Starting phenix.real_space_refine on Fri Aug 7 03:23:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jtu_61817/08_2026/9jtu_61817.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jtu_61817/08_2026/9jtu_61817.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jtu_61817/08_2026/9jtu_61817.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jtu_61817/08_2026/9jtu_61817.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jtu_61817/08_2026/9jtu_61817.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jtu_61817/08_2026/9jtu_61817.map" } resolution = 3.43 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= -0.001 sd= 0.023 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 160 5.49 5 S 106 5.16 5 C 11311 2.51 5 N 3311 2.21 5 O 3814 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18706 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4965 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 618, 4959 Classifications: {'peptide': 618} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 26, 'TRANS': 591} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Conformer: "B" Number of residues, atoms: 618, 4959 Classifications: {'peptide': 618} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 26, 'TRANS': 591} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 bond proxies already assigned to first conformer: 5055 Chain: "B" Number of atoms: 2704 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 344, 2683 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 19, 'TRANS': 324} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 344, 2683 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 19, 'TRANS': 324} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 2727 Chain: "C" Number of atoms: 5010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 5010 Classifications: {'peptide': 623} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 596} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 2673 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 343, 2663 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 19, 'TRANS': 323} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 343, 2663 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 19, 'TRANS': 323} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 2718 Chain: "G" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 795 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain: "L" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 607 Classifications: {'DNA': 30} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 29} Chain: "M" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 801 Classifications: {'DNA': 39} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 38} Chain: "F" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 617 Classifications: {'DNA': 30} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 29} Chain: "H" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 262 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "I" Number of atoms: 268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 268 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} 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 2632 SG CYS A 727 74.550 102.744 101.828 1.00 62.02 S ATOM 2653 SG CYS A 730 77.142 104.943 103.719 1.00 64.37 S ATOM 10356 SG CYS C 727 27.012 100.076 55.115 1.00 65.35 S ATOM 10377 SG CYS C 730 24.495 102.296 53.073 1.00 65.92 S Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" N ACYS A 907 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS A 907 " occ=0.50 residue: pdb=" N AHIS B 47 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS B 47 " occ=0.50 residue: pdb=" N AARG B 237 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG B 237 " occ=0.50 residue: pdb=" N AHIS D 47 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS D 47 " occ=0.50 residue: pdb=" P DT I 15 " occ=0.85 ... (18 atoms not shown) pdb=" C6 DT I 15 " occ=0.85 Time building chain proxies: 5.58, per 1000 atoms: 0.30 Number of scatterers: 18706 At special positions: 0 Unit cell: (110.24, 151.58, 159, 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 106 16.00 P 160 15.00 O 3814 8.00 N 3311 7.00 C 11311 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: 1.28 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1102 " pdb="ZN ZN A1102 " - pdb=" NE2 HIS A 937 " pdb="ZN ZN A1102 " - pdb=" NE2 HIS A 942 " pdb="ZN ZN A1102 " - pdb=" SG CYS A 727 " pdb="ZN ZN A1102 " - pdb=" SG CYS A 730 " pdb=" ZN C1102 " pdb="ZN ZN C1102 " - pdb=" NE2 HIS C 937 " pdb="ZN ZN C1102 " - pdb=" NE2 HIS C 942 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 730 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 727 " Number of angles added : 4 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3616 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 19 sheets defined 37.9% alpha, 22.9% beta 80 base pairs and 124 stacking pairs defined. Time for finding SS restraints: 2.21 Creating SS restraints... Processing helix chain 'A' and resid 408 through 422 removed outlier: 3.850A pdb=" N ILE A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N GLN A 414 " --> pdb=" O GLU A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 442 Processing helix chain 'A' and resid 444 through 456 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 507 Processing helix chain 'A' and resid 558 through 570 Processing helix chain 'A' and resid 570 through 581 Processing helix chain 'A' and resid 664 through 683 Proline residue: A 674 - end of helix Processing helix chain 'A' and resid 708 through 717 removed outlier: 3.568A pdb=" N GLY A 717 " --> pdb=" O ARG A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 741 Processing helix chain 'A' and resid 749 through 763 Processing helix chain 'A' and resid 768 through 777 Processing helix chain 'A' and resid 792 through 812 Processing helix chain 'A' and resid 822 through 842 Processing helix chain 'A' and resid 851 through 858 Processing helix chain 'A' and resid 859 through 868 removed outlier: 3.828A pdb=" N VAL A 863 " --> pdb=" O THR A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 890 Processing helix chain 'A' and resid 891 through 894 Processing helix chain 'A' and resid 897 through 902 removed outlier: 3.633A pdb=" N CYS A 902 " --> pdb=" O PRO A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 924 removed outlier: 4.842A pdb=" N SER A 910 " --> pdb=" O LEU A 906 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N PHE A 911 " --> pdb=" O ACYS A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 942 Processing helix chain 'A' and resid 942 through 951 Processing helix chain 'A' and resid 958 through 975 removed outlier: 3.622A pdb=" N ARG A 969 " --> pdb=" O ASN A 965 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG A 970 " --> pdb=" O LYS A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 996 Processing helix chain 'A' and resid 1000 through 1008 removed outlier: 4.922A pdb=" N HIS A1006 " --> pdb=" O MET A1003 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN A1007 " --> pdb=" O ASN A1004 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 15 removed outlier: 3.537A pdb=" N LEU B 14 " --> pdb=" O ASN B 11 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE B 15 " --> pdb=" O ILE B 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 11 through 15' Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'C' and resid 395 through 399 removed outlier: 3.814A pdb=" N LEU C 399 " --> pdb=" O LEU C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 408 Processing helix chain 'C' and resid 410 through 423 removed outlier: 3.536A pdb=" N LYS C 421 " --> pdb=" O GLU C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 442 removed outlier: 3.544A pdb=" N VAL C 430 " --> pdb=" O ASP C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 456 removed outlier: 3.646A pdb=" N ALA C 448 " --> pdb=" O GLU C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 474 Processing helix chain 'C' and resid 477 through 493 Processing helix chain 'C' and resid 499 through 511 removed outlier: 3.655A pdb=" N LYS C 508 " --> pdb=" O ARG C 504 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N VAL C 509 " --> pdb=" O ASN C 505 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LEU C 510 " --> pdb=" O ALA C 506 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU C 511 " --> pdb=" O GLU C 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 570 removed outlier: 3.684A pdb=" N MET C 570 " --> pdb=" O ALA C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 581 removed outlier: 3.617A pdb=" N GLN C 581 " --> pdb=" O GLY C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 665 through 683 Proline residue: C 674 - end of helix Processing helix chain 'C' and resid 708 through 716 Processing helix chain 'C' and resid 733 through 741 Processing helix chain 'C' and resid 749 through 763 removed outlier: 3.654A pdb=" N ASN C 753 " --> pdb=" O SER C 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 777 Processing helix chain 'C' and resid 792 through 812 Processing helix chain 'C' and resid 822 through 842 Processing helix chain 'C' and resid 850 through 858 Processing helix chain 'C' and resid 859 through 867 removed outlier: 3.812A pdb=" N VAL C 863 " --> pdb=" O THR C 859 " (cutoff:3.500A) Processing helix chain 'C' and resid 872 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 907 Processing helix chain 'C' and resid 908 through 923 Processing helix chain 'C' and resid 933 through 942 Processing helix chain 'C' and resid 942 through 951 Processing helix chain 'C' and resid 953 through 957 removed outlier: 3.519A pdb=" N ALA C 957 " --> pdb=" O GLY C 954 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 975 removed outlier: 3.865A pdb=" N LYS C 973 " --> pdb=" O ARG C 969 " (cutoff:3.500A) Processing helix chain 'C' and resid 983 through 995 Processing helix chain 'C' and resid 996 through 1002 removed outlier: 4.075A pdb=" N PHE C1002 " --> pdb=" O TYR C 998 " (cutoff:3.500A) Processing helix chain 'C' and resid 1003 through 1005 No H-bonds generated for 'chain 'C' and resid 1003 through 1005' Processing helix chain 'D' and resid 11 through 15 removed outlier: 3.876A pdb=" N ILE D 15 " --> pdb=" O ILE D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 313 Processing sheet with id=AA1, first strand: chain 'A' and resid 518 through 519 removed outlier: 3.600A pdb=" N ILE A 694 " --> pdb=" O MET A 691 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N PHE A 591 " --> pdb=" O LYS A 699 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N ILE A 701 " --> pdb=" O PHE A 591 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N VAL A 593 " --> pdb=" O ILE A 701 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ARG A 703 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N VAL A 595 " --> pdb=" O ARG A 703 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N THR A 705 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N GLU A 597 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLU A 632 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG A 628 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LYS A 596 " --> pdb=" O VAL A 626 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N VAL A 626 " --> pdb=" O LYS A 596 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N SER A 598 " --> pdb=" O PHE A 624 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N PHE A 624 " --> pdb=" O SER A 598 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ASP A 600 " --> pdb=" O PHE A 622 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N PHE A 622 " --> pdb=" O ASP A 600 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N VAL A 620 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LEU A 657 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N PHE A 622 " --> pdb=" O LEU A 655 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N LEU A 655 " --> pdb=" O PHE A 557 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 518 through 519 removed outlier: 3.600A pdb=" N ILE A 694 " --> pdb=" O MET A 691 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N PHE A 591 " --> pdb=" O LYS A 699 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N ILE A 701 " --> pdb=" O PHE A 591 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N VAL A 593 " --> pdb=" O ILE A 701 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ARG A 703 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N VAL A 595 " --> pdb=" O ARG A 703 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N THR A 705 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N GLU A 597 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLU A 632 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG A 628 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LYS A 596 " --> pdb=" O VAL A 626 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N VAL A 626 " --> pdb=" O LYS A 596 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N SER A 598 " --> pdb=" O PHE A 624 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N PHE A 624 " --> pdb=" O SER A 598 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ASP A 600 " --> pdb=" O PHE A 622 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N PHE A 622 " --> pdb=" O ASP A 600 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N MET A 627 " --> pdb=" O GLU A 642 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLU A 642 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE A 629 " --> pdb=" O VAL A 640 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE A 631 " --> pdb=" O VAL A 638 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 2 through 5 removed outlier: 3.590A pdb=" N SER B 320 " --> pdb=" O PHE B 328 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE B 318 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 7 through 8 removed outlier: 6.842A pdb=" N THR B 7 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 20 through 24 Processing sheet with id=AA6, first strand: chain 'B' and resid 46 through 47 removed outlier: 3.706A pdb=" N LYS B 58 " --> pdb=" O AHIS B 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 61 through 62 removed outlier: 7.094A pdb=" N ILE B 61 " --> pdb=" O PHE B 122 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N CYS B 124 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N LYS B 119 " --> pdb=" O LYS B 115 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N LYS B 115 " --> pdb=" O LYS B 119 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N THR B 121 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE B 107 " --> pdb=" O LYS B 127 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 130 through 131 removed outlier: 6.674A pdb=" N VAL B 130 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N SER B 194 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N CYS B 191 " --> pdb=" O ASP B 186 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AB1, first strand: chain 'B' and resid 208 through 211 removed outlier: 3.670A pdb=" N VAL B 208 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP B 239 " --> pdb=" O ALA B 246 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA B 246 " --> pdb=" O ASP B 239 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 262 through 265 removed outlier: 3.589A pdb=" N THR B 264 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU B 298 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 517 through 520 removed outlier: 3.588A pdb=" N GLU C 686 " --> pdb=" O GLN C 520 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE C 694 " --> pdb=" O MET C 691 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N PHE C 591 " --> pdb=" O LYS C 699 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE C 701 " --> pdb=" O PHE C 591 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N VAL C 593 " --> pdb=" O ILE C 701 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N ARG C 703 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL C 595 " --> pdb=" O ARG C 703 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ARG C 628 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N LYS C 596 " --> pdb=" O VAL C 626 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N VAL C 626 " --> pdb=" O LYS C 596 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N SER C 598 " --> pdb=" O PHE C 624 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N PHE C 624 " --> pdb=" O SER C 598 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N ASP C 600 " --> pdb=" O PHE C 622 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N PHE C 622 " --> pdb=" O ASP C 600 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N MET C 602 " --> pdb=" O VAL C 620 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N VAL C 620 " --> pdb=" O MET C 602 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N PHE C 624 " --> pdb=" O PRO C 654 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N LEU C 655 " --> pdb=" O PHE C 557 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 517 through 520 removed outlier: 3.588A pdb=" N GLU C 686 " --> pdb=" O GLN C 520 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE C 694 " --> pdb=" O MET C 691 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N PHE C 591 " --> pdb=" O LYS C 699 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE C 701 " --> pdb=" O PHE C 591 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N VAL C 593 " --> pdb=" O ILE C 701 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N ARG C 703 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL C 595 " --> pdb=" O ARG C 703 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ARG C 628 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N LYS C 596 " --> pdb=" O VAL C 626 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N VAL C 626 " --> pdb=" O LYS C 596 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N SER C 598 " --> pdb=" O PHE C 624 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N PHE C 624 " --> pdb=" O SER C 598 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N ASP C 600 " --> pdb=" O PHE C 622 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N PHE C 622 " --> pdb=" O ASP C 600 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N MET C 602 " --> pdb=" O VAL C 620 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N VAL C 620 " --> pdb=" O MET C 602 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N MET C 627 " --> pdb=" O GLU C 642 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLU C 642 " --> pdb=" O MET C 627 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE C 629 " --> pdb=" O VAL C 640 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN C 636 " --> pdb=" O HIS C 633 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 20 through 24 removed outlier: 4.334A pdb=" N VAL D 28 " --> pdb=" O PHE D 48 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS D 58 " --> pdb=" O AHIS D 47 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP D 49 " --> pdb=" O LYS D 56 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N LEU D 55 " --> pdb=" O MET D 5 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N THR D 7 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N LEU D 57 " --> pdb=" O THR D 7 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N PHE D 345 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N VAL D 8 " --> pdb=" O PHE D 343 " (cutoff:3.500A) removed outlier: 9.606A pdb=" N PHE D 343 " --> pdb=" O VAL D 8 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE D 328 " --> pdb=" O SER D 320 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER D 320 " --> pdb=" O PHE D 328 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE D 318 " --> pdb=" O GLY D 330 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 61 through 62 removed outlier: 7.155A pdb=" N ILE D 61 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N CYS D 124 " --> pdb=" O ILE D 61 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS D 119 " --> pdb=" O LYS D 115 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LYS D 115 " --> pdb=" O LYS D 119 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N THR D 121 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS D 127 " --> pdb=" O ILE D 107 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ILE D 107 " --> pdb=" O LYS D 127 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N SER D 104 " --> pdb=" O LYS D 97 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LYS D 97 " --> pdb=" O SER D 104 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LYS D 106 " --> pdb=" O GLY D 95 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE D 92 " --> pdb=" O CYS D 78 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 130 through 131 removed outlier: 6.408A pdb=" N VAL D 130 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N SER D 194 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 159 through 161 Processing sheet with id=AB9, first strand: chain 'D' and resid 208 through 211 removed outlier: 3.682A pdb=" N VAL D 208 " --> pdb=" O LEU D 219 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU D 219 " --> pdb=" O VAL D 208 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU D 233 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA D 246 " --> pdb=" O ASP D 239 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 262 through 267 removed outlier: 5.989A pdb=" N LEU D 263 " --> pdb=" O VAL D 274 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N VAL D 274 " --> pdb=" O LEU D 263 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N GLN D 265 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N VAL D 272 " --> pdb=" O GLN D 265 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN D 267 " --> pdb=" O GLU D 270 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU D 298 " --> pdb=" O SER D 291 " (cutoff:3.500A) 683 hydrogen bonds defined for protein. 1943 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 197 hydrogen bonds 390 hydrogen bond angles 0 basepair planarities 80 basepair parallelities 124 stacking parallelities Total time for adding SS restraints: 4.78 Time building geometry restraints manager: 1.79 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: 5391 1.34 - 1.46: 4187 1.46 - 1.58: 9397 1.58 - 1.69: 318 1.69 - 1.81: 161 Bond restraints: 19454 Sorted by residual: bond pdb=" C3' DA L 36 " pdb=" C2' DA L 36 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.16e+01 bond pdb=" C3' DT F 9 " pdb=" C2' DT F 9 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.14e+01 bond pdb=" C3' DG M 37 " pdb=" C2' DG M 37 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" C3' DA M 47 " pdb=" C2' DA M 47 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.25e+00 bond pdb=" C3' DT G 6 " pdb=" C2' DT G 6 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.91e+00 ... (remaining 19449 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 26666 2.45 - 4.90: 305 4.90 - 7.35: 13 7.35 - 9.80: 3 9.80 - 12.25: 1 Bond angle restraints: 26988 Sorted by residual: angle pdb=" N3 DT L 22 " pdb=" C4 DT L 22 " pdb=" O4 DT L 22 " ideal model delta sigma weight residual 119.90 122.76 -2.86 6.00e-01 2.78e+00 2.27e+01 angle pdb=" N3 DT G 38 " pdb=" C4 DT G 38 " pdb=" O4 DT G 38 " ideal model delta sigma weight residual 119.90 122.62 -2.72 6.00e-01 2.78e+00 2.05e+01 angle pdb=" N3 DT M 25 " pdb=" C4 DT M 25 " pdb=" O4 DT M 25 " ideal model delta sigma weight residual 119.90 122.60 -2.70 6.00e-01 2.78e+00 2.02e+01 angle pdb=" N3 DT G 28 " pdb=" C4 DT G 28 " pdb=" O4 DT G 28 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.98e+01 angle pdb=" O4' DA M 18 " pdb=" C4' DA M 18 " pdb=" C3' DA M 18 " ideal model delta sigma weight residual 106.00 103.34 2.66 6.00e-01 2.78e+00 1.97e+01 ... (remaining 26983 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 9258 17.94 - 35.88: 1318 35.88 - 53.81: 582 53.81 - 71.75: 130 71.75 - 89.69: 12 Dihedral angle restraints: 11300 sinusoidal: 5687 harmonic: 5613 Sorted by residual: dihedral pdb=" CA HIS A 406 " pdb=" C HIS A 406 " pdb=" N ARG A 407 " pdb=" CA ARG A 407 " ideal model delta harmonic sigma weight residual 180.00 152.61 27.39 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA LEU A 718 " pdb=" C LEU A 718 " pdb=" N GLU A 719 " pdb=" CA GLU A 719 " ideal model delta harmonic sigma weight residual 180.00 -155.59 -24.41 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA MET A 568 " pdb=" C MET A 568 " pdb=" N ASP A 569 " pdb=" CA ASP A 569 " ideal model delta harmonic sigma weight residual 180.00 156.61 23.39 0 5.00e+00 4.00e-02 2.19e+01 ... (remaining 11297 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1903 0.036 - 0.071: 706 0.071 - 0.107: 275 0.107 - 0.143: 64 0.143 - 0.178: 5 Chirality restraints: 2953 Sorted by residual: chirality pdb=" CA HIS A 406 " pdb=" N HIS A 406 " pdb=" C HIS A 406 " pdb=" CB HIS A 406 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.95e-01 chirality pdb=" CB ILE A 413 " pdb=" CA ILE A 413 " pdb=" CG1 ILE A 413 " pdb=" CG2 ILE A 413 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.91e-01 chirality pdb=" C3' DT L 22 " pdb=" C4' DT L 22 " pdb=" O3' DT L 22 " pdb=" C2' DT L 22 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 7.77e-01 ... (remaining 2950 not shown) Planarity restraints: 2913 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 179 " 0.064 5.00e-02 4.00e+02 9.70e-02 1.50e+01 pdb=" N PRO D 180 " -0.168 5.00e-02 4.00e+02 pdb=" CA PRO D 180 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO D 180 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 890 " -0.046 5.00e-02 4.00e+02 6.98e-02 7.80e+00 pdb=" N PRO A 891 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO A 891 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 891 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 890 " 0.043 5.00e-02 4.00e+02 6.47e-02 6.70e+00 pdb=" N PRO C 891 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO C 891 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 891 " 0.036 5.00e-02 4.00e+02 ... (remaining 2910 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1507 2.74 - 3.28: 17593 3.28 - 3.82: 32897 3.82 - 4.36: 37476 4.36 - 4.90: 61056 Nonbonded interactions: 150529 Sorted by model distance: nonbonded pdb=" NH2 ARG A 838 " pdb=" OE2 GLU C 607 " model vdw 2.200 3.120 nonbonded pdb=" NH2 ARG B 73 " pdb=" OD1 ASN B 101 " model vdw 2.212 3.120 nonbonded pdb=" OH TYR C 935 " pdb=" OP1 DG I 16 " model vdw 2.238 3.040 nonbonded pdb=" O VAL C 488 " pdb=" OG1 THR C 492 " model vdw 2.245 3.040 nonbonded pdb=" NZ LYS A 989 " pdb=" OP1 DA M 24 " model vdw 2.262 3.120 ... (remaining 150524 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 391 through 906 or resid 908 through 1006 or (resid 1007 a \ nd (name N or name CA or name C or name O or name CB )) or resid 1101 through 11 \ 02)) selection = (chain 'C' and (resid 391 through 392 or (resid 393 and (name N or name CA or na \ me C or name O or name CB )) or resid 394 through 457 or (resid 458 and (name N \ or name CA or name C or name O or name CB )) or resid 459 through 906 or resid 9 \ 08 through 958 or (resid 959 and (name N or name CA or name C or name O or name \ CB )) or resid 960 through 1102)) } ncs_group { reference = (chain 'B' and (resid 1 through 46 or resid 48 through 117 or (resid 118 and (na \ me N or name CA or name C or name O or name CB )) or resid 119 through 236 or re \ sid 238 through 335 or (resid 336 and (name N or name CA or name C or name O or \ name CB )) or resid 337 or resid 340 or (resid 341 through 342 and (name N or na \ me CA or name C or name O or name CB )) or resid 343 through 350)) selection = (chain 'D' and (resid 1 through 46 or resid 48 through 236 or resid 238 through \ 350)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.190 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: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 23.950 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 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:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 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 : 0.004 0.038 19462 Z= 0.325 Angle : 0.649 12.247 26992 Z= 0.477 Chirality : 0.044 0.178 2953 Planarity : 0.004 0.097 2913 Dihedral : 19.407 89.689 7684 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.12 % Allowed : 0.36 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % 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: -0.01 (0.19), residues: 1926 helix: 1.08 (0.21), residues: 663 sheet: 0.64 (0.28), residues: 369 loop : -1.12 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 407 TYR 0.020 0.001 TYR C 757 PHE 0.016 0.001 PHE C 557 TRP 0.025 0.001 TRP D 317 HIS 0.006 0.001 HIS A 876 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.32 (19454) covalent geometry : angle 0.64694 / 0.48 (26988) hydrogen bonds : bond 0.15482 / 10.63 ( 859) hydrogen bonds : angle 6.46814 / 4.65 ( 2333) metal coordination : bond 0.00690 / 0.35 ( 8) metal coordination : angle 4.08601 / 2.08 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 388 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 915 ARG cc_start: 0.7858 (tpm170) cc_final: 0.7287 (tpt170) REVERT: B 234 TYR cc_start: 0.7756 (m-80) cc_final: 0.7484 (m-80) REVERT: B 294 ASP cc_start: 0.6834 (t70) cc_final: 0.6634 (t0) REVERT: B 302 MET cc_start: 0.7645 (ppp) cc_final: 0.7324 (ppp) REVERT: C 602 MET cc_start: 0.8776 (mtp) cc_final: 0.8486 (mtm) REVERT: C 661 ASP cc_start: 0.8372 (t0) cc_final: 0.7710 (t0) REVERT: C 886 TYR cc_start: 0.8239 (t80) cc_final: 0.8036 (t80) REVERT: D 344 TYR cc_start: 0.7537 (m-10) cc_final: 0.7285 (m-10) outliers start: 0 outliers final: 0 residues processed: 388 average time/residue: 0.1396 time to fit residues: 83.3771 Evaluate side-chains 185 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 98 optimal weight: 20.0000 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 50.0000 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 495 GLN ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 836 HIS ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 750 HIS C 753 ASN C 818 HIS ** C1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 ASN D 27 GLN D 53 ASN D 337 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.114020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.076899 restraints weight = 142000.263| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 5.78 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3213 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 8 (15 function evaluations) r_final: 0.3212 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19462 Z= 0.173 Angle : 0.682 9.653 26992 Z= 0.377 Chirality : 0.044 0.247 2953 Planarity : 0.005 0.083 2913 Dihedral : 21.124 77.761 3904 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.37 % Allowed : 10.39 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % 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: -0.00 (0.19), residues: 1926 helix: 1.04 (0.20), residues: 655 sheet: 0.75 (0.29), residues: 354 loop : -1.09 (0.19), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 73 TYR 0.015 0.002 TYR A 559 PHE 0.026 0.002 PHE B 24 TRP 0.017 0.002 TRP D 317 HIS 0.007 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.17 (19454) covalent geometry : angle 0.68056 / 0.38 (26988) hydrogen bonds : bond 0.05057 / 3.43 ( 859) hydrogen bonds : angle 5.31688 / 3.85 ( 2333) metal coordination : bond 0.00743 / 0.37 ( 8) metal coordination : angle 3.52390 / 1.81 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 200 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 889 MET cc_start: 0.8440 (mmm) cc_final: 0.7835 (mmm) REVERT: B 52 GLN cc_start: 0.8820 (mp10) cc_final: 0.8390 (mp10) REVERT: B 294 ASP cc_start: 0.8628 (t70) cc_final: 0.8146 (t0) REVERT: B 339 MET cc_start: 0.8213 (mmm) cc_final: 0.7709 (mmm) REVERT: C 602 MET cc_start: 0.9054 (mtp) cc_final: 0.8090 (mtp) REVERT: C 661 ASP cc_start: 0.8062 (t0) cc_final: 0.7632 (t0) REVERT: C 809 GLN cc_start: 0.8218 (tt0) cc_final: 0.7925 (tm-30) REVERT: D 21 LEU cc_start: 0.9097 (mp) cc_final: 0.8812 (mm) REVERT: D 234 TYR cc_start: 0.6972 (m-10) cc_final: 0.5946 (m-10) outliers start: 22 outliers final: 11 residues processed: 212 average time/residue: 0.1207 time to fit residues: 40.9695 Evaluate side-chains 178 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 167 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 897 CYS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 267 ASN Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain C residue 536 ASP Chi-restraints excluded: chain C residue 862 THR Chi-restraints excluded: chain D residue 55 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 142 optimal weight: 6.9990 chunk 175 optimal weight: 7.9990 chunk 86 optimal weight: 6.9990 chunk 130 optimal weight: 0.9980 chunk 44 optimal weight: 0.4980 chunk 57 optimal weight: 0.6980 chunk 203 optimal weight: 20.0000 chunk 117 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 94 optimal weight: 8.9990 chunk 199 optimal weight: 50.0000 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 10 HIS ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 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 = 0.3908 r_free = 0.3908 target = 0.112707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.075624 restraints weight = 121100.845| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 5.35 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3187 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3187 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19462 Z= 0.176 Angle : 0.637 9.294 26992 Z= 0.353 Chirality : 0.043 0.367 2953 Planarity : 0.004 0.072 2913 Dihedral : 21.271 74.507 3904 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.31 % Allowed : 12.41 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % 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: -0.02 (0.19), residues: 1926 helix: 1.06 (0.20), residues: 655 sheet: 0.73 (0.29), residues: 352 loop : -1.11 (0.19), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 446 TYR 0.026 0.002 TYR B 234 PHE 0.038 0.002 PHE B 206 TRP 0.017 0.002 TRP D 317 HIS 0.017 0.001 HIS A 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.18 (19454) covalent geometry : angle 0.63508 / 0.35 (26988) hydrogen bonds : bond 0.04628 / 3.14 ( 859) hydrogen bonds : angle 5.01260 / 3.65 ( 2333) metal coordination : bond 0.00929 / 0.45 ( 8) metal coordination : angle 3.78354 / 1.95 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 168 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 435 PHE cc_start: 0.8664 (t80) cc_final: 0.8397 (t80) REVERT: A 442 ARG cc_start: 0.9343 (tpm170) cc_final: 0.9141 (mtm-85) REVERT: A 455 MET cc_start: 0.7542 (mmp) cc_final: 0.7311 (mmp) REVERT: B 142 ILE cc_start: 0.8956 (tt) cc_final: 0.8707 (tp) REVERT: B 162 MET cc_start: 0.8570 (mmp) cc_final: 0.8361 (mmm) REVERT: B 287 CYS cc_start: 0.8697 (m) cc_final: 0.8423 (t) REVERT: B 294 ASP cc_start: 0.8487 (t70) cc_final: 0.8053 (t0) REVERT: C 661 ASP cc_start: 0.8090 (t0) cc_final: 0.7695 (t0) REVERT: C 809 GLN cc_start: 0.8238 (tt0) cc_final: 0.8027 (tm-30) REVERT: C 965 ASN cc_start: 0.9565 (OUTLIER) cc_final: 0.9292 (t0) REVERT: D 19 PHE cc_start: 0.8539 (p90) cc_final: 0.8235 (p90) outliers start: 21 outliers final: 13 residues processed: 182 average time/residue: 0.1207 time to fit residues: 36.0648 Evaluate side-chains 173 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 159 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 862 THR Chi-restraints excluded: chain A residue 897 CYS Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain C residue 414 GLN Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain C residue 965 ASN Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 350 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 199 optimal weight: 50.0000 chunk 107 optimal weight: 0.7980 chunk 54 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 69.8077 > 50:) chunk 92 optimal weight: 8.9990 chunk 48 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 148 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 95 optimal weight: 40.0000 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 975 ASN ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 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 = 0.3925 r_free = 0.3925 target = 0.113782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.076259 restraints weight = 152943.700| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 6.02 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3200 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3200 r_free = 0.3200 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3200 r_free = 0.3200 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.3200 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19462 Z= 0.138 Angle : 0.608 10.447 26992 Z= 0.336 Chirality : 0.042 0.359 2953 Planarity : 0.004 0.067 2913 Dihedral : 21.318 72.749 3904 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.37 % Allowed : 13.18 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % 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: 0.05 (0.19), residues: 1926 helix: 1.11 (0.21), residues: 655 sheet: 0.67 (0.29), residues: 343 loop : -1.00 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 446 TYR 0.020 0.001 TYR B 234 PHE 0.033 0.002 PHE A 743 TRP 0.019 0.002 TRP D 317 HIS 0.015 0.001 HIS A 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.14 (19454) covalent geometry : angle 0.60667 / 0.34 (26988) hydrogen bonds : bond 0.04173 / 2.82 ( 859) hydrogen bonds : angle 4.79362 / 3.49 ( 2333) metal coordination : bond 0.00572 / 0.28 ( 8) metal coordination : angle 3.64304 / 1.87 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 170 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 435 PHE cc_start: 0.8690 (t80) cc_final: 0.8433 (t80) REVERT: A 556 ARG cc_start: 0.8518 (ttp80) cc_final: 0.8179 (ptm-80) REVERT: A 806 LYS cc_start: 0.9092 (tppp) cc_final: 0.8678 (tptp) REVERT: A 974 MET cc_start: 0.8173 (mtp) cc_final: 0.7781 (mtt) REVERT: B 55 LEU cc_start: 0.8588 (mm) cc_final: 0.8352 (mm) REVERT: B 142 ILE cc_start: 0.8899 (tt) cc_final: 0.8649 (tp) REVERT: B 162 MET cc_start: 0.8718 (mmt) cc_final: 0.8400 (mmm) REVERT: B 287 CYS cc_start: 0.8788 (m) cc_final: 0.8373 (t) REVERT: C 661 ASP cc_start: 0.7833 (t0) cc_final: 0.7408 (t0) REVERT: D 19 PHE cc_start: 0.8530 (p90) cc_final: 0.8161 (p90) outliers start: 22 outliers final: 17 residues processed: 185 average time/residue: 0.1213 time to fit residues: 36.5738 Evaluate side-chains 172 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 155 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 897 CYS Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain C residue 952 SER Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 349 ARG Chi-restraints excluded: chain D residue 350 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 170 optimal weight: 5.9990 chunk 147 optimal weight: 0.7980 chunk 189 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 63 optimal weight: 8.9990 chunk 101 optimal weight: 0.0570 chunk 190 optimal weight: 0.9980 chunk 94 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 120 optimal weight: 7.9990 chunk 124 optimal weight: 1.9990 overall best weight: 0.9700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 842 ASN ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 ASN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 447 GLN ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1000 GLN D 23 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.113520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.076490 restraints weight = 122297.108| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 5.41 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3208 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3208 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19462 Z= 0.136 Angle : 0.592 8.947 26992 Z= 0.330 Chirality : 0.042 0.360 2953 Planarity : 0.004 0.065 2913 Dihedral : 21.348 73.810 3904 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.60 % Allowed : 13.90 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % 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: 0.05 (0.19), residues: 1926 helix: 1.10 (0.21), residues: 657 sheet: 0.66 (0.28), residues: 343 loop : -1.00 (0.20), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 442 TYR 0.018 0.001 TYR B 234 PHE 0.023 0.001 PHE A 743 TRP 0.020 0.001 TRP D 317 HIS 0.015 0.001 HIS A 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.14 (19454) covalent geometry : angle 0.59068 / 0.33 (26988) hydrogen bonds : bond 0.04048 / 2.74 ( 859) hydrogen bonds : angle 4.74839 / 3.45 ( 2333) metal coordination : bond 0.00620 / 0.30 ( 8) metal coordination : angle 3.41150 / 1.75 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 156 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 446 ARG cc_start: 0.8959 (ttp80) cc_final: 0.8545 (ttp80) REVERT: A 556 ARG cc_start: 0.8523 (ttp80) cc_final: 0.8042 (ptm-80) REVERT: A 806 LYS cc_start: 0.9096 (tppp) cc_final: 0.8616 (tptp) REVERT: A 842 ASN cc_start: 0.6941 (OUTLIER) cc_final: 0.6638 (t0) REVERT: A 974 MET cc_start: 0.8195 (mtp) cc_final: 0.7757 (mtt) REVERT: B 55 LEU cc_start: 0.8499 (mm) cc_final: 0.8261 (mm) REVERT: B 142 ILE cc_start: 0.8918 (tt) cc_final: 0.8677 (tp) REVERT: B 152 MET cc_start: 0.8244 (ptm) cc_final: 0.7631 (ppp) REVERT: B 162 MET cc_start: 0.8742 (mmt) cc_final: 0.8435 (mmm) REVERT: B 287 CYS cc_start: 0.8820 (m) cc_final: 0.8528 (t) REVERT: C 661 ASP cc_start: 0.7848 (t0) cc_final: 0.7418 (t0) REVERT: C 847 MET cc_start: 0.8454 (pmm) cc_final: 0.8116 (ptm) REVERT: C 984 MET cc_start: 0.8681 (mmt) cc_final: 0.7877 (mmm) REVERT: D 19 PHE cc_start: 0.8559 (p90) cc_final: 0.8189 (p90) outliers start: 26 outliers final: 19 residues processed: 174 average time/residue: 0.1200 time to fit residues: 34.3590 Evaluate side-chains 171 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 151 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 515 HIS Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 842 ASN Chi-restraints excluded: chain A residue 897 CYS Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain C residue 837 LEU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 349 ARG Chi-restraints excluded: chain D residue 350 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 64 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 200 optimal weight: 50.0000 chunk 160 optimal weight: 1.9990 chunk 203 optimal weight: 20.0000 chunk 43 optimal weight: 4.9990 chunk 168 optimal weight: 8.9990 chunk 28 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 447 GLN ** C 473 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 = 0.3910 r_free = 0.3910 target = 0.112744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.075467 restraints weight = 129189.181| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 5.53 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3186 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3186 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19462 Z= 0.153 Angle : 0.585 8.184 26992 Z= 0.326 Chirality : 0.041 0.268 2953 Planarity : 0.004 0.062 2913 Dihedral : 21.388 74.599 3904 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.72 % Allowed : 14.07 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % 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: 0.09 (0.19), residues: 1926 helix: 1.15 (0.21), residues: 656 sheet: 0.53 (0.28), residues: 351 loop : -0.93 (0.20), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 828 TYR 0.021 0.001 TYR D 234 PHE 0.025 0.001 PHE A 743 TRP 0.023 0.001 TRP D 317 HIS 0.015 0.001 HIS A 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (19454) covalent geometry : angle 0.58318 / 0.33 (26988) hydrogen bonds : bond 0.04080 / 2.75 ( 859) hydrogen bonds : angle 4.72258 / 3.45 ( 2333) metal coordination : bond 0.00847 / 0.42 ( 8) metal coordination : angle 3.42552 / 1.75 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 155 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 446 ARG cc_start: 0.8956 (ttp80) cc_final: 0.8543 (ttp80) REVERT: A 556 ARG cc_start: 0.8608 (ttp80) cc_final: 0.7932 (ptm-80) REVERT: A 806 LYS cc_start: 0.9059 (tppp) cc_final: 0.8599 (tptp) REVERT: A 974 MET cc_start: 0.8235 (mtp) cc_final: 0.7805 (mtt) REVERT: B 55 LEU cc_start: 0.8508 (mm) cc_final: 0.8258 (mm) REVERT: B 142 ILE cc_start: 0.8911 (tt) cc_final: 0.8673 (tp) REVERT: B 162 MET cc_start: 0.8728 (mmt) cc_final: 0.8396 (mmm) REVERT: B 287 CYS cc_start: 0.8796 (m) cc_final: 0.8503 (t) REVERT: C 627 MET cc_start: 0.8583 (tpp) cc_final: 0.8266 (tpp) REVERT: C 661 ASP cc_start: 0.7914 (t0) cc_final: 0.7478 (t0) REVERT: D 5 MET cc_start: 0.8523 (ttm) cc_final: 0.8319 (tpp) REVERT: D 19 PHE cc_start: 0.8569 (p90) cc_final: 0.7918 (p90) outliers start: 28 outliers final: 22 residues processed: 174 average time/residue: 0.1279 time to fit residues: 36.6407 Evaluate side-chains 169 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 515 HIS Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 897 CYS Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain C residue 565 SER Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain C residue 837 LEU Chi-restraints excluded: chain C residue 862 THR Chi-restraints excluded: chain C residue 952 SER Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 349 ARG Chi-restraints excluded: chain D residue 350 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 43 optimal weight: 5.9990 chunk 141 optimal weight: 0.8980 chunk 148 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 chunk 150 optimal weight: 0.1980 chunk 57 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 197 optimal weight: 9.9990 chunk 125 optimal weight: 0.0040 chunk 113 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 ASN ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 447 GLN ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 809 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.113943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.076835 restraints weight = 125106.097| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 5.49 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3214 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3214 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 19462 Z= 0.123 Angle : 0.571 8.468 26992 Z= 0.318 Chirality : 0.041 0.186 2953 Planarity : 0.004 0.060 2913 Dihedral : 21.376 76.395 3904 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.31 % Allowed : 15.20 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % 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: 0.12 (0.19), residues: 1926 helix: 1.16 (0.21), residues: 657 sheet: 0.62 (0.29), residues: 330 loop : -0.90 (0.20), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 442 TYR 0.024 0.001 TYR D 234 PHE 0.019 0.001 PHE A 743 TRP 0.025 0.001 TRP D 317 HIS 0.015 0.001 HIS A 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 (19454) covalent geometry : angle 0.56918 / 0.32 (26988) hydrogen bonds : bond 0.03737 / 2.52 ( 859) hydrogen bonds : angle 4.62072 / 3.36 ( 2333) metal coordination : bond 0.00528 / 0.26 ( 8) metal coordination : angle 3.30048 / 1.69 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 159 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 617 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8331 (mt-10) REVERT: A 806 LYS cc_start: 0.9019 (tppp) cc_final: 0.8586 (tptp) REVERT: A 889 MET cc_start: 0.8429 (mmm) cc_final: 0.7909 (mmm) REVERT: A 974 MET cc_start: 0.8210 (mtp) cc_final: 0.7772 (mtt) REVERT: B 55 LEU cc_start: 0.8506 (mm) cc_final: 0.8252 (mm) REVERT: B 152 MET cc_start: 0.8288 (ptm) cc_final: 0.7754 (ppp) REVERT: B 162 MET cc_start: 0.8742 (mmt) cc_final: 0.8474 (mmm) REVERT: B 287 CYS cc_start: 0.8751 (m) cc_final: 0.8523 (t) REVERT: C 627 MET cc_start: 0.8533 (tpp) cc_final: 0.8199 (tpp) REVERT: C 661 ASP cc_start: 0.7803 (t0) cc_final: 0.7384 (t0) REVERT: C 841 MET cc_start: 0.8538 (mmm) cc_final: 0.8258 (mtt) REVERT: C 847 MET cc_start: 0.8456 (pmm) cc_final: 0.8092 (ptm) REVERT: C 984 MET cc_start: 0.8686 (mmt) cc_final: 0.8051 (mmm) REVERT: D 5 MET cc_start: 0.8448 (ttm) cc_final: 0.8245 (tpp) REVERT: D 21 LEU cc_start: 0.9058 (mp) cc_final: 0.8827 (mm) outliers start: 21 outliers final: 17 residues processed: 173 average time/residue: 0.1285 time to fit residues: 36.4882 Evaluate side-chains 163 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 515 HIS Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 897 CYS Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain C residue 837 LEU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 349 ARG Chi-restraints excluded: chain D residue 350 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 0 optimal weight: 50.0000 chunk 175 optimal weight: 10.0000 chunk 179 optimal weight: 8.9990 chunk 44 optimal weight: 1.9990 chunk 186 optimal weight: 6.9990 chunk 164 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 123 optimal weight: 7.9990 chunk 176 optimal weight: 0.7980 chunk 82 optimal weight: 9.9990 chunk 119 optimal weight: 1.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 609 HIS ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 753 ASN ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 447 GLN ** C 473 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 = 0.3877 r_free = 0.3877 target = 0.110480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.072962 restraints weight = 130528.812| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 5.58 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3134 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3134 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 19462 Z= 0.219 Angle : 0.644 10.220 26992 Z= 0.351 Chirality : 0.043 0.267 2953 Planarity : 0.004 0.059 2913 Dihedral : 21.539 78.275 3904 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.60 % Allowed : 15.50 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % 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: 0.08 (0.19), residues: 1926 helix: 1.12 (0.21), residues: 657 sheet: 0.47 (0.28), residues: 354 loop : -0.89 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 556 TYR 0.015 0.002 TYR A 559 PHE 0.020 0.002 PHE A 743 TRP 0.019 0.002 TRP D 317 HIS 0.015 0.001 HIS A 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.22 (19454) covalent geometry : angle 0.64231 / 0.35 (26988) hydrogen bonds : bond 0.04513 / 3.03 ( 859) hydrogen bonds : angle 4.69451 / 3.42 ( 2333) metal coordination : bond 0.01658 / 0.84 ( 8) metal coordination : angle 3.51239 / 1.79 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 0.753 Fit side-chains revert: symmetry clash REVERT: A 446 ARG cc_start: 0.8993 (ttp80) cc_final: 0.8549 (ttp80) REVERT: A 806 LYS cc_start: 0.9051 (tppp) cc_final: 0.8654 (tppt) REVERT: A 889 MET cc_start: 0.8473 (mmm) cc_final: 0.7891 (mmm) REVERT: A 974 MET cc_start: 0.8294 (mtp) cc_final: 0.7865 (mtt) REVERT: B 55 LEU cc_start: 0.8523 (mm) cc_final: 0.8272 (mm) REVERT: B 162 MET cc_start: 0.8711 (mmt) cc_final: 0.8423 (mmm) REVERT: B 287 CYS cc_start: 0.8773 (m) cc_final: 0.8472 (t) REVERT: C 627 MET cc_start: 0.8736 (tpp) cc_final: 0.8306 (tpp) REVERT: C 661 ASP cc_start: 0.8063 (t0) cc_final: 0.7628 (t0) REVERT: C 984 MET cc_start: 0.8933 (mmt) cc_final: 0.8125 (mmm) REVERT: D 5 MET cc_start: 0.8473 (ttm) cc_final: 0.8194 (tpp) REVERT: D 21 LEU cc_start: 0.9131 (mp) cc_final: 0.8928 (mm) REVERT: D 349 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.8088 (ttt-90) outliers start: 26 outliers final: 21 residues processed: 159 average time/residue: 0.1280 time to fit residues: 33.6149 Evaluate side-chains 159 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 515 HIS Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 897 CYS Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain C residue 536 ASP Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain C residue 812 ILE Chi-restraints excluded: chain C residue 837 LEU Chi-restraints excluded: chain C residue 952 SER Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 349 ARG Chi-restraints excluded: chain D residue 350 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 180 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 149 optimal weight: 0.9980 chunk 202 optimal weight: 20.0000 chunk 173 optimal weight: 6.9990 chunk 85 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 62 optimal weight: 0.0470 chunk 98 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 overall best weight: 0.7678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 447 GLN ** C 473 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 = 0.3911 r_free = 0.3911 target = 0.112641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.075361 restraints weight = 130722.546| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 5.55 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3185 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.3185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19462 Z= 0.127 Angle : 0.585 8.739 26992 Z= 0.323 Chirality : 0.041 0.251 2953 Planarity : 0.004 0.058 2913 Dihedral : 21.454 80.351 3904 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.19 % Allowed : 16.09 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % 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: 1926 helix: 1.28 (0.21), residues: 654 sheet: 0.59 (0.28), residues: 351 loop : -0.87 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 446 TYR 0.023 0.001 TYR D 234 PHE 0.016 0.001 PHE A 743 TRP 0.022 0.001 TRP D 317 HIS 0.016 0.001 HIS A 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.13 (19454) covalent geometry : angle 0.58377 / 0.32 (26988) hydrogen bonds : bond 0.03756 / 2.53 ( 859) hydrogen bonds : angle 4.58557 / 3.34 ( 2333) metal coordination : bond 0.00601 / 0.29 ( 8) metal coordination : angle 3.63521 / 1.84 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.701 Fit side-chains revert: symmetry clash REVERT: A 446 ARG cc_start: 0.8977 (ttp80) cc_final: 0.8553 (ttp80) REVERT: A 806 LYS cc_start: 0.9019 (tppp) cc_final: 0.8643 (tppt) REVERT: A 889 MET cc_start: 0.8365 (mmm) cc_final: 0.7861 (mmm) REVERT: A 974 MET cc_start: 0.8235 (mtp) cc_final: 0.7790 (mtt) REVERT: B 55 LEU cc_start: 0.8505 (mm) cc_final: 0.8256 (mm) REVERT: B 162 MET cc_start: 0.8780 (mmt) cc_final: 0.8481 (mmm) REVERT: B 287 CYS cc_start: 0.8748 (m) cc_final: 0.8501 (t) REVERT: C 627 MET cc_start: 0.8726 (tpp) cc_final: 0.8299 (tpp) REVERT: C 661 ASP cc_start: 0.7914 (t0) cc_final: 0.7543 (t0) REVERT: C 841 MET cc_start: 0.8561 (mmm) cc_final: 0.8191 (mtt) REVERT: C 984 MET cc_start: 0.8831 (mmt) cc_final: 0.8103 (mmm) REVERT: D 5 MET cc_start: 0.8464 (ttm) cc_final: 0.8229 (tpp) REVERT: D 21 LEU cc_start: 0.9109 (mp) cc_final: 0.8904 (mm) REVERT: D 349 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.8143 (tpt170) outliers start: 19 outliers final: 16 residues processed: 157 average time/residue: 0.1290 time to fit residues: 33.4217 Evaluate side-chains 154 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 515 HIS Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 897 CYS Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain C residue 837 LEU Chi-restraints excluded: chain C residue 952 SER Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 349 ARG Chi-restraints excluded: chain D residue 350 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 30 optimal weight: 0.9990 chunk 132 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 chunk 45 optimal weight: 0.0010 chunk 93 optimal weight: 0.9980 chunk 162 optimal weight: 0.5980 chunk 83 optimal weight: 0.5980 chunk 201 optimal weight: 40.0000 chunk 175 optimal weight: 9.9990 chunk 156 optimal weight: 3.9990 chunk 3 optimal weight: 20.0000 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 447 GLN ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 495 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.113198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.075439 restraints weight = 161478.206| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 6.21 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3191 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.3191 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 19462 Z= 0.124 Angle : 0.594 12.210 26992 Z= 0.325 Chirality : 0.041 0.225 2953 Planarity : 0.004 0.059 2913 Dihedral : 21.424 81.289 3904 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.25 % Allowed : 16.33 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % 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: 0.22 (0.19), residues: 1926 helix: 1.24 (0.21), residues: 655 sheet: 0.62 (0.28), residues: 351 loop : -0.85 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 446 TYR 0.019 0.001 TYR A 559 PHE 0.017 0.001 PHE A 743 TRP 0.024 0.001 TRP D 317 HIS 0.017 0.001 HIS A 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 (19454) covalent geometry : angle 0.59271 / 0.32 (26988) hydrogen bonds : bond 0.03681 / 2.47 ( 859) hydrogen bonds : angle 4.55899 / 3.32 ( 2333) metal coordination : bond 0.00606 / 0.29 ( 8) metal coordination : angle 3.18079 / 1.62 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 144 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 446 ARG cc_start: 0.8963 (ttp80) cc_final: 0.8550 (ttp80) REVERT: A 617 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8304 (mt-10) REVERT: A 806 LYS cc_start: 0.9021 (tppp) cc_final: 0.8666 (tppt) REVERT: A 974 MET cc_start: 0.8235 (mtp) cc_final: 0.7771 (mtt) REVERT: B 55 LEU cc_start: 0.8501 (mm) cc_final: 0.8253 (mm) REVERT: B 162 MET cc_start: 0.8772 (mmt) cc_final: 0.8530 (mmm) REVERT: B 287 CYS cc_start: 0.8876 (m) cc_final: 0.8552 (t) REVERT: C 627 MET cc_start: 0.8678 (tpp) cc_final: 0.8246 (tpp) REVERT: C 661 ASP cc_start: 0.7810 (t0) cc_final: 0.7395 (t0) REVERT: C 841 MET cc_start: 0.8553 (mmm) cc_final: 0.8243 (mtt) REVERT: C 847 MET cc_start: 0.8458 (pmm) cc_final: 0.8009 (ptm) REVERT: C 984 MET cc_start: 0.8812 (mmt) cc_final: 0.8460 (mmm) outliers start: 20 outliers final: 18 residues processed: 157 average time/residue: 0.1334 time to fit residues: 33.9933 Evaluate side-chains 158 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 515 HIS Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 897 CYS Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain C residue 447 GLN Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain C residue 837 LEU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 349 ARG Chi-restraints excluded: chain D residue 350 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 191 optimal weight: 50.0000 chunk 46 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 193 optimal weight: 40.0000 chunk 109 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 447 GLN ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 495 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.112983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.075511 restraints weight = 154676.191| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 5.99 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3191 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.3191 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.198 19462 Z= 0.221 Angle : 0.772 59.200 26992 Z= 0.457 Chirality : 0.042 0.399 2953 Planarity : 0.004 0.067 2913 Dihedral : 21.423 81.268 3904 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.19 % Allowed : 16.51 % Favored : 82.30 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 1.11 % 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: 1926 helix: 1.24 (0.20), residues: 655 sheet: 0.62 (0.28), residues: 351 loop : -0.85 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.037 0.001 ARG A 828 TYR 0.018 0.001 TYR A 559 PHE 0.017 0.001 PHE A 743 TRP 0.024 0.001 TRP D 317 HIS 0.016 0.001 HIS A 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.22 (19454) covalent geometry : angle 0.77059 / 0.46 (26988) hydrogen bonds : bond 0.03703 / 2.49 ( 859) hydrogen bonds : angle 4.56383 / 3.32 ( 2333) metal coordination : bond 0.00640 / 0.32 ( 8) metal coordination : angle 3.18067 / 1.62 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4064.35 seconds wall clock time: 70 minutes 44.37 seconds (4244.37 seconds total)