Starting phenix.real_space_refine on Sun Feb 18 01:46:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cij_7480/02_2024/6cij_7480.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cij_7480/02_2024/6cij_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cij_7480/02_2024/6cij_7480.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cij_7480/02_2024/6cij_7480.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cij_7480/02_2024/6cij_7480.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cij_7480/02_2024/6cij_7480.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 Residue "A ARG 402": "NH1" <-> "NH2" Residue "A ARG 407": "NH1" <-> "NH2" Residue "A ARG 409": "NH1" <-> "NH2" Residue "A ARG 471": "NH1" <-> "NH2" Residue "A ARG 579": "NH1" <-> "NH2" Residue "A TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 628": "NH1" <-> "NH2" Residue "A ARG 696": "NH1" <-> "NH2" Residue "A GLU 719": "OE1" <-> "OE2" Residue "A ARG 734": "NH1" <-> "NH2" Residue "A ARG 773": "NH1" <-> "NH2" Residue "A ARG 855": "NH1" <-> "NH2" Residue "A ARG 977": "NH1" <-> "NH2" Residue "C ARG 401": "NH1" <-> "NH2" Residue "C ARG 407": "NH1" <-> "NH2" Residue "C ARG 628": "NH1" <-> "NH2" Residue "C ARG 679": "NH1" <-> "NH2" Residue "C ARG 713": "NH1" <-> "NH2" Residue "C ARG 826": "NH1" <-> "NH2" Residue "C ARG 838": "NH1" <-> "NH2" Residue "C GLU 959": "OE1" <-> "OE2" Residue "C ARG 972": "NH1" <-> "NH2" Residue "D ARG 148": "NH1" <-> "NH2" Residue "D ARG 235": "NH1" <-> "NH2" Residue "D ARG 237": "NH1" <-> "NH2" Residue "D ARG 349": "NH1" <-> "NH2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B ARG 229": "NH1" <-> "NH2" Residue "B ARG 235": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/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: {'GLU:plan': 1, 'HIS: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: {'GLN:plan1': 1, 'ARG:plan': 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: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 5} 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: 11.27, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.97 Conformation dependent library (CDL) restraints added in 3.0 seconds 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: 8.33 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: 9.53 Time building geometry restraints manager: 9.62 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: 98.01 - 105.20: 1206 105.20 - 112.40: 11139 112.40 - 119.59: 6547 119.59 - 126.79: 9983 126.79 - 133.98: 822 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 2.520 nonbonded pdb=" OG1 THR D 308 " pdb=" OD1 ASP D 310 " model vdw 2.214 2.440 nonbonded pdb=" N MET B 1 " pdb=" O ARG B 349 " model vdw 2.215 2.520 nonbonded pdb=" OD1 ASP C 569 " pdb=" OG SER C 996 " model vdw 2.228 2.440 ... (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 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 1007 or resid 1101 \ 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: 0.010 Normalize map: mean=0, sd=1: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.960 Check model and map are aligned: 0.300 Set scattering table: 0.180 Process input model: 66.840 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.090 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.370 ------------------------------------------------------------------------------- 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 : 0.003 0.040 21295 Z= 0.155 Angle : 0.578 8.430 29697 Z= 0.365 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (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 TRP 0.011 0.001 TRP A 829 HIS 0.003 0.000 HIS N 27 PHE 0.011 0.001 PHE A 916 TYR 0.012 0.001 TYR A 805 ARG 0.004 0.000 ARG C 679 *********************** 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 fitting. rotamer outliers: 39 poor density : 258 time to evaluate : 1.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 ARG cc_start: 0.9380 (OUTLIER) cc_final: 0.9107 (ttp80) REVERT: A 504 ARG cc_start: 0.8931 (OUTLIER) cc_final: 0.8677 (ttm170) REVERT: C 780 SER cc_start: 0.9032 (m) cc_final: 0.8500 (p) REVERT: N 27 HIS cc_start: 0.6185 (p-80) cc_final: 0.5516 (m90) REVERT: N 67 ASP cc_start: 0.4382 (t0) cc_final: 0.4178 (t70) REVERT: N 109 TYR cc_start: 0.8054 (m-80) cc_final: 0.7124 (t80) REVERT: D 16 GLN cc_start: 0.8719 (pt0) cc_final: 0.8434 (pt0) REVERT: D 283 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8288 (ttpp) REVERT: B 110 MET cc_start: 0.8877 (mmm) cc_final: 0.8524 (mmp) REVERT: B 214 ASP cc_start: 0.8104 (p0) cc_final: 0.7743 (p0) REVERT: B 283 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8009 (ptmm) outliers start: 39 outliers final: 14 residues processed: 291 average time/residue: 0.4223 time to fit residues: 173.3325 Evaluate side-chains 138 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 120 time to evaluate : 2.139 ------------------------------------------------------------------------------- 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 187 optimal weight: 0.7980 chunk 168 optimal weight: 1.9990 chunk 93 optimal weight: 7.9990 chunk 57 optimal weight: 0.8980 chunk 113 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 174 optimal weight: 9.9990 chunk 67 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 129 optimal weight: 10.0000 chunk 201 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 912 ASN A 978 GLN A 990 HIS C 495 GLN C 800 ASN C 809 GLN C 860 GLN ** C 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 HIS ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21295 Z= 0.177 Angle : 0.572 8.349 29697 Z= 0.314 Chirality : 0.038 0.203 3261 Planarity : 0.004 0.048 3091 Dihedral : 23.813 175.380 4605 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.39 % Allowed : 8.49 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.18), residues: 2021 helix: 0.53 (0.19), residues: 739 sheet: -1.22 (0.28), residues: 341 loop : -2.18 (0.18), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 893 HIS 0.005 0.001 HIS N 27 PHE 0.011 0.001 PHE N 41 TYR 0.014 0.001 TYR A 805 ARG 0.007 0.001 ARG C 713 *********************** 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 156 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 132 time to evaluate : 2.168 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 471 ARG cc_start: 0.9375 (OUTLIER) cc_final: 0.8910 (ttt90) REVERT: C 578 MET cc_start: 0.8179 (mtp) cc_final: 0.7737 (mtm) REVERT: C 780 SER cc_start: 0.9017 (m) cc_final: 0.8526 (p) REVERT: C 823 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8515 (mmtp) REVERT: C 828 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.7707 (mpt-90) REVERT: C 883 MET cc_start: 0.8494 (mmm) cc_final: 0.7924 (tpt) REVERT: N 109 TYR cc_start: 0.8155 (m-80) cc_final: 0.7038 (t80) REVERT: B 214 ASP cc_start: 0.8205 (p0) cc_final: 0.7780 (p0) outliers start: 24 outliers final: 6 residues processed: 155 average time/residue: 0.3567 time to fit residues: 83.7292 Evaluate side-chains 112 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 103 time to evaluate : 2.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 ARG Chi-restraints excluded: chain A residue 784 PHE Chi-restraints excluded: chain C residue 582 ASP Chi-restraints excluded: chain C residue 823 LYS Chi-restraints excluded: chain C residue 824 GLU Chi-restraints excluded: chain C residue 828 ARG 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 112 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 167 optimal weight: 4.9990 chunk 137 optimal weight: 7.9990 chunk 55 optimal weight: 0.9990 chunk 201 optimal weight: 4.9990 chunk 218 optimal weight: 5.9990 chunk 179 optimal weight: 10.0000 chunk 200 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 162 optimal weight: 0.0020 overall best weight: 2.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 800 ASN C 912 ASN ** C 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 961 ASN ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 4 GLN ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21295 Z= 0.250 Angle : 0.582 8.940 29697 Z= 0.319 Chirality : 0.039 0.142 3261 Planarity : 0.004 0.046 3091 Dihedral : 23.914 174.225 4566 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.44 % Allowed : 8.89 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.19), residues: 2021 helix: 0.92 (0.20), residues: 758 sheet: -0.88 (0.29), residues: 349 loop : -1.95 (0.19), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 893 HIS 0.004 0.001 HIS D 313 PHE 0.018 0.002 PHE A 418 TYR 0.014 0.001 TYR A 805 ARG 0.005 0.000 ARG B 349 *********************** 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 130 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 105 time to evaluate : 2.172 Fit side-chains REVERT: A 929 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7322 (mm-30) REVERT: C 578 MET cc_start: 0.8190 (mtp) cc_final: 0.7952 (mtm) REVERT: C 780 SER cc_start: 0.9040 (m) cc_final: 0.8543 (p) REVERT: C 883 MET cc_start: 0.8466 (mmm) cc_final: 0.8119 (tpt) REVERT: N 105 PHE cc_start: 0.7785 (t80) cc_final: 0.7256 (t80) REVERT: N 109 TYR cc_start: 0.8201 (m-80) cc_final: 0.7984 (m-80) REVERT: B 162 MET cc_start: 0.8811 (mmm) cc_final: 0.8556 (mmm) REVERT: B 214 ASP cc_start: 0.8296 (p0) cc_final: 0.7854 (p0) outliers start: 25 outliers final: 13 residues processed: 126 average time/residue: 0.3504 time to fit residues: 68.7839 Evaluate side-chains 110 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 97 time to evaluate : 2.113 ------------------------------------------------------------------------------- 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 582 ASP Chi-restraints excluded: chain C residue 824 GLU 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 287 CYS Chi-restraints excluded: chain B residue 22 MET Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain B residue 283 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 199 optimal weight: 3.9990 chunk 151 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 135 optimal weight: 20.0000 chunk 202 optimal weight: 8.9990 chunk 214 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 192 optimal weight: 0.4980 chunk 57 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21295 Z= 0.191 Angle : 0.553 11.810 29697 Z= 0.301 Chirality : 0.038 0.136 3261 Planarity : 0.003 0.040 3091 Dihedral : 23.878 174.431 4552 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.39 % Allowed : 9.41 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.19), residues: 2021 helix: 1.12 (0.20), residues: 755 sheet: -0.72 (0.29), residues: 349 loop : -1.76 (0.20), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 893 HIS 0.003 0.001 HIS N 27 PHE 0.014 0.001 PHE N 41 TYR 0.014 0.001 TYR C 909 ARG 0.005 0.000 ARG C 828 *********************** 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 fitting. rotamer outliers: 24 poor density : 103 time to evaluate : 2.227 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 408 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.9030 (tp) REVERT: C 578 MET cc_start: 0.8208 (mtp) cc_final: 0.7867 (mtm) REVERT: C 780 SER cc_start: 0.8969 (m) cc_final: 0.8530 (p) REVERT: C 883 MET cc_start: 0.8393 (mmm) cc_final: 0.8123 (tpt) REVERT: N 105 PHE cc_start: 0.7863 (t80) cc_final: 0.7323 (t80) REVERT: N 109 TYR cc_start: 0.8160 (m-80) cc_final: 0.7938 (m-80) REVERT: B 189 PHE cc_start: 0.7202 (m-80) cc_final: 0.6996 (m-80) REVERT: B 214 ASP cc_start: 0.8268 (p0) cc_final: 0.7838 (p0) outliers start: 24 outliers final: 17 residues processed: 119 average time/residue: 0.3274 time to fit residues: 62.1831 Evaluate side-chains 118 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 100 time to evaluate : 2.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 996 SER Chi-restraints excluded: chain A residue 1003 MET Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 460 SER Chi-restraints excluded: chain C residue 507 GLU Chi-restraints excluded: chain C residue 582 ASP Chi-restraints excluded: chain C residue 824 GLU Chi-restraints excluded: chain C residue 947 ILE Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain D residue 12 ILE 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 B residue 8 VAL Chi-restraints excluded: chain B residue 22 MET Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain B residue 283 LYS Chi-restraints excluded: chain B residue 302 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 178 optimal weight: 7.9990 chunk 121 optimal weight: 0.6980 chunk 3 optimal weight: 6.9990 chunk 159 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 183 optimal weight: 4.9990 chunk 148 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 109 optimal weight: 3.9990 chunk 192 optimal weight: 0.0170 chunk 54 optimal weight: 4.9990 overall best weight: 2.9424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 912 ASN C 406 HIS C 860 GLN ** C 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 21295 Z= 0.310 Angle : 0.609 12.366 29697 Z= 0.329 Chirality : 0.040 0.137 3261 Planarity : 0.004 0.042 3091 Dihedral : 24.027 173.488 4552 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.67 % Allowed : 9.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.19), residues: 2021 helix: 1.28 (0.20), residues: 755 sheet: -0.53 (0.29), residues: 337 loop : -1.78 (0.19), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 893 HIS 0.005 0.001 HIS D 313 PHE 0.020 0.002 PHE A 418 TYR 0.014 0.002 TYR C 757 ARG 0.006 0.001 ARG C 828 *********************** 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 fitting. rotamer outliers: 29 poor density : 99 time to evaluate : 1.955 Fit side-chains REVERT: A 929 GLU cc_start: 0.7538 (mm-30) cc_final: 0.7270 (mm-30) REVERT: C 408 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.9051 (tp) REVERT: C 445 HIS cc_start: 0.8151 (m-70) cc_final: 0.7926 (m-70) REVERT: C 578 MET cc_start: 0.8231 (mtp) cc_final: 0.7957 (mtm) REVERT: C 780 SER cc_start: 0.9016 (m) cc_final: 0.8559 (p) REVERT: C 883 MET cc_start: 0.8602 (mmm) cc_final: 0.8256 (tpt) REVERT: C 936 PHE cc_start: 0.9112 (OUTLIER) cc_final: 0.8874 (m-80) REVERT: N 105 PHE cc_start: 0.7801 (t80) cc_final: 0.7387 (t80) REVERT: N 109 TYR cc_start: 0.8224 (m-80) cc_final: 0.8021 (m-80) REVERT: N 131 GLU cc_start: 0.8434 (mm-30) cc_final: 0.8176 (tp30) REVERT: B 214 ASP cc_start: 0.8317 (p0) cc_final: 0.7782 (p0) outliers start: 29 outliers final: 18 residues processed: 120 average time/residue: 0.3473 time to fit residues: 65.2608 Evaluate side-chains 115 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 95 time to evaluate : 2.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 996 SER Chi-restraints excluded: chain A residue 1003 MET Chi-restraints excluded: chain C residue 406 HIS Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 460 SER Chi-restraints excluded: chain C residue 582 ASP Chi-restraints excluded: chain C residue 716 GLU Chi-restraints excluded: chain C residue 824 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 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 302 MET Chi-restraints excluded: chain B residue 22 MET Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain B residue 283 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 72 optimal weight: 0.8980 chunk 193 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 125 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 214 optimal weight: 0.2980 chunk 178 optimal weight: 7.9990 chunk 99 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 71 optimal weight: 4.9990 chunk 112 optimal weight: 0.8980 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 C 406 HIS ** C 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21295 Z= 0.156 Angle : 0.556 13.622 29697 Z= 0.299 Chirality : 0.038 0.135 3261 Planarity : 0.003 0.041 3091 Dihedral : 23.911 174.124 4552 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.44 % Allowed : 9.87 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.19), residues: 2021 helix: 1.38 (0.20), residues: 754 sheet: -0.37 (0.28), residues: 348 loop : -1.58 (0.20), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 893 HIS 0.008 0.001 HIS C 406 PHE 0.018 0.001 PHE A 641 TYR 0.012 0.001 TYR C 909 ARG 0.004 0.000 ARG C 828 *********************** 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 125 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 100 time to evaluate : 2.179 Fit side-chains REVERT: C 408 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.9031 (tp) REVERT: C 780 SER cc_start: 0.8966 (m) cc_final: 0.8559 (p) REVERT: C 883 MET cc_start: 0.8461 (mmm) cc_final: 0.8208 (tpt) REVERT: N 105 PHE cc_start: 0.7725 (t80) cc_final: 0.7377 (t80) REVERT: N 131 GLU cc_start: 0.8383 (mm-30) cc_final: 0.8032 (tp30) REVERT: B 189 PHE cc_start: 0.7173 (m-80) cc_final: 0.6897 (m-10) REVERT: B 214 ASP cc_start: 0.8230 (p0) cc_final: 0.7833 (p0) outliers start: 25 outliers final: 13 residues processed: 120 average time/residue: 0.3236 time to fit residues: 62.0091 Evaluate side-chains 112 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 98 time to evaluate : 2.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 658 MET Chi-restraints excluded: chain A residue 996 SER Chi-restraints excluded: chain C residue 406 HIS Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 460 SER Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 178 CYS Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 322 MET Chi-restraints excluded: chain B residue 22 MET Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain B residue 283 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 207 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 chunk 156 optimal weight: 8.9990 chunk 121 optimal weight: 1.9990 chunk 180 optimal weight: 0.9990 chunk 119 optimal weight: 5.9990 chunk 213 optimal weight: 5.9990 chunk 133 optimal weight: 10.0000 chunk 130 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 456 GLN C 912 ASN ** C 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1000 GLN ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 21295 Z= 0.277 Angle : 0.584 9.822 29697 Z= 0.316 Chirality : 0.039 0.136 3261 Planarity : 0.004 0.040 3091 Dihedral : 23.982 173.547 4552 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.33 % Allowed : 10.62 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.19), residues: 2021 helix: 1.38 (0.20), residues: 760 sheet: -0.41 (0.29), residues: 342 loop : -1.64 (0.20), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 893 HIS 0.005 0.001 HIS C 406 PHE 0.019 0.002 PHE A 641 TYR 0.018 0.001 TYR N 109 ARG 0.004 0.000 ARG C 442 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4042 Ramachandran restraints generated. 2021 Oldfield, 0 Emsley, 2021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4042 Ramachandran restraints generated. 2021 Oldfield, 0 Emsley, 2021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 99 time to evaluate : 2.144 Fit side-chains REVERT: A 929 GLU cc_start: 0.7453 (mm-30) cc_final: 0.7179 (mm-30) REVERT: C 445 HIS cc_start: 0.8083 (m-70) cc_final: 0.7825 (m-70) REVERT: C 780 SER cc_start: 0.9034 (m) cc_final: 0.8591 (p) REVERT: C 883 MET cc_start: 0.8639 (mmm) cc_final: 0.8270 (tpt) REVERT: N 131 GLU cc_start: 0.8452 (mm-30) cc_final: 0.7912 (tp30) REVERT: D 41 CYS cc_start: 0.8344 (OUTLIER) cc_final: 0.7917 (p) REVERT: B 189 PHE cc_start: 0.7216 (m-80) cc_final: 0.6964 (m-10) REVERT: B 214 ASP cc_start: 0.8267 (p0) cc_final: 0.7830 (p0) outliers start: 23 outliers final: 16 residues processed: 113 average time/residue: 0.3207 time to fit residues: 57.7066 Evaluate side-chains 114 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 97 time to evaluate : 2.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 996 SER Chi-restraints excluded: chain A residue 1003 MET Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 460 SER Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 33 GLN Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 178 CYS Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 322 MET Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain B residue 283 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 132 optimal weight: 6.9990 chunk 85 optimal weight: 9.9990 chunk 127 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 chunk 41 optimal weight: 0.8980 chunk 136 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 168 optimal weight: 4.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 406 HIS ** C 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 21295 Z= 0.346 Angle : 0.636 13.692 29697 Z= 0.340 Chirality : 0.040 0.193 3261 Planarity : 0.004 0.045 3091 Dihedral : 24.127 172.886 4552 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.56 % Allowed : 10.85 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.19), residues: 2021 helix: 1.31 (0.20), residues: 756 sheet: -0.30 (0.30), residues: 314 loop : -1.65 (0.19), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 893 HIS 0.004 0.001 HIS D 313 PHE 0.021 0.002 PHE N 105 TYR 0.015 0.002 TYR A 485 ARG 0.005 0.001 ARG C 442 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4042 Ramachandran restraints generated. 2021 Oldfield, 0 Emsley, 2021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4042 Ramachandran restraints generated. 2021 Oldfield, 0 Emsley, 2021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 98 time to evaluate : 2.010 Fit side-chains REVERT: C 408 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9055 (tp) REVERT: C 780 SER cc_start: 0.8990 (m) cc_final: 0.8569 (p) REVERT: C 823 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8548 (mmtp) REVERT: C 883 MET cc_start: 0.8731 (mmm) cc_final: 0.8245 (tpt) REVERT: N 131 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8384 (tp30) REVERT: B 162 MET cc_start: 0.8802 (mmm) cc_final: 0.8492 (mmm) REVERT: B 189 PHE cc_start: 0.7252 (m-80) cc_final: 0.6937 (m-10) REVERT: B 214 ASP cc_start: 0.8274 (p0) cc_final: 0.7830 (p0) outliers start: 27 outliers final: 16 residues processed: 118 average time/residue: 0.3270 time to fit residues: 60.6143 Evaluate side-chains 112 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 94 time to evaluate : 2.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 658 MET Chi-restraints excluded: chain A residue 996 SER Chi-restraints excluded: chain C residue 406 HIS Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 460 SER Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 823 LYS Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 41 PHE Chi-restraints excluded: chain D residue 33 GLN Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 178 CYS Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 322 MET Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain B residue 283 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 194 optimal weight: 1.9990 chunk 204 optimal weight: 9.9990 chunk 187 optimal weight: 0.7980 chunk 199 optimal weight: 0.6980 chunk 120 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 chunk 156 optimal weight: 0.0870 chunk 61 optimal weight: 0.6980 chunk 180 optimal weight: 0.9980 chunk 188 optimal weight: 0.6980 chunk 198 optimal weight: 1.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21295 Z= 0.153 Angle : 0.568 10.611 29697 Z= 0.307 Chirality : 0.038 0.161 3261 Planarity : 0.004 0.067 3091 Dihedral : 23.998 173.850 4552 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.10 % Allowed : 11.20 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.19), residues: 2021 helix: 1.37 (0.20), residues: 753 sheet: -0.19 (0.29), residues: 344 loop : -1.43 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 893 HIS 0.014 0.001 HIS C 406 PHE 0.017 0.001 PHE N 105 TYR 0.013 0.001 TYR N 109 ARG 0.009 0.000 ARG C 407 *********************** 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 117 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 98 time to evaluate : 2.000 Fit side-chains REVERT: A 711 LEU cc_start: 0.8990 (tp) cc_final: 0.8689 (mp) REVERT: C 780 SER cc_start: 0.8924 (m) cc_final: 0.8518 (p) REVERT: C 823 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8411 (mmtp) REVERT: C 883 MET cc_start: 0.8492 (mmm) cc_final: 0.8220 (tpt) REVERT: N 131 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8189 (tp30) REVERT: B 162 MET cc_start: 0.8788 (mmm) cc_final: 0.8492 (mmm) REVERT: B 189 PHE cc_start: 0.7109 (m-80) cc_final: 0.6833 (m-10) REVERT: B 214 ASP cc_start: 0.8152 (p0) cc_final: 0.7752 (p0) outliers start: 19 outliers final: 12 residues processed: 112 average time/residue: 0.3349 time to fit residues: 59.2829 Evaluate side-chains 108 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 95 time to evaluate : 2.412 ------------------------------------------------------------------------------- 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 432 LEU Chi-restraints excluded: chain C residue 460 SER Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 823 LYS Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 178 CYS Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain B residue 283 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 130 optimal weight: 10.0000 chunk 210 optimal weight: 4.9990 chunk 128 optimal weight: 10.0000 chunk 100 optimal weight: 0.9980 chunk 146 optimal weight: 7.9990 chunk 221 optimal weight: 10.0000 chunk 203 optimal weight: 1.9990 chunk 176 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 136 optimal weight: 20.0000 chunk 107 optimal weight: 4.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 818 HIS C 406 HIS ** C 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 21295 Z= 0.373 Angle : 0.661 14.743 29697 Z= 0.351 Chirality : 0.041 0.142 3261 Planarity : 0.004 0.039 3091 Dihedral : 24.170 172.665 4552 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.75 % Allowed : 11.61 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.19), residues: 2021 helix: 1.35 (0.20), residues: 755 sheet: -0.14 (0.30), residues: 316 loop : -1.56 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 133 HIS 0.005 0.001 HIS A1006 PHE 0.022 0.002 PHE A 418 TYR 0.015 0.002 TYR A 485 ARG 0.007 0.001 ARG A 504 ********************** 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 108 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 95 time to evaluate : 2.078 Fit side-chains REVERT: C 780 SER cc_start: 0.8982 (m) cc_final: 0.8582 (p) REVERT: C 823 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8546 (mmtp) REVERT: C 883 MET cc_start: 0.8773 (mmm) cc_final: 0.8210 (tpt) REVERT: N 131 GLU cc_start: 0.8517 (mm-30) cc_final: 0.8271 (tp30) REVERT: B 162 MET cc_start: 0.8820 (mmm) cc_final: 0.8535 (mmm) REVERT: B 189 PHE cc_start: 0.7237 (m-80) cc_final: 0.6936 (m-10) REVERT: B 214 ASP cc_start: 0.8247 (p0) cc_final: 0.7836 (p0) outliers start: 13 outliers final: 10 residues processed: 105 average time/residue: 0.3288 time to fit residues: 54.3465 Evaluate side-chains 105 residues out of total 1798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 94 time to evaluate : 2.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 996 SER Chi-restraints excluded: chain A residue 1003 MET Chi-restraints excluded: chain C residue 460 SER Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 823 LYS Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 178 CYS Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain B residue 283 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 139 optimal weight: 8.9990 chunk 187 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 162 optimal weight: 6.9990 chunk 26 optimal weight: 0.4980 chunk 48 optimal weight: 0.9980 chunk 176 optimal weight: 6.9990 chunk 73 optimal weight: 0.9990 chunk 181 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 32 optimal weight: 0.0980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 GLN ** 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 = 0.3371 r_free = 0.3371 target = 0.066818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.046065 restraints weight = 81935.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.047346 restraints weight = 40246.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.048171 restraints weight = 25325.154| |-----------------------------------------------------------------------------| r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21295 Z= 0.157 Angle : 0.572 9.968 29697 Z= 0.306 Chirality : 0.038 0.135 3261 Planarity : 0.003 0.040 3091 Dihedral : 24.028 173.671 4552 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.81 % Allowed : 11.55 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.19), residues: 2021 helix: 1.44 (0.20), residues: 754 sheet: -0.13 (0.29), residues: 338 loop : -1.35 (0.20), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 893 HIS 0.004 0.001 HIS N 27 PHE 0.025 0.001 PHE A 418 TYR 0.014 0.001 TYR N 109 ARG 0.004 0.000 ARG C 442 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3121.62 seconds wall clock time: 58 minutes 28.44 seconds (3508.44 seconds total)