Starting phenix.real_space_refine on Sat Jul 4 06:54:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jtu_61817/07_2026/9jtu_61817.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jtu_61817/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9jtu_61817/07_2026/9jtu_61817.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jtu_61817/07_2026/9jtu_61817.map" model { file = "/net/cci-nas-00/data/ceres_data/9jtu_61817/07_2026/9jtu_61817.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jtu_61817/07_2026/9jtu_61817.cif" } 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-dev-6108/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, 1 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 1 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain breaks: 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: 5.40, per 1000 atoms: 0.29 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: 1.62 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: 2.38 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: 4.45 Time building geometry restraints manager: 2.12 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: 26667 2.45 - 4.90: 304 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: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 23.880 Find NCS groups from input model: 0.270 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.910 ------------------------------------------------------------------------------- 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 : 0.647 12.247 26992 Z= 0.475 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 0.64516 / 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 : 0.658 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: A 915 ARG cc_start: 0.7858 (tpm170) cc_final: 0.7288 (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: 0.7721 (t0) REVERT: C 886 TYR cc_start: 0.8239 (t80) cc_final: 0.8037 (t80) REVERT: D 344 TYR cc_start: 0.7537 (m-10) cc_final: 0.7286 (m-10) outliers start: 0 outliers final: 0 residues processed: 388 average time/residue: 0.1443 time to fit residues: 86.0494 Evaluate side-chains 183 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.667 ------------------------------------------------------------------------------- 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: 10.9990 chunk 107 optimal weight: 2.9990 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: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 GLN ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 836 HIS B 10 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.113388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.076146 restraints weight = 142105.539| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 5.89 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3196 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (12 function evaluations) r_final: 0.3195 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19462 Z= 0.186 Angle : 0.687 9.785 26992 Z= 0.380 Chirality : 0.044 0.248 2953 Planarity : 0.005 0.082 2913 Dihedral : 21.170 78.440 3904 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.43 % Allowed : 10.63 % Favored : 87.95 % 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: -0.03 (0.19), residues: 1926 helix: 1.03 (0.20), residues: 655 sheet: 0.71 (0.29), residues: 354 loop : -1.11 (0.19), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 73 TYR 0.016 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 0.00391 / 0.19 (19454) covalent geometry : angle 0.68584 / 0.38 (26988) hydrogen bonds : bond 0.05080 / 3.45 ( 859) hydrogen bonds : angle 5.28355 / 3.83 ( 2333) metal coordination : bond 0.00895 / 0.44 ( 8) metal coordination : angle 3.51116 / 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 218 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 195 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 442 ARG cc_start: 0.9338 (tpm170) cc_final: 0.9137 (mtm-85) REVERT: B 294 ASP cc_start: 0.8621 (t70) cc_final: 0.8139 (t0) REVERT: B 339 MET cc_start: 0.8205 (mmm) cc_final: 0.7714 (mmm) REVERT: C 602 MET cc_start: 0.9080 (mtp) cc_final: 0.8774 (mtp) REVERT: C 661 ASP cc_start: 0.8125 (t0) cc_final: 0.7706 (t0) REVERT: C 809 GLN cc_start: 0.8281 (tt0) cc_final: 0.7995 (tm-30) REVERT: D 21 LEU cc_start: 0.9106 (mp) cc_final: 0.8818 (mm) REVERT: D 234 TYR cc_start: 0.6980 (m-10) cc_final: 0.5952 (m-10) outliers start: 23 outliers final: 12 residues processed: 208 average time/residue: 0.1296 time to fit residues: 43.0453 Evaluate side-chains 179 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 167 time to evaluate : 0.765 ------------------------------------------------------------------------------- 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 5 MET 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: 5.9990 chunk 175 optimal weight: 9.9990 chunk 86 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 203 optimal weight: 20.0000 chunk 117 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 chunk 199 optimal weight: 50.0000 overall best weight: 2.7986 ------------------------------------------------------------------------------- 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 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 447 GLN C1000 GLN D 23 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.111046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.073959 restraints weight = 121516.451| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 5.27 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3149 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (12 function evaluations) r_final: 0.3149 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 19462 Z= 0.220 Angle : 0.662 9.100 26992 Z= 0.366 Chirality : 0.044 0.379 2953 Planarity : 0.005 0.072 2913 Dihedral : 21.384 75.849 3904 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.78 % Allowed : 12.71 % Favored : 85.51 % 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: 0.97 (0.20), residues: 654 sheet: 0.41 (0.28), residues: 360 loop : -1.05 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 828 TYR 0.027 0.002 TYR B 234 PHE 0.036 0.002 PHE B 206 TRP 0.016 0.002 TRP C 893 HIS 0.017 0.001 HIS A 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.22 (19454) covalent geometry : angle 0.66008 / 0.37 (26988) hydrogen bonds : bond 0.04844 / 3.28 ( 859) hydrogen bonds : angle 5.03997 / 3.67 ( 2333) metal coordination : bond 0.01347 / 0.66 ( 8) metal coordination : angle 4.09419 / 2.10 ( 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 190 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 161 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 435 PHE cc_start: 0.8703 (t80) cc_final: 0.8430 (t80) REVERT: A 442 ARG cc_start: 0.9332 (tpm170) cc_final: 0.9086 (mtm-85) REVERT: A 974 MET cc_start: 0.8160 (mtm) cc_final: 0.7885 (mtp) REVERT: B 52 GLN cc_start: 0.8972 (mp10) cc_final: 0.8536 (mp10) REVERT: B 142 ILE cc_start: 0.8943 (tt) cc_final: 0.8694 (tp) REVERT: B 162 MET cc_start: 0.8633 (mmp) cc_final: 0.8409 (mmm) REVERT: B 287 CYS cc_start: 0.8771 (m) cc_final: 0.8486 (t) REVERT: C 627 MET cc_start: 0.8649 (mmm) cc_final: 0.8389 (tpp) REVERT: C 661 ASP cc_start: 0.8097 (t0) cc_final: 0.7664 (t0) REVERT: D 21 LEU cc_start: 0.9198 (mp) cc_final: 0.8868 (mm) outliers start: 29 outliers final: 17 residues processed: 181 average time/residue: 0.1282 time to fit residues: 37.7010 Evaluate side-chains 166 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 149 time to evaluate : 0.656 ------------------------------------------------------------------------------- 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 C residue 414 GLN Chi-restraints excluded: chain C residue 536 ASP Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 780 SER Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain C residue 862 THR 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: 0.0470 chunk 54 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 148 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 95 optimal weight: 40.0000 overall best weight: 0.9882 ------------------------------------------------------------------------------- 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** C 447 GLN ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.112837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.075205 restraints weight = 152872.085| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 5.96 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3177 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.3177 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19462 Z= 0.139 Angle : 0.606 10.413 26992 Z= 0.336 Chirality : 0.042 0.415 2953 Planarity : 0.004 0.067 2913 Dihedral : 21.395 73.154 3904 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.37 % Allowed : 13.06 % Favored : 85.57 % 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: 654 sheet: 0.59 (0.28), residues: 354 loop : -1.03 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 828 TYR 0.020 0.001 TYR B 234 PHE 0.034 0.002 PHE A 743 TRP 0.018 0.002 TRP D 317 HIS 0.015 0.001 HIS A 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.14 (19454) covalent geometry : angle 0.60391 / 0.34 (26988) hydrogen bonds : bond 0.04245 / 2.88 ( 859) hydrogen bonds : angle 4.81853 / 3.51 ( 2333) metal coordination : bond 0.00648 / 0.32 ( 8) metal coordination : angle 3.93095 / 2.01 ( 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 189 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 167 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 435 PHE cc_start: 0.8675 (t80) cc_final: 0.8397 (t80) REVERT: A 556 ARG cc_start: 0.8547 (ttp80) cc_final: 0.8227 (ptm-80) REVERT: A 806 LYS cc_start: 0.9098 (tppp) cc_final: 0.8682 (tptp) REVERT: A 842 ASN cc_start: 0.7637 (OUTLIER) cc_final: 0.7084 (t0) REVERT: A 974 MET cc_start: 0.8070 (mtm) cc_final: 0.7795 (mtp) REVERT: B 52 GLN cc_start: 0.9011 (mp10) cc_final: 0.8581 (mp10) REVERT: B 55 LEU cc_start: 0.8509 (mm) cc_final: 0.8298 (mm) REVERT: B 142 ILE cc_start: 0.8900 (tt) cc_final: 0.8657 (tp) REVERT: B 162 MET cc_start: 0.8707 (mmt) cc_final: 0.8419 (mmm) REVERT: B 287 CYS cc_start: 0.8764 (m) cc_final: 0.8483 (t) REVERT: C 661 ASP cc_start: 0.7905 (t0) cc_final: 0.7494 (t0) REVERT: C 984 MET cc_start: 0.8764 (mmt) cc_final: 0.8007 (mmm) outliers start: 22 outliers final: 13 residues processed: 181 average time/residue: 0.1134 time to fit residues: 33.9884 Evaluate side-chains 167 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 153 time to evaluate : 0.805 ------------------------------------------------------------------------------- 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 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 C residue 447 GLN Chi-restraints excluded: chain C residue 787 THR 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 170 optimal weight: 7.9990 chunk 147 optimal weight: 7.9990 chunk 189 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 63 optimal weight: 8.9990 chunk 101 optimal weight: 5.9990 chunk 190 optimal weight: 2.9990 chunk 94 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 609 HIS ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 744 HIS ** 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** C 912 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.110658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.073381 restraints weight = 122122.939| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 5.29 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3141 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.3141 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 19462 Z= 0.210 Angle : 0.632 9.087 26992 Z= 0.348 Chirality : 0.043 0.326 2953 Planarity : 0.004 0.063 2913 Dihedral : 21.489 74.162 3904 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.90 % Allowed : 13.66 % Favored : 84.44 % 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: -0.03 (0.19), residues: 1926 helix: 1.05 (0.21), residues: 654 sheet: 0.47 (0.29), residues: 349 loop : -0.99 (0.20), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 442 TYR 0.017 0.002 TYR B 234 PHE 0.024 0.002 PHE A 743 TRP 0.021 0.002 TRP D 317 HIS 0.016 0.001 HIS A 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.21 (19454) covalent geometry : angle 0.63055 / 0.35 (26988) hydrogen bonds : bond 0.04509 / 3.05 ( 859) hydrogen bonds : angle 4.87761 / 3.56 ( 2333) metal coordination : bond 0.01292 / 0.65 ( 8) metal coordination : angle 3.83653 / 1.95 ( 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: 31 poor density : 151 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 556 ARG cc_start: 0.8597 (ttp80) cc_final: 0.8059 (ptm-80) REVERT: A 806 LYS cc_start: 0.9095 (tppp) cc_final: 0.8683 (tptp) REVERT: A 974 MET cc_start: 0.8323 (mtm) cc_final: 0.8042 (mtp) REVERT: B 52 GLN cc_start: 0.8978 (mp10) cc_final: 0.8596 (mp10) REVERT: B 55 LEU cc_start: 0.8523 (mm) cc_final: 0.8294 (mm) REVERT: B 142 ILE cc_start: 0.8947 (tt) cc_final: 0.8699 (tp) REVERT: B 162 MET cc_start: 0.8693 (mmt) cc_final: 0.8439 (mmm) REVERT: B 287 CYS cc_start: 0.8777 (m) cc_final: 0.8476 (t) REVERT: C 661 ASP cc_start: 0.8079 (t0) cc_final: 0.7671 (t0) REVERT: D 234 TYR cc_start: 0.6887 (m-10) cc_final: 0.6179 (m-10) outliers start: 31 outliers final: 25 residues processed: 171 average time/residue: 0.1132 time to fit residues: 32.2119 Evaluate side-chains 171 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 146 time to evaluate : 0.643 ------------------------------------------------------------------------------- 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 651 CYS 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 536 ASP Chi-restraints excluded: chain C residue 565 SER Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 766 HIS 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 264 THR Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 302 MET 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: 4.9990 chunk 111 optimal weight: 2.9990 chunk 200 optimal weight: 40.0000 chunk 160 optimal weight: 0.9980 chunk 203 optimal weight: 20.0000 chunk 43 optimal weight: 2.9990 chunk 168 optimal weight: 6.9990 chunk 28 optimal weight: 0.6980 chunk 123 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.112023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.074560 restraints weight = 128721.364| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 5.58 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3164 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.3164 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19462 Z= 0.136 Angle : 0.584 8.488 26992 Z= 0.326 Chirality : 0.042 0.254 2953 Planarity : 0.004 0.061 2913 Dihedral : 21.463 74.882 3904 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.60 % Allowed : 14.43 % Favored : 83.97 % 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: 1.15 (0.21), residues: 654 sheet: 0.52 (0.28), residues: 355 loop : -0.94 (0.20), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 828 TYR 0.018 0.001 TYR B 234 PHE 0.024 0.002 PHE A 743 TRP 0.022 0.001 TRP D 317 HIS 0.010 0.001 HIS A 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.14 (19454) covalent geometry : angle 0.58208 / 0.33 (26988) hydrogen bonds : bond 0.04042 / 2.74 ( 859) hydrogen bonds : angle 4.73284 / 3.45 ( 2333) metal coordination : bond 0.00715 / 0.35 ( 8) metal coordination : angle 3.86448 / 1.97 ( 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 177 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 556 ARG cc_start: 0.8566 (ttp80) cc_final: 0.8294 (ptm-80) REVERT: A 806 LYS cc_start: 0.9054 (tppp) cc_final: 0.8609 (tptp) REVERT: B 52 GLN cc_start: 0.8996 (mp10) cc_final: 0.8637 (mp10) REVERT: B 55 LEU cc_start: 0.8489 (mm) cc_final: 0.8256 (mm) REVERT: B 142 ILE cc_start: 0.8918 (tt) cc_final: 0.8676 (tp) REVERT: B 152 MET cc_start: 0.8334 (ptm) cc_final: 0.7793 (ppp) REVERT: B 162 MET cc_start: 0.8690 (mmt) cc_final: 0.8467 (mmm) REVERT: B 287 CYS cc_start: 0.8714 (m) cc_final: 0.8464 (t) REVERT: C 661 ASP cc_start: 0.8017 (t0) cc_final: 0.7597 (t0) REVERT: C 984 MET cc_start: 0.8900 (mmm) cc_final: 0.8196 (mmm) REVERT: D 234 TYR cc_start: 0.6880 (m-10) cc_final: 0.6612 (m-10) outliers start: 26 outliers final: 21 residues processed: 167 average time/residue: 0.1253 time to fit residues: 34.1185 Evaluate side-chains 169 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 0.478 ------------------------------------------------------------------------------- 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 766 HIS 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 142 ILE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 320 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 43 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 148 optimal weight: 0.9980 chunk 75 optimal weight: 10.0000 chunk 150 optimal weight: 0.0040 chunk 57 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 197 optimal weight: 10.0000 chunk 125 optimal weight: 0.8980 chunk 113 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.1796 ------------------------------------------------------------------------------- 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 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 = 0.3900 r_free = 0.3900 target = 0.111969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.074817 restraints weight = 124391.850| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 5.38 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3174 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3174 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19462 Z= 0.137 Angle : 0.580 8.926 26992 Z= 0.322 Chirality : 0.041 0.201 2953 Planarity : 0.004 0.062 2913 Dihedral : 21.476 76.880 3904 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.48 % Allowed : 14.90 % Favored : 83.61 % 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: 1.12 (0.21), residues: 655 sheet: 0.56 (0.28), residues: 351 loop : -0.91 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 442 TYR 0.016 0.001 TYR B 234 PHE 0.020 0.001 PHE A 743 TRP 0.024 0.001 TRP D 317 HIS 0.007 0.001 HIS A 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.14 (19454) covalent geometry : angle 0.57864 / 0.32 (26988) hydrogen bonds : bond 0.03965 / 2.68 ( 859) hydrogen bonds : angle 4.67208 / 3.41 ( 2333) metal coordination : bond 0.00760 / 0.37 ( 8) metal coordination : angle 3.54466 / 1.80 ( 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 178 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 154 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 806 LYS cc_start: 0.9024 (tppp) cc_final: 0.8605 (tptp) REVERT: B 52 GLN cc_start: 0.8997 (mp10) cc_final: 0.8647 (mp10) REVERT: B 55 LEU cc_start: 0.8497 (mm) cc_final: 0.8262 (mm) REVERT: B 142 ILE cc_start: 0.8892 (tt) cc_final: 0.8650 (tp) REVERT: B 152 MET cc_start: 0.8362 (ptm) cc_final: 0.7690 (ppp) REVERT: B 162 MET cc_start: 0.8798 (mmt) cc_final: 0.8483 (mmm) REVERT: B 287 CYS cc_start: 0.8744 (m) cc_final: 0.8440 (t) REVERT: C 627 MET cc_start: 0.8515 (mmm) cc_final: 0.8042 (tpp) REVERT: C 661 ASP cc_start: 0.7965 (t0) cc_final: 0.7545 (t0) REVERT: C 984 MET cc_start: 0.8881 (mmm) cc_final: 0.8157 (mmm) REVERT: D 5 MET cc_start: 0.8607 (tpp) cc_final: 0.8378 (mmt) outliers start: 24 outliers final: 22 residues processed: 170 average time/residue: 0.1246 time to fit residues: 34.6212 Evaluate side-chains 171 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 0.683 ------------------------------------------------------------------------------- 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 414 GLN Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 769 VAL 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 142 ILE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 302 MET 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: 7.9990 chunk 179 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 186 optimal weight: 20.0000 chunk 164 optimal weight: 0.3980 chunk 74 optimal weight: 0.8980 chunk 123 optimal weight: 0.9990 chunk 176 optimal weight: 0.0670 chunk 82 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 overall best weight: 1.0722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.112274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.074929 restraints weight = 131027.236| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 5.52 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3178 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3178 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19462 Z= 0.133 Angle : 0.589 10.494 26992 Z= 0.324 Chirality : 0.041 0.224 2953 Planarity : 0.004 0.060 2913 Dihedral : 21.484 78.956 3904 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.60 % Allowed : 15.44 % Favored : 82.96 % 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: 0.11 (0.19), residues: 1926 helix: 1.16 (0.21), residues: 655 sheet: 0.64 (0.29), residues: 339 loop : -0.92 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 556 TYR 0.017 0.001 TYR D 234 PHE 0.020 0.001 PHE A 743 TRP 0.020 0.001 TRP D 317 HIS 0.004 0.001 HIS A 937 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 (19454) covalent geometry : angle 0.58780 / 0.32 (26988) hydrogen bonds : bond 0.03791 / 2.55 ( 859) hydrogen bonds : angle 4.61814 / 3.37 ( 2333) metal coordination : bond 0.00691 / 0.34 ( 8) metal coordination : angle 3.54202 / 1.80 ( 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 177 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 806 LYS cc_start: 0.9015 (tppp) cc_final: 0.8654 (tppt) REVERT: B 52 GLN cc_start: 0.9010 (mp10) cc_final: 0.8732 (mp10) REVERT: B 55 LEU cc_start: 0.8448 (mm) cc_final: 0.8209 (mm) REVERT: B 142 ILE cc_start: 0.8880 (tt) cc_final: 0.8645 (tp) REVERT: B 162 MET cc_start: 0.8799 (mmt) cc_final: 0.8532 (mmm) REVERT: B 287 CYS cc_start: 0.8744 (m) cc_final: 0.8493 (t) REVERT: C 627 MET cc_start: 0.8518 (mmm) cc_final: 0.8022 (tpp) REVERT: C 661 ASP cc_start: 0.7860 (t0) cc_final: 0.7475 (t0) REVERT: C 841 MET cc_start: 0.8592 (mmm) cc_final: 0.8308 (mtt) REVERT: C 984 MET cc_start: 0.8869 (mmm) cc_final: 0.8129 (mmm) REVERT: D 5 MET cc_start: 0.8549 (tpp) cc_final: 0.8314 (mmt) outliers start: 26 outliers final: 23 residues processed: 169 average time/residue: 0.1264 time to fit residues: 34.9699 Evaluate side-chains 169 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 0.640 ------------------------------------------------------------------------------- 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 414 GLN Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 769 VAL 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 142 ILE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 320 SER 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: 1.9990 chunk 59 optimal weight: 0.9990 chunk 149 optimal weight: 0.8980 chunk 202 optimal weight: 10.0000 chunk 173 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 chunk 62 optimal weight: 0.3980 chunk 98 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.112328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.074925 restraints weight = 130327.234| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 5.62 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3177 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3177 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19462 Z= 0.132 Angle : 0.584 8.722 26992 Z= 0.322 Chirality : 0.041 0.225 2953 Planarity : 0.004 0.060 2913 Dihedral : 21.476 80.431 3904 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.66 % Allowed : 15.50 % Favored : 82.84 % 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: 0.15 (0.19), residues: 1926 helix: 1.19 (0.20), residues: 656 sheet: 0.70 (0.29), residues: 332 loop : -0.91 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 442 TYR 0.017 0.001 TYR A 559 PHE 0.017 0.001 PHE A 743 TRP 0.022 0.001 TRP D 317 HIS 0.005 0.001 HIS A 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 (19454) covalent geometry : angle 0.58226 / 0.32 (26988) hydrogen bonds : bond 0.03764 / 2.53 ( 859) hydrogen bonds : angle 4.59086 / 3.35 ( 2333) metal coordination : bond 0.00707 / 0.34 ( 8) metal coordination : angle 3.37281 / 1.71 ( 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 178 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 151 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 806 LYS cc_start: 0.9013 (tppp) cc_final: 0.8669 (tppt) REVERT: B 52 GLN cc_start: 0.9005 (mp10) cc_final: 0.8731 (mp10) REVERT: B 55 LEU cc_start: 0.8451 (mm) cc_final: 0.8214 (mm) REVERT: B 142 ILE cc_start: 0.8874 (tt) cc_final: 0.8644 (tp) REVERT: B 152 MET cc_start: 0.8413 (ptm) cc_final: 0.7883 (ppp) REVERT: B 162 MET cc_start: 0.8786 (mmt) cc_final: 0.8542 (mmm) REVERT: B 287 CYS cc_start: 0.8823 (m) cc_final: 0.8506 (t) REVERT: C 627 MET cc_start: 0.8537 (mmm) cc_final: 0.8028 (tpp) REVERT: C 661 ASP cc_start: 0.7860 (t0) cc_final: 0.7442 (t0) REVERT: C 841 MET cc_start: 0.8579 (mmm) cc_final: 0.8336 (mtt) REVERT: C 984 MET cc_start: 0.8874 (mmm) cc_final: 0.8104 (mmm) REVERT: D 5 MET cc_start: 0.8561 (tpp) cc_final: 0.8324 (mmt) outliers start: 27 outliers final: 25 residues processed: 169 average time/residue: 0.1244 time to fit residues: 34.1264 Evaluate side-chains 171 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 146 time to evaluate : 0.709 ------------------------------------------------------------------------------- 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 285 MET Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain C residue 414 GLN Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 769 VAL 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 142 ILE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 287 CYS Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 320 SER 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: 3.9990 chunk 132 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 45 optimal weight: 0.0470 chunk 93 optimal weight: 0.9980 chunk 162 optimal weight: 5.9990 chunk 83 optimal weight: 10.0000 chunk 201 optimal weight: 50.0000 chunk 175 optimal weight: 4.9990 chunk 156 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 overall best weight: 2.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.110541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.072675 restraints weight = 160923.496| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 6.11 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3131 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3131 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 19462 Z= 0.181 Angle : 0.615 9.182 26992 Z= 0.336 Chirality : 0.042 0.246 2953 Planarity : 0.004 0.059 2913 Dihedral : 21.563 81.544 3904 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.54 % Allowed : 15.62 % Favored : 82.84 % 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: 0.11 (0.19), residues: 1926 helix: 1.17 (0.20), residues: 657 sheet: 0.51 (0.28), residues: 350 loop : -0.91 (0.20), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 442 TYR 0.020 0.002 TYR A 559 PHE 0.018 0.002 PHE A 743 TRP 0.020 0.002 TRP D 317 HIS 0.008 0.001 HIS A 937 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.18 (19454) covalent geometry : angle 0.61318 / 0.34 (26988) hydrogen bonds : bond 0.04199 / 2.82 ( 859) hydrogen bonds : angle 4.65349 / 3.40 ( 2333) metal coordination : bond 0.01263 / 0.64 ( 8) metal coordination : angle 3.53244 / 1.79 ( 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 171 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 146 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 446 ARG cc_start: 0.8919 (ttp-110) cc_final: 0.8659 (ttp80) REVERT: A 806 LYS cc_start: 0.8992 (tppp) cc_final: 0.8652 (tppt) REVERT: A 889 MET cc_start: 0.8248 (mmm) cc_final: 0.7633 (mmm) REVERT: B 52 GLN cc_start: 0.9022 (mp10) cc_final: 0.8752 (mp10) REVERT: B 142 ILE cc_start: 0.8881 (tt) cc_final: 0.8651 (tp) REVERT: B 162 MET cc_start: 0.8719 (mmt) cc_final: 0.8495 (mmm) REVERT: B 281 ASN cc_start: 0.9108 (p0) cc_final: 0.8877 (t0) REVERT: B 287 CYS cc_start: 0.8885 (m) cc_final: 0.8529 (t) REVERT: C 627 MET cc_start: 0.8651 (mmm) cc_final: 0.8108 (tpp) REVERT: C 661 ASP cc_start: 0.8025 (t0) cc_final: 0.7605 (t0) REVERT: C 841 MET cc_start: 0.8658 (mmm) cc_final: 0.8296 (mtt) REVERT: C 984 MET cc_start: 0.8975 (mmm) cc_final: 0.8597 (mmt) REVERT: D 5 MET cc_start: 0.8568 (tpp) cc_final: 0.8338 (mmt) outliers start: 25 outliers final: 23 residues processed: 162 average time/residue: 0.1239 time to fit residues: 32.6732 Evaluate side-chains 165 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 0.642 ------------------------------------------------------------------------------- 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 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 766 HIS Chi-restraints excluded: chain C residue 769 VAL 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 142 ILE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 287 CYS Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 320 SER 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: 0.0570 chunk 103 optimal weight: 0.0040 chunk 76 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 chunk 50 optimal weight: 0.7980 chunk 140 optimal weight: 6.9990 chunk 193 optimal weight: 40.0000 chunk 109 optimal weight: 5.9990 chunk 1 optimal weight: 0.0670 chunk 160 optimal weight: 3.9990 overall best weight: 0.7850 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.112071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.074518 restraints weight = 154069.086| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 6.03 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3169 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.3169 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19462 Z= 0.128 Angle : 0.603 11.586 26992 Z= 0.330 Chirality : 0.042 0.313 2953 Planarity : 0.004 0.058 2913 Dihedral : 21.500 82.138 3904 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.31 % Allowed : 16.45 % Favored : 82.24 % 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: 0.20 (0.19), residues: 1926 helix: 1.24 (0.21), residues: 655 sheet: 0.76 (0.29), residues: 332 loop : -0.90 (0.20), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG A 442 TYR 0.017 0.001 TYR A 559 PHE 0.015 0.001 PHE A 743 TRP 0.020 0.001 TRP D 317 HIS 0.006 0.001 HIS A 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.13 (19454) covalent geometry : angle 0.60165 / 0.33 (26988) hydrogen bonds : bond 0.03779 / 2.56 ( 859) hydrogen bonds : angle 4.61246 / 3.37 ( 2333) metal coordination : bond 0.00670 / 0.33 ( 8) metal coordination : angle 3.55931 / 1.80 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3984.43 seconds wall clock time: 69 minutes 20.47 seconds (4160.47 seconds total)