Starting phenix.real_space_refine on Thu Sep 18 18:29:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jtu_61817/09_2025/9jtu_61817.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jtu_61817/09_2025/9jtu_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_61817/09_2025/9jtu_61817.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jtu_61817/09_2025/9jtu_61817.map" model { file = "/net/cci-nas-00/data/ceres_data/9jtu_61817/09_2025/9jtu_61817.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jtu_61817/09_2025/9jtu_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-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18706 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4965 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 618, 4959 Classifications: {'peptide': 618} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 26, 'TRANS': 591} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Conformer: "B" Number of residues, atoms: 618, 4959 Classifications: {'peptide': 618} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 26, 'TRANS': 591} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 bond proxies already assigned to first conformer: 5055 Chain: "B" Number of atoms: 2704 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 344, 2683 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 19, 'TRANS': 324} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 344, 2683 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 19, 'TRANS': 324} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 2727 Chain: "C" Number of atoms: 5010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 5010 Classifications: {'peptide': 623} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 596} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 2673 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 343, 2663 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 19, 'TRANS': 323} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 343, 2663 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 19, 'TRANS': 323} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 2718 Chain: "G" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 795 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain: "L" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 607 Classifications: {'DNA': 30} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 29} Chain: "M" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 801 Classifications: {'DNA': 39} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 38} Chain: "F" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 617 Classifications: {'DNA': 30} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 29} Chain: "H" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 262 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "I" Number of atoms: 268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 268 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2632 SG CYS A 727 74.550 102.744 101.828 1.00 62.02 S ATOM 2653 SG CYS A 730 77.142 104.943 103.719 1.00 64.37 S ATOM 10356 SG CYS C 727 27.012 100.076 55.115 1.00 65.35 S ATOM 10377 SG CYS C 730 24.495 102.296 53.073 1.00 65.92 S Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" N ACYS A 907 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS A 907 " occ=0.50 residue: pdb=" N AHIS B 47 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS B 47 " occ=0.50 residue: pdb=" N AARG B 237 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG B 237 " occ=0.50 residue: pdb=" N AHIS D 47 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS D 47 " occ=0.50 residue: pdb=" P DT I 15 " occ=0.85 ... (18 atoms not shown) pdb=" C6 DT I 15 " occ=0.85 Time building chain proxies: 6.47, per 1000 atoms: 0.35 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: 2.04 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 2.48 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: 5.23 Time building geometry restraints manager: 2.54 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=" C LYS A 890 " pdb=" N PRO A 891 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.28e-02 6.10e+03 2.07e+00 bond pdb=" CA HIS A 406 " pdb=" C HIS A 406 " ideal model delta sigma weight residual 1.522 1.537 -0.015 1.37e-02 5.33e+03 1.14e+00 bond pdb=" CG GLN C 414 " pdb=" CD GLN C 414 " ideal model delta sigma weight residual 1.516 1.491 0.025 2.50e-02 1.60e+03 1.01e+00 bond pdb=" SD MET C 883 " pdb=" CE MET C 883 " ideal model delta sigma weight residual 1.791 1.767 0.024 2.50e-02 1.60e+03 9.47e-01 bond pdb=" C4' DG F 30 " pdb=" O4' DG F 30 " ideal model delta sigma weight residual 1.450 1.431 0.019 2.00e-02 2.50e+03 9.37e-01 ... (remaining 19449 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 26752 2.45 - 4.90: 219 4.90 - 7.35: 13 7.35 - 9.80: 3 9.80 - 12.25: 1 Bond angle restraints: 26988 Sorted by residual: angle pdb=" C LEU A 567 " pdb=" N MET A 568 " pdb=" CA MET A 568 " ideal model delta sigma weight residual 122.38 114.75 7.63 1.81e+00 3.05e-01 1.78e+01 angle pdb=" CB MET C 858 " pdb=" CG MET C 858 " pdb=" SD MET C 858 " ideal model delta sigma weight residual 112.70 124.95 -12.25 3.00e+00 1.11e-01 1.67e+01 angle pdb=" CG ARG A 407 " pdb=" CD ARG A 407 " pdb=" NE ARG A 407 " ideal model delta sigma weight residual 112.00 120.87 -8.87 2.20e+00 2.07e-01 1.63e+01 angle pdb=" C ILE C 413 " pdb=" N GLN C 414 " pdb=" CA GLN C 414 " ideal model delta sigma weight residual 120.68 115.39 5.29 1.70e+00 3.46e-01 9.68e+00 angle pdb=" CA ARG A 407 " pdb=" CB ARG A 407 " pdb=" CG ARG A 407 " ideal model delta sigma weight residual 114.10 120.04 -5.94 2.00e+00 2.50e-01 8.81e+00 ... (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: 2116 0.036 - 0.071: 591 0.071 - 0.107: 186 0.107 - 0.143: 56 0.143 - 0.178: 4 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=" CA MET A 568 " pdb=" N MET A 568 " pdb=" C MET A 568 " pdb=" CB MET A 568 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.74e-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: 0.010 Normalize map: mean=0, sd=1: 1.260 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 27.120 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19462 Z= 0.135 Angle : 0.577 12.247 26992 Z= 0.316 Chirality : 0.039 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 aren 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 covalent geometry : bond 0.00291 (19454) covalent geometry : angle 0.57469 (26988) hydrogen bonds : bond 0.15482 ( 859) hydrogen bonds : angle 6.46814 ( 2333) metal coordination : bond 0.00690 ( 8) metal coordination : angle 4.08601 ( 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 : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 915 ARG cc_start: 0.7858 (tpm170) cc_final: 0.7287 (tpt170) REVERT: B 234 TYR cc_start: 0.7756 (m-80) cc_final: 0.7484 (m-80) REVERT: B 294 ASP cc_start: 0.6834 (t70) cc_final: 0.6634 (t0) REVERT: B 302 MET cc_start: 0.7645 (ppp) cc_final: 0.7324 (ppp) REVERT: C 602 MET cc_start: 0.8776 (mtp) cc_final: 0.8486 (mtm) REVERT: C 661 ASP cc_start: 0.8372 (t0) cc_final: 0.7710 (t0) REVERT: C 886 TYR cc_start: 0.8239 (t80) cc_final: 0.8036 (t80) REVERT: D 344 TYR cc_start: 0.7537 (m-10) cc_final: 0.7285 (m-10) outliers start: 0 outliers final: 0 residues processed: 388 average time/residue: 0.1529 time to fit residues: 90.6650 Evaluate side-chains 185 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.687 ------------------------------------------------------------------------------- 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: 4.9990 chunk 107 optimal weight: 1.9990 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: 20.0000 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3921 r_free = 0.3921 target = 0.113426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.076287 restraints weight = 142201.418| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 5.78 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3199 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3199 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 19462 Z= 0.174 Angle : 0.665 12.465 26992 Z= 0.357 Chirality : 0.042 0.186 2953 Planarity : 0.005 0.083 2913 Dihedral : 20.953 81.033 3904 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.19 % Allowed : 10.93 % Favored : 87.89 % 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 aren not related in a simple way. whole: -0.01 (0.19), residues: 1926 helix: 1.02 (0.20), residues: 660 sheet: 0.76 (0.29), residues: 350 loop : -1.09 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 73 TYR 0.017 0.002 TYR A 559 PHE 0.025 0.002 PHE B 24 TRP 0.013 0.002 TRP A 760 HIS 0.008 0.001 HIS A 515 Details of bonding type rmsd covalent geometry : bond 0.00399 (19454) covalent geometry : angle 0.66309 (26988) hydrogen bonds : bond 0.04606 ( 859) hydrogen bonds : angle 5.14279 ( 2333) metal coordination : bond 0.00765 ( 8) metal coordination : angle 3.63908 ( 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 216 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 197 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 435 PHE cc_start: 0.8845 (t80) cc_final: 0.8301 (t80) REVERT: A 442 ARG cc_start: 0.9336 (tpm170) cc_final: 0.9131 (mtm-85) REVERT: A 455 MET cc_start: 0.7594 (mmp) cc_final: 0.7359 (mmp) REVERT: B 52 GLN cc_start: 0.8854 (mp10) cc_final: 0.8560 (mp10) REVERT: B 294 ASP cc_start: 0.8635 (t70) cc_final: 0.8168 (t0) REVERT: B 339 MET cc_start: 0.8106 (mmm) cc_final: 0.7603 (mmm) REVERT: C 602 MET cc_start: 0.8968 (mtp) cc_final: 0.8764 (mtp) REVERT: C 661 ASP cc_start: 0.8091 (t0) cc_final: 0.7649 (t0) REVERT: D 21 LEU cc_start: 0.9120 (mp) cc_final: 0.8823 (mm) outliers start: 19 outliers final: 11 residues processed: 208 average time/residue: 0.1348 time to fit residues: 45.0270 Evaluate side-chains 174 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 163 time to evaluate : 0.747 ------------------------------------------------------------------------------- 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 55 LEU Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain C residue 862 THR Chi-restraints excluded: chain D residue 55 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 142 optimal weight: 5.9990 chunk 175 optimal weight: 10.0000 chunk 86 optimal weight: 6.9990 chunk 130 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 203 optimal weight: 7.9990 chunk 117 optimal weight: 2.9990 chunk 48 optimal weight: 0.3980 chunk 94 optimal weight: 0.1980 chunk 199 optimal weight: 20.0000 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** C1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.113588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.076630 restraints weight = 120906.242| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 5.36 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3207 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3207 r_free = 0.3207 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3206 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 19462 Z= 0.143 Angle : 0.606 9.575 26992 Z= 0.325 Chirality : 0.040 0.204 2953 Planarity : 0.004 0.072 2913 Dihedral : 20.970 78.396 3904 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.48 % Allowed : 11.94 % Favored : 86.58 % 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 aren not related in a simple way. whole: 0.05 (0.19), residues: 1926 helix: 1.08 (0.20), residues: 656 sheet: 0.68 (0.28), residues: 355 loop : -1.01 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 349 TYR 0.027 0.002 TYR B 234 PHE 0.017 0.002 PHE D 29 TRP 0.015 0.002 TRP C 893 HIS 0.017 0.001 HIS A 515 Details of bonding type rmsd covalent geometry : bond 0.00326 (19454) covalent geometry : angle 0.60460 (26988) hydrogen bonds : bond 0.03963 ( 859) hydrogen bonds : angle 4.82614 ( 2333) metal coordination : bond 0.00611 ( 8) metal coordination : angle 3.73974 ( 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 200 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 176 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 435 PHE cc_start: 0.8764 (t80) cc_final: 0.8470 (t80) REVERT: A 442 ARG cc_start: 0.9328 (tpm170) cc_final: 0.9093 (mtm-85) REVERT: A 556 ARG cc_start: 0.8521 (ttp80) cc_final: 0.8039 (ptm-80) REVERT: A 806 LYS cc_start: 0.9054 (tppp) cc_final: 0.8629 (tptp) REVERT: A 842 ASN cc_start: 0.7406 (OUTLIER) cc_final: 0.7044 (t0) REVERT: A 868 GLU cc_start: 0.9040 (tp30) cc_final: 0.8573 (tm-30) REVERT: A 974 MET cc_start: 0.8000 (mtm) cc_final: 0.7759 (mtt) REVERT: B 55 LEU cc_start: 0.8682 (mm) cc_final: 0.8452 (mm) REVERT: B 162 MET cc_start: 0.8762 (mmp) cc_final: 0.8486 (mmm) REVERT: B 287 CYS cc_start: 0.8646 (m) cc_final: 0.8348 (t) REVERT: B 339 MET cc_start: 0.7997 (mmm) cc_final: 0.7737 (mmm) REVERT: C 627 MET cc_start: 0.8556 (mmm) cc_final: 0.8351 (tpp) REVERT: C 661 ASP cc_start: 0.7962 (t0) cc_final: 0.7536 (t0) REVERT: C 984 MET cc_start: 0.8734 (mmt) cc_final: 0.8358 (mmm) REVERT: D 23 ASN cc_start: 0.8433 (OUTLIER) cc_final: 0.8232 (m110) outliers start: 24 outliers final: 16 residues processed: 194 average time/residue: 0.1217 time to fit residues: 38.1979 Evaluate side-chains 177 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 HIS Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 842 ASN Chi-restraints excluded: chain A residue 862 THR Chi-restraints excluded: chain A residue 897 CYS Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain C residue 780 SER Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain D residue 23 ASN Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 349 ARG 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: 30.0000 chunk 107 optimal weight: 0.1980 chunk 54 optimal weight: 5.9990 chunk 92 optimal weight: 0.4980 chunk 48 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 148 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 133 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 95 optimal weight: 50.0000 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** C1000 GLN ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.113839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.076403 restraints weight = 155593.541| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 6.05 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3205 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3205 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19462 Z= 0.130 Angle : 0.583 8.441 26992 Z= 0.314 Chirality : 0.040 0.237 2953 Planarity : 0.004 0.068 2913 Dihedral : 20.972 76.207 3904 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.31 % Allowed : 13.18 % 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 aren not related in a simple way. whole: 0.04 (0.19), residues: 1926 helix: 1.08 (0.20), residues: 662 sheet: 0.73 (0.28), residues: 344 loop : -1.04 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 828 TYR 0.023 0.001 TYR B 234 PHE 0.027 0.001 PHE A 743 TRP 0.013 0.001 TRP D 317 HIS 0.017 0.001 HIS A 515 Details of bonding type rmsd covalent geometry : bond 0.00295 (19454) covalent geometry : angle 0.58163 (26988) hydrogen bonds : bond 0.03732 ( 859) hydrogen bonds : angle 4.68383 ( 2333) metal coordination : bond 0.00551 ( 8) metal coordination : angle 3.48481 ( 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 187 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 166 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 556 ARG cc_start: 0.8506 (ttp80) cc_final: 0.7936 (ptm-80) REVERT: A 806 LYS cc_start: 0.9066 (tppp) cc_final: 0.8610 (tptp) REVERT: B 162 MET cc_start: 0.8717 (mmp) cc_final: 0.8464 (mmm) REVERT: B 287 CYS cc_start: 0.8713 (m) cc_final: 0.8386 (t) REVERT: B 339 MET cc_start: 0.8137 (mmm) cc_final: 0.7820 (mmm) REVERT: C 627 MET cc_start: 0.8522 (mmm) cc_final: 0.8318 (tpp) REVERT: C 661 ASP cc_start: 0.7869 (t0) cc_final: 0.7415 (t0) REVERT: C 984 MET cc_start: 0.8740 (mmt) cc_final: 0.8321 (mmt) REVERT: D 21 LEU cc_start: 0.9135 (mp) cc_final: 0.8802 (mm) outliers start: 21 outliers final: 18 residues processed: 181 average time/residue: 0.1212 time to fit residues: 35.6825 Evaluate side-chains 169 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 151 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 HIS Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 897 CYS Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain C residue 780 SER Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain D residue 55 LEU 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 350 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 170 optimal weight: 6.9990 chunk 147 optimal weight: 0.9990 chunk 189 optimal weight: 0.3980 chunk 3 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 101 optimal weight: 8.9990 chunk 190 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 753 ASN B 173 ASN ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.112890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.075781 restraints weight = 122239.743| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 5.37 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3192 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3192 r_free = 0.3192 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3192 r_free = 0.3192 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3192 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19462 Z= 0.140 Angle : 0.579 10.993 26992 Z= 0.311 Chirality : 0.040 0.170 2953 Planarity : 0.004 0.064 2913 Dihedral : 21.034 76.864 3904 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.90 % Allowed : 13.90 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.19), residues: 1926 helix: 1.19 (0.21), residues: 665 sheet: 0.71 (0.29), residues: 330 loop : -0.96 (0.20), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG A 442 TYR 0.017 0.001 TYR A 559 PHE 0.023 0.001 PHE A 743 TRP 0.011 0.001 TRP C 893 HIS 0.026 0.001 HIS A 515 Details of bonding type rmsd covalent geometry : bond 0.00319 (19454) covalent geometry : angle 0.57729 (26988) hydrogen bonds : bond 0.03707 ( 859) hydrogen bonds : angle 4.55085 ( 2333) metal coordination : bond 0.00810 ( 8) metal coordination : angle 3.38391 ( 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 188 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 157 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 435 PHE cc_start: 0.8556 (t80) cc_final: 0.8338 (t80) REVERT: A 442 ARG cc_start: 0.9309 (mmm160) cc_final: 0.9056 (mtm180) REVERT: A 806 LYS cc_start: 0.9024 (tppp) cc_final: 0.8603 (tptp) REVERT: B 162 MET cc_start: 0.8745 (mmt) cc_final: 0.8506 (mmm) REVERT: B 287 CYS cc_start: 0.8761 (m) cc_final: 0.8517 (t) REVERT: C 661 ASP cc_start: 0.7939 (t0) cc_final: 0.7538 (t0) REVERT: C 984 MET cc_start: 0.8836 (mmt) cc_final: 0.8523 (mmm) REVERT: D 5 MET cc_start: 0.8608 (tpp) cc_final: 0.8184 (tpp) REVERT: D 317 TRP cc_start: 0.8144 (p90) cc_final: 0.7725 (p90) REVERT: D 349 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.8101 (ttt-90) outliers start: 31 outliers final: 23 residues processed: 178 average time/residue: 0.1338 time to fit residues: 38.6251 Evaluate side-chains 170 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 0.658 ------------------------------------------------------------------------------- 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 862 THR Chi-restraints excluded: chain A residue 897 CYS Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain 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 780 SER Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain C residue 837 LEU Chi-restraints excluded: chain C residue 952 SER Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 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 349 ARG Chi-restraints excluded: chain D residue 350 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 64 optimal weight: 0.3980 chunk 45 optimal weight: 7.9990 chunk 111 optimal weight: 0.1980 chunk 200 optimal weight: 20.0000 chunk 160 optimal weight: 1.9990 chunk 203 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 168 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3916 r_free = 0.3916 target = 0.112983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.075906 restraints weight = 129468.746| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 5.52 r_work (final): 0.3197 ------------------------------------------------------------------------------- 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 = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3196 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19462 Z= 0.132 Angle : 0.565 10.366 26992 Z= 0.304 Chirality : 0.039 0.193 2953 Planarity : 0.004 0.061 2913 Dihedral : 21.078 80.370 3904 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.54 % Allowed : 14.96 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.19), residues: 1926 helix: 1.22 (0.21), residues: 663 sheet: 0.69 (0.29), residues: 339 loop : -0.94 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 442 TYR 0.016 0.001 TYR A 559 PHE 0.020 0.001 PHE A 743 TRP 0.011 0.001 TRP C 893 HIS 0.004 0.001 HIS A 937 Details of bonding type rmsd covalent geometry : bond 0.00299 (19454) covalent geometry : angle 0.56363 (26988) hydrogen bonds : bond 0.03505 ( 859) hydrogen bonds : angle 4.51703 ( 2333) metal coordination : bond 0.00670 ( 8) metal coordination : angle 3.14883 ( 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: 25 poor density : 152 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 617 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8350 (mt-10) REVERT: A 806 LYS cc_start: 0.9012 (tppp) cc_final: 0.8654 (tppt) REVERT: A 974 MET cc_start: 0.8068 (mtp) cc_final: 0.7670 (mtt) REVERT: B 152 MET cc_start: 0.8453 (ptm) cc_final: 0.8064 (ppp) REVERT: B 162 MET cc_start: 0.8725 (mmt) cc_final: 0.8510 (mmm) REVERT: B 287 CYS cc_start: 0.8737 (m) cc_final: 0.8511 (t) REVERT: C 661 ASP cc_start: 0.7872 (t0) cc_final: 0.7441 (t0) REVERT: C 818 HIS cc_start: 0.9080 (m90) cc_final: 0.8688 (m90) REVERT: C 841 MET cc_start: 0.8521 (mmm) cc_final: 0.8191 (mtt) REVERT: C 984 MET cc_start: 0.8829 (mmt) cc_final: 0.8495 (mmm) REVERT: D 5 MET cc_start: 0.8587 (tpp) cc_final: 0.8082 (tpp) REVERT: D 317 TRP cc_start: 0.8105 (p90) cc_final: 0.7822 (p90) REVERT: D 349 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.8056 (ttt-90) outliers start: 25 outliers final: 21 residues processed: 168 average time/residue: 0.1184 time to fit residues: 32.8782 Evaluate side-chains 169 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 478 CYS 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 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 787 THR Chi-restraints excluded: chain C residue 837 LEU Chi-restraints excluded: chain C residue 952 SER Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 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 349 ARG Chi-restraints excluded: chain D residue 350 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 43 optimal weight: 6.9990 chunk 141 optimal weight: 0.6980 chunk 148 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 150 optimal weight: 0.3980 chunk 57 optimal weight: 0.6980 chunk 10 optimal weight: 7.9990 chunk 197 optimal weight: 3.9990 chunk 125 optimal weight: 0.6980 chunk 113 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 809 GLN ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** 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 = 0.3926 r_free = 0.3926 target = 0.113572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.076633 restraints weight = 125375.858| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 5.58 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3215 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3215 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19462 Z= 0.119 Angle : 0.561 8.505 26992 Z= 0.301 Chirality : 0.039 0.196 2953 Planarity : 0.004 0.060 2913 Dihedral : 21.096 81.768 3904 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.48 % Allowed : 15.38 % Favored : 83.14 % 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 aren not related in a simple way. whole: 0.26 (0.19), residues: 1926 helix: 1.27 (0.21), residues: 656 sheet: 0.76 (0.29), residues: 328 loop : -0.84 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 442 TYR 0.023 0.001 TYR D 234 PHE 0.019 0.001 PHE A 743 TRP 0.012 0.001 TRP B 317 HIS 0.008 0.001 HIS A 515 Details of bonding type rmsd covalent geometry : bond 0.00267 (19454) covalent geometry : angle 0.56005 (26988) hydrogen bonds : bond 0.03385 ( 859) hydrogen bonds : angle 4.44632 ( 2333) metal coordination : bond 0.00577 ( 8) metal coordination : angle 3.05558 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 156 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 435 PHE cc_start: 0.8646 (t80) cc_final: 0.8194 (t80) REVERT: A 442 ARG cc_start: 0.9311 (mmm160) cc_final: 0.9053 (mtm180) REVERT: A 617 GLU cc_start: 0.8559 (mt-10) cc_final: 0.8346 (mt-10) REVERT: A 806 LYS cc_start: 0.8981 (tppp) cc_final: 0.8644 (tppt) REVERT: A 974 MET cc_start: 0.8010 (mtp) cc_final: 0.7608 (mtt) REVERT: A 984 MET cc_start: 0.8358 (mmm) cc_final: 0.8116 (tpt) REVERT: B 152 MET cc_start: 0.8475 (ptm) cc_final: 0.7945 (ppp) REVERT: B 287 CYS cc_start: 0.8680 (m) cc_final: 0.8443 (t) REVERT: C 570 MET cc_start: 0.9231 (ptp) cc_final: 0.9019 (ptp) REVERT: C 661 ASP cc_start: 0.7822 (t0) cc_final: 0.7457 (t0) REVERT: C 841 MET cc_start: 0.8498 (mmm) cc_final: 0.8278 (mtt) REVERT: C 847 MET cc_start: 0.8464 (pmm) cc_final: 0.7974 (ptm) REVERT: C 984 MET cc_start: 0.8779 (mmt) cc_final: 0.8411 (mmm) REVERT: D 114 CYS cc_start: 0.8864 (t) cc_final: 0.8082 (p) REVERT: D 317 TRP cc_start: 0.8097 (p90) cc_final: 0.7777 (p90) REVERT: D 349 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.8120 (ptm-80) outliers start: 24 outliers final: 20 residues processed: 169 average time/residue: 0.1153 time to fit residues: 31.9443 Evaluate side-chains 170 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 478 CYS 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 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 787 THR Chi-restraints excluded: chain C residue 837 LEU Chi-restraints excluded: chain C residue 952 SER Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 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 349 ARG Chi-restraints excluded: chain D residue 350 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 0 optimal weight: 50.0000 chunk 175 optimal weight: 7.9990 chunk 179 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 186 optimal weight: 5.9990 chunk 164 optimal weight: 2.9990 chunk 74 optimal weight: 0.0070 chunk 123 optimal weight: 0.9980 chunk 176 optimal weight: 7.9990 chunk 82 optimal weight: 10.0000 chunk 119 optimal weight: 3.9990 overall best weight: 1.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 809 GLN ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** 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 = 0.3893 r_free = 0.3893 target = 0.111468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.074230 restraints weight = 131091.359| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 5.62 r_work (final): 0.3162 ------------------------------------------------------------------------------- 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 = 0.11 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 = 0.09 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3164 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19462 Z= 0.162 Angle : 0.596 14.921 26992 Z= 0.316 Chirality : 0.040 0.211 2953 Planarity : 0.004 0.058 2913 Dihedral : 21.183 82.009 3904 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.48 % Allowed : 15.62 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.19), residues: 1926 helix: 1.30 (0.21), residues: 656 sheet: 0.75 (0.29), residues: 338 loop : -0.83 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 446 TYR 0.014 0.001 TYR A 559 PHE 0.018 0.001 PHE A 743 TRP 0.012 0.001 TRP B 317 HIS 0.009 0.001 HIS A 515 Details of bonding type rmsd covalent geometry : bond 0.00371 (19454) covalent geometry : angle 0.59461 (26988) hydrogen bonds : bond 0.03846 ( 859) hydrogen bonds : angle 4.48148 ( 2333) metal coordination : bond 0.01131 ( 8) metal coordination : angle 3.19787 ( 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 164 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 446 ARG cc_start: 0.8960 (ttp80) cc_final: 0.8556 (ttp80) REVERT: A 617 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8363 (mt-10) REVERT: A 806 LYS cc_start: 0.9004 (tppp) cc_final: 0.8654 (tppt) REVERT: A 889 MET cc_start: 0.8397 (mmm) cc_final: 0.7782 (mmm) REVERT: A 974 MET cc_start: 0.8011 (mtp) cc_final: 0.7576 (mtt) REVERT: B 152 MET cc_start: 0.8520 (ptm) cc_final: 0.7948 (ppp) REVERT: B 162 MET cc_start: 0.8607 (mmm) cc_final: 0.8333 (mmp) REVERT: B 287 CYS cc_start: 0.8723 (m) cc_final: 0.8407 (t) REVERT: C 627 MET cc_start: 0.8620 (mmm) cc_final: 0.8112 (tpp) REVERT: C 661 ASP cc_start: 0.7961 (t0) cc_final: 0.7580 (t0) REVERT: C 841 MET cc_start: 0.8592 (mmm) cc_final: 0.8284 (mtt) REVERT: C 984 MET cc_start: 0.8918 (mmt) cc_final: 0.8578 (mmm) REVERT: D 5 MET cc_start: 0.8548 (tpp) cc_final: 0.8155 (tpp) REVERT: D 349 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.8064 (ttt-90) outliers start: 24 outliers final: 19 residues processed: 156 average time/residue: 0.1167 time to fit residues: 29.8815 Evaluate side-chains 158 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 478 CYS 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 414 GLN Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain C residue 837 LEU Chi-restraints excluded: chain C residue 952 SER Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 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 349 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 180 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 chunk 202 optimal weight: 5.9990 chunk 173 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 98 optimal weight: 10.0000 chunk 19 optimal weight: 0.5980 chunk 4 optimal weight: 10.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 912 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.111477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.074006 restraints weight = 131322.178| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 5.64 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3157 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3157 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19462 Z= 0.157 Angle : 0.595 15.461 26992 Z= 0.316 Chirality : 0.040 0.278 2953 Planarity : 0.004 0.057 2913 Dihedral : 21.202 81.510 3904 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.60 % Allowed : 15.86 % Favored : 82.54 % 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 aren not related in a simple way. whole: 0.32 (0.19), residues: 1926 helix: 1.31 (0.21), residues: 658 sheet: 0.78 (0.29), residues: 343 loop : -0.81 (0.20), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 442 TYR 0.020 0.001 TYR D 234 PHE 0.017 0.001 PHE A 743 TRP 0.017 0.001 TRP D 317 HIS 0.008 0.001 HIS A 515 Details of bonding type rmsd covalent geometry : bond 0.00359 (19454) covalent geometry : angle 0.59335 (26988) hydrogen bonds : bond 0.03678 ( 859) hydrogen bonds : angle 4.47915 ( 2333) metal coordination : bond 0.00907 ( 8) metal coordination : angle 3.33693 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 0.527 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: 0.8664 (tppt) REVERT: A 889 MET cc_start: 0.8360 (mmm) cc_final: 0.7688 (mmm) REVERT: A 974 MET cc_start: 0.8084 (mtp) cc_final: 0.7623 (mtt) REVERT: B 162 MET cc_start: 0.8572 (mmm) cc_final: 0.8323 (mmp) REVERT: B 287 CYS cc_start: 0.8733 (m) cc_final: 0.8425 (t) REVERT: C 576 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.7866 (pp20) REVERT: C 627 MET cc_start: 0.8662 (mmm) cc_final: 0.8132 (tpp) REVERT: C 661 ASP cc_start: 0.8037 (t0) cc_final: 0.7674 (t0) REVERT: C 841 MET cc_start: 0.8636 (mmm) cc_final: 0.8343 (mtt) REVERT: C 984 MET cc_start: 0.8904 (mmt) cc_final: 0.8570 (mmm) REVERT: D 5 MET cc_start: 0.8516 (tpp) cc_final: 0.8131 (tpp) outliers start: 26 outliers final: 19 residues processed: 155 average time/residue: 0.1223 time to fit residues: 30.9215 Evaluate side-chains 155 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 478 CYS 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 289 LEU Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain C residue 414 GLN Chi-restraints excluded: chain C residue 576 GLU Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain C residue 837 LEU Chi-restraints excluded: chain C residue 952 SER Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 30 optimal weight: 7.9990 chunk 132 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 93 optimal weight: 6.9990 chunk 162 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 201 optimal weight: 10.0000 chunk 175 optimal weight: 9.9990 chunk 156 optimal weight: 0.6980 chunk 3 optimal weight: 20.0000 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 609 HIS ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 744 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 753 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 = 0.3855 r_free = 0.3855 target = 0.109011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.071145 restraints weight = 159800.468| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 6.03 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3098 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3098 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 19462 Z= 0.223 Angle : 0.651 15.464 26992 Z= 0.343 Chirality : 0.042 0.270 2953 Planarity : 0.004 0.057 2913 Dihedral : 21.381 79.904 3904 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.54 % Allowed : 16.03 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.19), residues: 1926 helix: 1.25 (0.20), residues: 655 sheet: 0.61 (0.29), residues: 348 loop : -0.84 (0.20), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 442 TYR 0.016 0.002 TYR A 559 PHE 0.020 0.002 PHE A 916 TRP 0.013 0.002 TRP B 317 HIS 0.008 0.001 HIS A 515 Details of bonding type rmsd covalent geometry : bond 0.00510 (19454) covalent geometry : angle 0.64959 (26988) hydrogen bonds : bond 0.04369 ( 859) hydrogen bonds : angle 4.62151 ( 2333) metal coordination : bond 0.01629 ( 8) metal coordination : angle 3.81684 ( 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 161 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 136 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 806 LYS cc_start: 0.9028 (tppp) cc_final: 0.8676 (tppt) REVERT: A 889 MET cc_start: 0.8311 (mmm) cc_final: 0.7604 (mmm) REVERT: A 974 MET cc_start: 0.8140 (mtp) cc_final: 0.7745 (mtt) REVERT: B 152 MET cc_start: 0.8493 (ptm) cc_final: 0.8167 (ppp) REVERT: B 162 MET cc_start: 0.8660 (mmm) cc_final: 0.8383 (mmp) REVERT: B 287 CYS cc_start: 0.8838 (m) cc_final: 0.8511 (t) REVERT: C 576 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.7863 (pp20) REVERT: C 604 ASP cc_start: 0.9095 (m-30) cc_final: 0.8796 (t70) REVERT: C 627 MET cc_start: 0.8697 (mmm) cc_final: 0.8156 (tpp) REVERT: C 661 ASP cc_start: 0.8350 (t0) cc_final: 0.7962 (t0) REVERT: C 887 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8915 (mm) REVERT: C 984 MET cc_start: 0.9035 (mmt) cc_final: 0.8689 (mmt) outliers start: 25 outliers final: 22 residues processed: 153 average time/residue: 0.1062 time to fit residues: 26.5131 Evaluate side-chains 156 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 576 GLU Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 672 LEU 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 887 LEU Chi-restraints excluded: chain C residue 952 SER Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 191 optimal weight: 30.0000 chunk 46 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 50 optimal weight: 0.1980 chunk 140 optimal weight: 3.9990 chunk 193 optimal weight: 10.0000 chunk 109 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 160 optimal weight: 2.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 744 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** 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 = 0.3865 r_free = 0.3865 target = 0.109659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.071790 restraints weight = 155204.881| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 6.01 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3114 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3114 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19462 Z= 0.185 Angle : 0.626 15.406 26992 Z= 0.331 Chirality : 0.041 0.254 2953 Planarity : 0.004 0.056 2913 Dihedral : 21.354 80.179 3904 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.54 % Allowed : 16.39 % Favored : 82.07 % 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 aren not related in a simple way. whole: 0.19 (0.19), residues: 1926 helix: 1.27 (0.20), residues: 654 sheet: 0.56 (0.28), residues: 357 loop : -0.88 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 442 TYR 0.022 0.002 TYR D 234 PHE 0.018 0.002 PHE A 698 TRP 0.014 0.002 TRP B 317 HIS 0.008 0.001 HIS A 515 Details of bonding type rmsd covalent geometry : bond 0.00423 (19454) covalent geometry : angle 0.62472 (26988) hydrogen bonds : bond 0.03999 ( 859) hydrogen bonds : angle 4.58599 ( 2333) metal coordination : bond 0.01137 ( 8) metal coordination : angle 3.73080 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3994.26 seconds wall clock time: 69 minutes 29.03 seconds (4169.03 seconds total)