 88.51 % 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: 755 sheet: -0.27 (0.29), residues: 344 loop : -1.34 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 442 TYR 0.018 0.001 TYR N 109 PHE 0.024 0.001 PHE D 189 TRP 0.011 0.001 TRP C 893 HIS 0.007 0.001 HIS N 27 Details of bonding type rmsd covalent geometry : bond 0.00327 (21295) covalent geometry : angle 0.56280 (29697) hydrogen bonds : bond 0.03969 ( 915) hydrogen bonds : angle 4.00961 ( 2472) metal coordination : bond 0.01301 ( 8) metal coordination : angle 1.73002 ( 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 118 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.556 Fit side-chains revert: symmetry clash REVERT: A 409 ARG cc_start: 0.9182 (OUTLIER) cc_final: 0.8782 (mtm180) REVERT: C 476 LEU cc_start: 0.9451 (OUTLIER) cc_final: 0.9241 (mm) REVERT: C 780 SER cc_start: 0.9071 (m) cc_final: 0.8682 (p) REVERT: C 849 MET cc_start: 0.8086 (tpt) cc_final: 0.7816 (tpt) REVERT: C 883 MET cc_start: 0.8756 (mmm) cc_final: 0.8427 (tpt) REVERT: N 131 GLU cc_start: 0.8410 (mm-30) cc_final: 0.8124 (tp30) REVERT: D 41 CYS cc_start: 0.8414 (OUTLIER) cc_final: 0.7867 (p) REVERT: B 110 MET cc_start: 0.9194 (mmm) cc_final: 0.8895 (mmm) REVERT: B 189 PHE cc_start: 0.7445 (m-80) cc_final: 0.7101 (m-10) REVERT: B 214 ASP cc_start: 0.8364 (p0) cc_final: 0.7986 (p0) outliers start: 21 outliers final: 15 residues processed: 113 average time/residue: 0.1592 time to fit residues: 28.3486 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 : 0.729 ------------------------------------------------------------------------------- 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 996 SER Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 501 HIS Chi-restraints excluded: chain C residue 507 GLU Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain N residue 41 PHE Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 41 CYS 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 322 MET Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain B residue 260 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 220 optimal weight: 10.0000 chunk 192 optimal weight: 5.9990 chunk 212 optimal weight: 8.9990 chunk 64 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 41 optimal weight: 0.7980 chunk 177 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 221 optimal weight: 10.0000 chunk 40 optimal weight: 0.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 934 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 = 0.3321 r_free = 0.3321 target = 0.065268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.044008 restraints weight = 81686.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.045220 restraints weight = 41087.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.045986 restraints weight = 26515.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 66)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.046463 restraints weight = 20020.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.046739 restraints weight = 17040.251| |-----------------------------------------------------------------------------| r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 21303 Z= 0.238 Angle : 0.641 15.858 29701 Z= 0.341 Chirality : 0.040 0.154 3261 Planarity : 0.004 0.047 3091 Dihedral : 24.067 172.786 4548 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.15 % Allowed : 10.51 % Favored : 88.34 % 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: -0.24 (0.19), residues: 2021 helix: 1.37 (0.20), residues: 755 sheet: -0.23 (0.29), residues: 336 loop : -1.45 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 409 TYR 0.015 0.002 TYR C 757 PHE 0.027 0.002 PHE D 189 TRP 0.016 0.001 TRP N 133 HIS 0.005 0.001 HIS D 313 Details of bonding type rmsd covalent geometry : bond 0.00531 (21295) covalent geometry : angle 0.64016 (29697) hydrogen bonds : bond 0.04799 ( 915) hydrogen bonds : angle 4.22923 ( 2472) metal coordination : bond 0.02722 ( 8) metal coordination : angle 2.62409 ( 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 117 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.745 Fit side-chains revert: symmetry clash REVERT: A 409 ARG cc_start: 0.9163 (OUTLIER) cc_final: 0.8744 (mtm180) REVERT: C 476 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.9278 (mm) REVERT: C 780 SER cc_start: 0.9051 (m) cc_final: 0.8634 (p) REVERT: N 131 GLU cc_start: 0.8442 (mm-30) cc_final: 0.8145 (tp30) REVERT: D 41 CYS cc_start: 0.8436 (OUTLIER) cc_final: 0.7855 (p) REVERT: B 110 MET cc_start: 0.9173 (mmm) cc_final: 0.8895 (mmm) REVERT: B 189 PHE cc_start: 0.7556 (m-80) cc_final: 0.7283 (m-10) REVERT: B 214 ASP cc_start: 0.8295 (p0) cc_final: 0.7913 (p0) outliers start: 20 outliers final: 15 residues processed: 111 average time/residue: 0.1476 time to fit residues: 26.2036 Evaluate side-chains 114 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 409 ARG Chi-restraints excluded: chain A residue 658 MET Chi-restraints excluded: chain A residue 996 SER Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 501 HIS Chi-restraints excluded: chain C residue 507 GLU Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 889 MET Chi-restraints excluded: chain N residue 41 PHE Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 178 CYS Chi-restraints excluded: chain D residue 322 MET Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain B residue 260 SER 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: 6.9990 chunk 210 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 51 optimal weight: 0.0370 chunk 166 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 overall best weight: 1.1664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.066776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.045731 restraints weight = 81322.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.047023 restraints weight = 39683.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.047843 restraints weight = 25049.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.048350 restraints weight = 18745.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.048650 restraints weight = 15755.078| |-----------------------------------------------------------------------------| r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21303 Z= 0.131 Angle : 0.569 10.651 29701 Z= 0.305 Chirality : 0.038 0.151 3261 Planarity : 0.003 0.043 3091 Dihedral : 23.963 173.674 4548 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.92 % Allowed : 10.68 % Favored : 88.39 % 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: -0.06 (0.19), residues: 2021 helix: 1.49 (0.20), residues: 749 sheet: -0.17 (0.29), residues: 333 loop : -1.28 (0.20), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 442 TYR 0.016 0.001 TYR N 109 PHE 0.020 0.001 PHE D 189 TRP 0.015 0.001 TRP N 133 HIS 0.006 0.001 HIS N 27 Details of bonding type rmsd covalent geometry : bond 0.00288 (21295) covalent geometry : angle 0.56875 (29697) hydrogen bonds : bond 0.03928 ( 915) hydrogen bonds : angle 4.03336 ( 2472) metal coordination : bond 0.00844 ( 8) metal coordination : angle 2.00143 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3378.14 seconds wall clock time: 59 minutes 10.09 seconds (3550.09 seconds total)