Starting phenix.real_space_refine on Sun Aug 24 15:11:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ss3_40742/08_2025/8ss3_40742.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ss3_40742/08_2025/8ss3_40742.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ss3_40742/08_2025/8ss3_40742.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ss3_40742/08_2025/8ss3_40742.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ss3_40742/08_2025/8ss3_40742.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ss3_40742/08_2025/8ss3_40742.map" } resolution = 3.21 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= 0.049 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: 6 Type Number sf(0) Gaussians P 30 5.49 5 S 130 5.16 5 C 13297 2.51 5 N 2919 2.21 5 O 3499 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19887 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4671 Classifications: {'peptide': 596} Link IDs: {'PCIS': 3, 'PTRANS': 14, 'TRANS': 578} Chain breaks: 4 Chain: "B" Number of atoms: 3156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3156 Classifications: {'peptide': 404} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 390} Chain breaks: 2 Chain: "C" Number of atoms: 4671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4671 Classifications: {'peptide': 596} Link IDs: {'PCIS': 3, 'PTRANS': 14, 'TRANS': 578} Chain breaks: 4 Chain: "D" Number of atoms: 3156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3156 Classifications: {'peptide': 404} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 390} Chain breaks: 2 Chain: "E" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1166 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain breaks: 1 Chain: "F" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1166 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain breaks: 1 Chain: "A" Number of atoms: 613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 613 Unusual residues: {'AJP': 3, 'CLR': 2, 'PCW': 12, 'SPD': 1, 'ZK1': 1} Classifications: {'undetermined': 19} Link IDs: {None: 18} Unresolved non-hydrogen bonds: 395 Unresolved non-hydrogen angles: 512 Unresolved non-hydrogen dihedrals: 543 Unresolved non-hydrogen chiralities: 65 Planarities with less than four sites: {'PCW:plan-2': 2, 'PCW:plan-1': 5, 'PCW:plan-3': 5, 'PCW:plan-4': 5} Unresolved non-hydrogen planarities: 63 Chain: "B" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 358 Unusual residues: {'PCW': 10, 'ZK1': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 209 Unresolved non-hydrogen angles: 236 Unresolved non-hydrogen dihedrals: 197 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PCW:plan-1': 3, 'PCW:plan-3': 3, 'PCW:plan-4': 4, 'PCW:plan-2': 3} Unresolved non-hydrogen planarities: 47 Chain: "C" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 449 Unusual residues: {'AJP': 3, 'CLR': 2, 'PCW': 9, 'ZK1': 1} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 387 Unresolved non-hydrogen angles: 505 Unresolved non-hydrogen dihedrals: 538 Unresolved non-hydrogen chiralities: 66 Planarities with less than four sites: {'PCW:plan-2': 2, 'PCW:plan-1': 5, 'PCW:plan-3': 5, 'PCW:plan-4': 5} Unresolved non-hydrogen planarities: 63 Chain: "D" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 307 Unusual residues: {'PCW': 9, 'ZK1': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 206 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 194 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PCW:plan-1': 3, 'PCW:plan-3': 3, 'PCW:plan-4': 4, 'PCW:plan-2': 3} Unresolved non-hydrogen planarities: 47 Chain: "E" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 87 Unusual residues: {'PCW': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 183 Unresolved non-hydrogen angles: 219 Unresolved non-hydrogen dihedrals: 167 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PCW:plan-1': 4, 'PCW:plan-3': 4, 'PCW:plan-4': 4, 'PCW:plan-2': 1} Unresolved non-hydrogen planarities: 49 Chain: "F" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 87 Unusual residues: {'PCW': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 183 Unresolved non-hydrogen angles: 219 Unresolved non-hydrogen dihedrals: 167 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PCW:plan-1': 4, 'PCW:plan-3': 4, 'PCW:plan-4': 4, 'PCW:plan-2': 1} Unresolved non-hydrogen planarities: 49 Time building chain proxies: 4.74, per 1000 atoms: 0.24 Number of scatterers: 19887 At special positions: 0 Unit cell: (118.69, 130.31, 138.61, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 130 16.00 P 30 15.00 F 12 9.00 O 3499 8.00 N 2919 7.00 C 13297 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.02 Simple disulfide: pdb=" SG CYS A 890 " - pdb=" SG CYS A 900 " distance=2.04 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.01 Simple disulfide: pdb=" SG CYS C 890 " - pdb=" SG CYS C 900 " distance=2.04 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.81 Conformation dependent library (CDL) restraints added in 851.0 milliseconds Enol-peptide restraints added in 1.4 microseconds 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4208 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 24 sheets defined 57.4% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 416 through 419 removed outlier: 3.980A pdb=" N GLU A 419 " --> pdb=" O GLU A 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 416 through 419' Processing helix chain 'A' and resid 423 through 435 Processing helix chain 'A' and resid 462 through 469 Processing helix chain 'A' and resid 482 through 487 removed outlier: 3.534A pdb=" N GLU A 487 " --> pdb=" O LEU A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 543 removed outlier: 3.831A pdb=" N VAL A 530 " --> pdb=" O TRP A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 585 removed outlier: 3.631A pdb=" N SER A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU A 581 " --> pdb=" O LEU A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 630 removed outlier: 3.862A pdb=" N VAL A 601 " --> pdb=" O SER A 597 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 626 " --> pdb=" O ALA A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 642 Processing helix chain 'A' and resid 653 through 661 removed outlier: 3.588A pdb=" N PHE A 659 " --> pdb=" O THR A 655 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG A 661 " --> pdb=" O GLU A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 676 removed outlier: 3.829A pdb=" N SER A 676 " --> pdb=" O THR A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 696 Processing helix chain 'A' and resid 706 through 714 Processing helix chain 'A' and resid 740 through 742 No H-bonds generated for 'chain 'A' and resid 740 through 742' Processing helix chain 'A' and resid 743 through 756 Processing helix chain 'A' and resid 757 through 767 removed outlier: 3.763A pdb=" N TRP A 766 " --> pdb=" O LEU A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 822 removed outlier: 3.544A pdb=" N LEU A 808 " --> pdb=" O GLY A 804 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG A 819 " --> pdb=" O CYS A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 858 removed outlier: 3.526A pdb=" N SER A 857 " --> pdb=" O GLY A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 952 removed outlier: 3.995A pdb=" N LEU A 933 " --> pdb=" O THR A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 986 removed outlier: 3.676A pdb=" N PHE A 960 " --> pdb=" O THR A 956 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER A 962 " --> pdb=" O LEU A 958 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP A 986 " --> pdb=" O SER A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1033 removed outlier: 3.732A pdb=" N PHE A1009 " --> pdb=" O TRP A1005 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU A1015 " --> pdb=" O ALA A1011 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL A1025 " --> pdb=" O GLY A1021 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 437 removed outlier: 3.594A pdb=" N ALA B 429 " --> pdb=" O CYS B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 469 removed outlier: 3.510A pdb=" N TYR B 469 " --> pdb=" O GLY B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 522 through 546 removed outlier: 3.525A pdb=" N VAL B 530 " --> pdb=" O TRP B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 585 removed outlier: 3.643A pdb=" N TRP B 578 " --> pdb=" O PHE B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 626 removed outlier: 3.661A pdb=" N VAL B 601 " --> pdb=" O SER B 597 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE B 613 " --> pdb=" O THR B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 641 Processing helix chain 'B' and resid 653 through 662 Processing helix chain 'B' and resid 665 through 677 removed outlier: 4.086A pdb=" N LYS B 669 " --> pdb=" O ALA B 665 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N MET B 674 " --> pdb=" O MET B 670 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER B 676 " --> pdb=" O THR B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 695 Processing helix chain 'B' and resid 706 through 714 removed outlier: 3.644A pdb=" N GLN B 714 " --> pdb=" O GLU B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 756 Processing helix chain 'B' and resid 757 through 767 removed outlier: 3.511A pdb=" N TRP B 766 " --> pdb=" O LEU B 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 791 Processing helix chain 'B' and resid 792 through 819 removed outlier: 3.848A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 415 Processing helix chain 'C' and resid 416 through 419 removed outlier: 3.980A pdb=" N GLU C 419 " --> pdb=" O GLU C 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 416 through 419' Processing helix chain 'C' and resid 423 through 435 Processing helix chain 'C' and resid 462 through 469 Processing helix chain 'C' and resid 482 through 487 removed outlier: 3.534A pdb=" N GLU C 487 " --> pdb=" O LEU C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 543 removed outlier: 3.831A pdb=" N VAL C 530 " --> pdb=" O TRP C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 585 removed outlier: 3.631A pdb=" N SER C 580 " --> pdb=" O SER C 576 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU C 581 " --> pdb=" O LEU C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 597 through 630 removed outlier: 3.863A pdb=" N VAL C 601 " --> pdb=" O SER C 597 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL C 626 " --> pdb=" O ALA C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 642 Processing helix chain 'C' and resid 653 through 661 removed outlier: 3.588A pdb=" N PHE C 659 " --> pdb=" O THR C 655 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG C 661 " --> pdb=" O GLU C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 676 removed outlier: 3.828A pdb=" N SER C 676 " --> pdb=" O THR C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 685 through 696 Processing helix chain 'C' and resid 706 through 714 Processing helix chain 'C' and resid 740 through 742 No H-bonds generated for 'chain 'C' and resid 740 through 742' Processing helix chain 'C' and resid 743 through 756 Processing helix chain 'C' and resid 757 through 767 removed outlier: 3.763A pdb=" N TRP C 766 " --> pdb=" O LEU C 762 " (cutoff:3.500A) Processing helix chain 'C' and resid 794 through 822 removed outlier: 3.545A pdb=" N LEU C 808 " --> pdb=" O GLY C 804 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG C 819 " --> pdb=" O CYS C 815 " (cutoff:3.500A) Processing helix chain 'C' and resid 834 through 858 removed outlier: 3.526A pdb=" N SER C 857 " --> pdb=" O GLY C 853 " (cutoff:3.500A) Processing helix chain 'C' and resid 929 through 952 removed outlier: 3.996A pdb=" N LEU C 933 " --> pdb=" O THR C 929 " (cutoff:3.500A) Processing helix chain 'C' and resid 956 through 986 removed outlier: 3.677A pdb=" N PHE C 960 " --> pdb=" O THR C 956 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER C 962 " --> pdb=" O LEU C 958 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP C 986 " --> pdb=" O SER C 982 " (cutoff:3.500A) Processing helix chain 'C' and resid 1004 through 1033 removed outlier: 3.731A pdb=" N PHE C1009 " --> pdb=" O TRP C1005 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU C1015 " --> pdb=" O ALA C1011 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL C1025 " --> pdb=" O GLY C1021 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 437 removed outlier: 3.595A pdb=" N ALA D 429 " --> pdb=" O CYS D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 469 removed outlier: 3.509A pdb=" N TYR D 469 " --> pdb=" O GLY D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 515 through 519 Processing helix chain 'D' and resid 522 through 546 removed outlier: 3.525A pdb=" N VAL D 530 " --> pdb=" O TRP D 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 585 removed outlier: 3.643A pdb=" N TRP D 578 " --> pdb=" O PHE D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 626 removed outlier: 3.661A pdb=" N VAL D 601 " --> pdb=" O SER D 597 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE D 613 " --> pdb=" O THR D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 641 Processing helix chain 'D' and resid 653 through 662 Processing helix chain 'D' and resid 665 through 677 removed outlier: 4.086A pdb=" N LYS D 669 " --> pdb=" O ALA D 665 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N MET D 674 " --> pdb=" O MET D 670 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER D 676 " --> pdb=" O THR D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 695 Processing helix chain 'D' and resid 706 through 714 removed outlier: 3.643A pdb=" N GLN D 714 " --> pdb=" O GLU D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 756 Processing helix chain 'D' and resid 757 through 767 removed outlier: 3.512A pdb=" N TRP D 766 " --> pdb=" O LEU D 762 " (cutoff:3.500A) Processing helix chain 'D' and resid 788 through 791 Processing helix chain 'D' and resid 792 through 819 removed outlier: 3.849A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 37 removed outlier: 3.892A pdb=" N SER E 19 " --> pdb=" O VAL E 15 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE E 22 " --> pdb=" O ALA E 18 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE E 31 " --> pdb=" O HIS E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 66 removed outlier: 3.675A pdb=" N LEU E 64 " --> pdb=" O ILE E 60 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG E 65 " --> pdb=" O CYS E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 85 removed outlier: 3.598A pdb=" N HIS E 75 " --> pdb=" O GLU E 71 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY E 76 " --> pdb=" O TYR E 72 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU E 83 " --> pdb=" O CYS E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 107 removed outlier: 3.614A pdb=" N ASN E 94 " --> pdb=" O THR E 90 " (cutoff:3.500A) Proline residue: E 96 - end of helix Processing helix chain 'E' and resid 124 through 159 removed outlier: 3.626A pdb=" N TRP E 136 " --> pdb=" O GLN E 132 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N CYS E 137 " --> pdb=" O LYS E 133 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU E 139 " --> pdb=" O SER E 135 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE E 147 " --> pdb=" O LEU E 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 37 removed outlier: 3.892A pdb=" N SER F 19 " --> pdb=" O VAL F 15 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE F 22 " --> pdb=" O ALA F 18 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE F 31 " --> pdb=" O HIS F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 66 removed outlier: 3.675A pdb=" N LEU F 64 " --> pdb=" O ILE F 60 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG F 65 " --> pdb=" O CYS F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 85 removed outlier: 3.598A pdb=" N HIS F 75 " --> pdb=" O GLU F 71 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU F 83 " --> pdb=" O CYS F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 107 removed outlier: 3.614A pdb=" N ASN F 94 " --> pdb=" O THR F 90 " (cutoff:3.500A) Proline residue: F 96 - end of helix Processing helix chain 'F' and resid 124 through 159 removed outlier: 3.627A pdb=" N TRP F 136 " --> pdb=" O GLN F 132 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N CYS F 137 " --> pdb=" O LYS F 133 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU F 139 " --> pdb=" O SER F 135 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE F 147 " --> pdb=" O LEU F 143 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 395 through 399 removed outlier: 6.418A pdb=" N VAL A 395 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N THR A 443 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL A 397 " --> pdb=" O THR A 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AA3, first strand: chain 'A' and resid 490 through 491 Processing sheet with id=AA4, first strand: chain 'A' and resid 496 through 498 removed outlier: 4.073A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU A 498 " --> pdb=" O LYS A 730 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 682 through 683 removed outlier: 7.455A pdb=" N VAL A 683 " --> pdb=" O TYR A 647 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N THR A 649 " --> pdb=" O VAL A 683 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 10.821A pdb=" N LEU A 650 " --> pdb=" O GLU A 705 " (cutoff:3.500A) removed outlier: 9.152A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 875 through 880 removed outlier: 6.547A pdb=" N GLU A 866 " --> pdb=" O LYS A 879 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU A 865 " --> pdb=" O ASN A1000 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR A 998 " --> pdb=" O GLY A 867 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 888 through 890 Processing sheet with id=AA8, first strand: chain 'B' and resid 394 through 399 removed outlier: 6.723A pdb=" N VAL B 395 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N THR B 443 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AB1, first strand: chain 'B' and resid 489 through 491 Processing sheet with id=AB2, first strand: chain 'B' and resid 496 through 498 removed outlier: 3.864A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 702 through 705 removed outlier: 4.383A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 395 through 399 removed outlier: 6.418A pdb=" N VAL C 395 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N THR C 443 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL C 397 " --> pdb=" O THR C 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AB6, first strand: chain 'C' and resid 490 through 491 Processing sheet with id=AB7, first strand: chain 'C' and resid 496 through 498 removed outlier: 4.073A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU C 498 " --> pdb=" O LYS C 730 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 682 through 683 removed outlier: 7.455A pdb=" N VAL C 683 " --> pdb=" O TYR C 647 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N THR C 649 " --> pdb=" O VAL C 683 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 10.820A pdb=" N LEU C 650 " --> pdb=" O GLU C 705 " (cutoff:3.500A) removed outlier: 9.151A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 875 through 880 removed outlier: 6.547A pdb=" N GLU C 866 " --> pdb=" O LYS C 879 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU C 865 " --> pdb=" O ASN C1000 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR C 998 " --> pdb=" O GLY C 867 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 888 through 890 Processing sheet with id=AC2, first strand: chain 'D' and resid 394 through 399 removed outlier: 6.723A pdb=" N VAL D 395 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N THR D 443 " --> pdb=" O VAL D 395 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N VAL D 397 " --> pdb=" O THR D 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AC4, first strand: chain 'D' and resid 489 through 491 Processing sheet with id=AC5, first strand: chain 'D' and resid 496 through 498 removed outlier: 3.864A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 702 through 705 removed outlier: 4.384A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) 960 hydrogen bonds defined for protein. 2808 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.54 Time building geometry restraints manager: 2.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.02 - 0.46: 5 0.46 - 0.90: 6 0.90 - 1.34: 5363 1.34 - 1.78: 14681 1.78 - 2.22: 253 Warning: very small bond lengths. Bond restraints: 20308 Sorted by residual: bond pdb=" C27 AJP C1110 " pdb=" O78 AJP C1110 " ideal model delta sigma weight residual 1.406 0.016 1.390 2.00e-02 2.50e+03 4.83e+03 bond pdb=" C27 AJP A1111 " pdb=" O78 AJP A1111 " ideal model delta sigma weight residual 1.406 0.048 1.358 2.00e-02 2.50e+03 4.61e+03 bond pdb=" C27 AJP C1114 " pdb=" O78 AJP C1114 " ideal model delta sigma weight residual 1.406 0.058 1.348 2.00e-02 2.50e+03 4.54e+03 bond pdb=" C27 AJP A1110 " pdb=" O78 AJP A1110 " ideal model delta sigma weight residual 1.406 0.070 1.336 2.00e-02 2.50e+03 4.46e+03 bond pdb=" C27 AJP A1116 " pdb=" O78 AJP A1116 " ideal model delta sigma weight residual 1.406 0.088 1.318 2.00e-02 2.50e+03 4.34e+03 ... (remaining 20303 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.71: 26292 4.71 - 9.41: 799 9.41 - 14.12: 152 14.12 - 18.82: 15 18.82 - 23.53: 6 Bond angle restraints: 27264 Sorted by residual: angle pdb=" C17 CLR A1107 " pdb=" C13 CLR A1107 " pdb=" C18 CLR A1107 " ideal model delta sigma weight residual 110.18 86.65 23.53 3.00e+00 1.11e-01 6.15e+01 angle pdb=" C17 CLR C1106 " pdb=" C13 CLR C1106 " pdb=" C18 CLR C1106 " ideal model delta sigma weight residual 110.18 86.77 23.41 3.00e+00 1.11e-01 6.09e+01 angle pdb=" C17 CLR A1112 " pdb=" C13 CLR A1112 " pdb=" C18 CLR A1112 " ideal model delta sigma weight residual 110.18 88.52 21.66 3.00e+00 1.11e-01 5.21e+01 angle pdb=" N VAL B 514 " pdb=" CA VAL B 514 " pdb=" C VAL B 514 " ideal model delta sigma weight residual 112.83 105.74 7.09 9.90e-01 1.02e+00 5.14e+01 angle pdb=" N VAL D 514 " pdb=" CA VAL D 514 " pdb=" C VAL D 514 " ideal model delta sigma weight residual 112.83 105.74 7.09 9.90e-01 1.02e+00 5.13e+01 ... (remaining 27259 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 12006 35.97 - 71.94: 635 71.94 - 107.91: 187 107.91 - 143.88: 97 143.88 - 179.85: 48 Dihedral angle restraints: 12973 sinusoidal: 6391 harmonic: 6582 Sorted by residual: dihedral pdb=" CA PRO F 109 " pdb=" C PRO F 109 " pdb=" N ALA F 110 " pdb=" CA ALA F 110 " ideal model delta harmonic sigma weight residual -180.00 -118.55 -61.45 0 5.00e+00 4.00e-02 1.51e+02 dihedral pdb=" CA PRO E 109 " pdb=" C PRO E 109 " pdb=" N ALA E 110 " pdb=" CA ALA E 110 " ideal model delta harmonic sigma weight residual -180.00 -118.58 -61.42 0 5.00e+00 4.00e-02 1.51e+02 dihedral pdb=" CA MET E 116 " pdb=" C MET E 116 " pdb=" N TYR E 117 " pdb=" CA TYR E 117 " ideal model delta harmonic sigma weight residual 180.00 120.86 59.14 0 5.00e+00 4.00e-02 1.40e+02 ... (remaining 12970 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.098: 2878 1.098 - 2.196: 14 2.196 - 3.294: 11 3.294 - 4.392: 16 4.392 - 5.489: 42 Chirality restraints: 2961 Sorted by residual: chirality pdb=" C15 AJP A1110 " pdb=" C14 AJP A1110 " pdb=" C16 AJP A1110 " pdb=" C20 AJP A1110 " both_signs ideal model delta sigma weight residual False -2.42 3.07 -5.49 2.00e-01 2.50e+01 7.53e+02 chirality pdb=" C15 AJP C1109 " pdb=" C14 AJP C1109 " pdb=" C16 AJP C1109 " pdb=" C20 AJP C1109 " both_signs ideal model delta sigma weight residual False -2.42 3.07 -5.49 2.00e-01 2.50e+01 7.53e+02 chirality pdb=" C02 AJP A1110 " pdb=" C01 AJP A1110 " pdb=" C03 AJP A1110 " pdb=" C85 AJP A1110 " both_signs ideal model delta sigma weight residual False 2.60 -2.84 5.44 2.00e-01 2.50e+01 7.40e+02 ... (remaining 2958 not shown) Planarity restraints: 3162 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET E 116 " 0.014 2.00e-02 2.50e+03 2.77e-02 7.69e+00 pdb=" C MET E 116 " -0.048 2.00e-02 2.50e+03 pdb=" O MET E 116 " 0.018 2.00e-02 2.50e+03 pdb=" N TYR E 117 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET F 116 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.64e+00 pdb=" C MET F 116 " 0.048 2.00e-02 2.50e+03 pdb=" O MET F 116 " -0.018 2.00e-02 2.50e+03 pdb=" N TYR F 117 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 406 " -0.013 2.00e-02 2.50e+03 2.57e-02 6.61e+00 pdb=" C VAL D 406 " 0.044 2.00e-02 2.50e+03 pdb=" O VAL D 406 " -0.017 2.00e-02 2.50e+03 pdb=" N MET D 407 " -0.015 2.00e-02 2.50e+03 ... (remaining 3159 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 530 2.68 - 3.23: 17707 3.23 - 3.79: 29684 3.79 - 4.34: 41312 4.34 - 4.90: 68155 Nonbonded interactions: 157388 Sorted by model distance: nonbonded pdb=" OE2 GLU C 705 " pdb=" OH TYR C 732 " model vdw 2.123 3.040 nonbonded pdb=" OE2 GLU A 705 " pdb=" OH TYR A 732 " model vdw 2.123 3.040 nonbonded pdb=" O25 AJP A1111 " pdb=" O79 AJP A1111 " model vdw 2.172 2.432 nonbonded pdb=" O25 AJP C1110 " pdb=" O79 AJP C1110 " model vdw 2.176 2.432 nonbonded pdb=" O31 AJP A1110 " pdb=" O78 AJP A1110 " model vdw 2.196 2.432 ... (remaining 157383 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 392 through 1104 or (resid 1105 and (name C13 or name C14 \ or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name \ C21 or name C22 or name C23)) or resid 1108 or resid 1110 or (resid 1113 and (na \ me C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 o \ r name C20 or name C21 or name C22 or name C23)) or resid 1115)) selection = (chain 'C' and (resid 392 through 1105 or resid 1108 or resid 1110 or resid 1113 \ or resid 1115)) } ncs_group { reference = (chain 'B' and (resid 392 through 1109 or (resid 1110 and (name C13 or name C14 \ or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name \ C21 or name C22 or name C23)))) selection = (chain 'D' and (resid 392 through 1108 or (resid 1109 through 1110 and (name C13 \ or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name \ C20 or name C21 or name C22 or name C23)))) } ncs_group { reference = (chain 'E' and (resid 2 through 201 or (resid 202 and (name C13 or name C14 or n \ ame C15 or name C16 or name C17 or name C18 or name C19 or name C20)) or resid 2 \ 04 through 205)) selection = (chain 'F' and (resid 2 through 201 or (resid 202 and (name C13 or name C14 or n \ ame C15 or name C16 or name C17 or name C18 or name C19 or name C20)) or resid 2 \ 04 through 205)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.650 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 18.830 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 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 : 0.047 1.390 20314 Z= 2.351 Angle : 1.899 23.526 27276 Z= 0.849 Chirality : 0.688 5.489 2961 Planarity : 0.007 0.062 3162 Dihedral : 28.238 179.849 8747 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.71 % Allowed : 7.59 % Favored : 91.70 % Rotamer: Outliers : 0.52 % Allowed : 3.92 % Favored : 95.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.82 % 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: -6.01 (0.11), residues: 2240 helix: -4.03 (0.07), residues: 1304 sheet: -3.28 (0.29), residues: 216 loop : -3.62 (0.17), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 485 TYR 0.033 0.003 TYR C 702 PHE 0.033 0.003 PHE A 574 TRP 0.017 0.003 TRP C 861 HIS 0.007 0.002 HIS E 27 Details of bonding type rmsd covalent geometry : bond 0.04733 (20308) covalent geometry : angle 1.89900 (27264) SS BOND : bond 0.01022 ( 6) SS BOND : angle 2.17489 ( 12) hydrogen bonds : bond 0.30028 ( 960) hydrogen bonds : angle 10.45065 ( 2808) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 511 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 663 LYS cc_start: 0.8768 (mptp) cc_final: 0.8485 (mttt) REVERT: A 674 MET cc_start: 0.8782 (mtm) cc_final: 0.8517 (mtp) REVERT: A 1005 TRP cc_start: 0.8230 (p-90) cc_final: 0.7932 (p-90) REVERT: B 638 ASP cc_start: 0.8032 (m-30) cc_final: 0.7796 (m-30) REVERT: B 642 GLN cc_start: 0.8075 (pp30) cc_final: 0.7471 (pp30) REVERT: C 519 ASP cc_start: 0.8612 (m-30) cc_final: 0.8408 (m-30) REVERT: C 630 VAL cc_start: 0.8564 (t) cc_final: 0.8361 (m) REVERT: C 674 MET cc_start: 0.8866 (mtm) cc_final: 0.8641 (mtp) REVERT: C 1005 TRP cc_start: 0.8137 (p-90) cc_final: 0.7896 (p-90) REVERT: D 527 MET cc_start: 0.7638 (mmm) cc_final: 0.7387 (mmt) REVERT: D 657 GLU cc_start: 0.7760 (tp30) cc_final: 0.7496 (mm-30) REVERT: D 661 ARG cc_start: 0.7850 (ptt180) cc_final: 0.7637 (ttp-170) REVERT: D 770 LYS cc_start: 0.7660 (mmtp) cc_final: 0.7437 (tttp) REVERT: F 64 LEU cc_start: 0.8041 (mt) cc_final: 0.7837 (mt) outliers start: 10 outliers final: 0 residues processed: 519 average time/residue: 0.1581 time to fit residues: 122.6610 Evaluate side-chains 295 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.5980 chunk 200 optimal weight: 2.9990 chunk 212 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 GLN A 575 ASN A 747 ASN ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 947 ASN B 461 ASN B 586 GLN B 587 GLN C 412 HIS C 575 ASN ** C 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 947 ASN ** C 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 461 ASN D 586 GLN D 587 GLN E 75 HIS E 94 ASN E 124 ASN E 132 GLN F 94 ASN F 124 ASN F 132 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.172988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.124425 restraints weight = 21984.372| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.03 r_work: 0.3131 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20314 Z= 0.174 Angle : 1.321 31.780 27276 Z= 0.521 Chirality : 0.152 2.488 2961 Planarity : 0.006 0.061 3162 Dihedral : 28.237 178.697 4619 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.74 % Favored : 92.86 % Rotamer: Outliers : 2.94 % Allowed : 8.61 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.64 % 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: -3.23 (0.15), residues: 2240 helix: -1.32 (0.12), residues: 1310 sheet: -2.73 (0.32), residues: 194 loop : -3.32 (0.18), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 684 TYR 0.020 0.002 TYR C 702 PHE 0.024 0.002 PHE D 541 TRP 0.015 0.001 TRP D 766 HIS 0.008 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00385 (20308) covalent geometry : angle 1.32129 (27264) SS BOND : bond 0.00347 ( 6) SS BOND : angle 1.20268 ( 12) hydrogen bonds : bond 0.05135 ( 960) hydrogen bonds : angle 4.73291 ( 2808) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 321 time to evaluate : 0.867 Fit side-chains revert: symmetry clash REVERT: A 663 LYS cc_start: 0.8972 (mptp) cc_final: 0.8640 (mttt) REVERT: A 669 LYS cc_start: 0.7911 (ttmt) cc_final: 0.7300 (mtpt) REVERT: A 860 TYR cc_start: 0.8354 (m-80) cc_final: 0.8038 (m-80) REVERT: A 891 PHE cc_start: 0.7760 (m-80) cc_final: 0.7501 (m-80) REVERT: A 986 ASP cc_start: 0.7898 (p0) cc_final: 0.7697 (p0) REVERT: B 695 LYS cc_start: 0.7239 (OUTLIER) cc_final: 0.6228 (mptt) REVERT: C 860 TYR cc_start: 0.8439 (m-80) cc_final: 0.8082 (m-80) REVERT: C 879 LYS cc_start: 0.8664 (ttmt) cc_final: 0.8194 (mtpp) REVERT: C 998 TYR cc_start: 0.7700 (p90) cc_final: 0.7457 (p90) REVERT: D 397 VAL cc_start: 0.8509 (OUTLIER) cc_final: 0.8304 (m) REVERT: D 439 LYS cc_start: 0.8650 (mtmm) cc_final: 0.8358 (mmtm) REVERT: D 695 LYS cc_start: 0.6571 (OUTLIER) cc_final: 0.5530 (mptt) REVERT: D 715 ARG cc_start: 0.7980 (tpp-160) cc_final: 0.7738 (mmt-90) REVERT: D 770 LYS cc_start: 0.8026 (mmtp) cc_final: 0.7696 (tttp) REVERT: D 817 LYS cc_start: 0.7699 (tppt) cc_final: 0.7389 (ttpt) outliers start: 57 outliers final: 24 residues processed: 360 average time/residue: 0.1468 time to fit residues: 81.6766 Evaluate side-chains 304 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 277 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 631 SER Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 695 LYS Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 729 SER Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 962 SER Chi-restraints excluded: chain C residue 964 ILE Chi-restraints excluded: chain C residue 1013 SER Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 631 SER Chi-restraints excluded: chain D residue 644 GLU Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 729 SER Chi-restraints excluded: chain D residue 790 SER Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain F residue 122 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 125 optimal weight: 4.9990 chunk 218 optimal weight: 4.9990 chunk 113 optimal weight: 0.7980 chunk 96 optimal weight: 0.5980 chunk 206 optimal weight: 5.9990 chunk 91 optimal weight: 0.1980 chunk 145 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 131 optimal weight: 0.7980 chunk 40 optimal weight: 9.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 587 GLN C 747 ASN ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 985 ASN D 587 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.169361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.122561 restraints weight = 22037.229| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.86 r_work: 0.3024 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20314 Z= 0.189 Angle : 1.272 33.786 27276 Z= 0.496 Chirality : 0.145 2.400 2961 Planarity : 0.005 0.048 3162 Dihedral : 27.069 179.952 4619 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.96 % Favored : 92.68 % Rotamer: Outliers : 3.56 % Allowed : 10.31 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.41 % 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: -1.56 (0.17), residues: 2240 helix: 0.33 (0.14), residues: 1310 sheet: -2.76 (0.31), residues: 198 loop : -3.05 (0.19), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 684 TYR 0.023 0.002 TYR D 673 PHE 0.019 0.002 PHE A 495 TRP 0.015 0.002 TRP C 861 HIS 0.014 0.002 HIS C 883 Details of bonding type rmsd covalent geometry : bond 0.00447 (20308) covalent geometry : angle 1.27210 (27264) SS BOND : bond 0.00789 ( 6) SS BOND : angle 1.20901 ( 12) hydrogen bonds : bond 0.04361 ( 960) hydrogen bonds : angle 4.18589 ( 2808) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 295 time to evaluate : 0.753 Fit side-chains REVERT: A 511 LYS cc_start: 0.8446 (mmmt) cc_final: 0.8069 (tptp) REVERT: A 585 MET cc_start: 0.9029 (OUTLIER) cc_final: 0.8755 (mmt) REVERT: A 587 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.6839 (mm-40) REVERT: A 663 LYS cc_start: 0.8920 (mptp) cc_final: 0.8584 (mttt) REVERT: A 669 LYS cc_start: 0.7875 (ttmt) cc_final: 0.7330 (mtpt) REVERT: A 952 ARG cc_start: 0.6805 (ptp-170) cc_final: 0.6516 (ptp-170) REVERT: B 415 LEU cc_start: 0.7908 (mt) cc_final: 0.7613 (mt) REVERT: B 461 ASN cc_start: 0.7586 (t0) cc_final: 0.7000 (t0) REVERT: B 695 LYS cc_start: 0.7404 (OUTLIER) cc_final: 0.6322 (mptt) REVERT: C 585 MET cc_start: 0.9015 (OUTLIER) cc_final: 0.8266 (mmt) REVERT: C 697 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8053 (pttp) REVERT: C 860 TYR cc_start: 0.8368 (m-80) cc_final: 0.8050 (m-80) REVERT: C 877 GLU cc_start: 0.8086 (tt0) cc_final: 0.7857 (tt0) REVERT: C 879 LYS cc_start: 0.8571 (ttmt) cc_final: 0.8110 (mtpp) REVERT: C 985 ASN cc_start: 0.8139 (m-40) cc_final: 0.7903 (m110) REVERT: C 998 TYR cc_start: 0.7959 (p90) cc_final: 0.7612 (p90) REVERT: D 461 ASN cc_start: 0.7725 (t0) cc_final: 0.7124 (t0) REVERT: D 635 SER cc_start: 0.8697 (t) cc_final: 0.8199 (p) REVERT: D 695 LYS cc_start: 0.7251 (OUTLIER) cc_final: 0.6180 (mptt) REVERT: D 764 ASN cc_start: 0.8370 (m110) cc_final: 0.7907 (m-40) REVERT: D 770 LYS cc_start: 0.7988 (mmtp) cc_final: 0.7750 (tttp) REVERT: D 817 LYS cc_start: 0.7707 (tppt) cc_final: 0.7380 (ttpt) REVERT: E 148 TYR cc_start: 0.8151 (t80) cc_final: 0.7741 (t80) outliers start: 69 outliers final: 38 residues processed: 343 average time/residue: 0.1474 time to fit residues: 78.6237 Evaluate side-chains 318 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 274 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 719 ASP Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 695 LYS Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 729 SER Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 661 ARG Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 719 ASP Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 962 SER Chi-restraints excluded: chain C residue 964 ILE Chi-restraints excluded: chain C residue 1013 SER Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 631 SER Chi-restraints excluded: chain D residue 644 GLU Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 729 SER Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 790 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 56 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 121 optimal weight: 0.0000 chunk 101 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 185 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 196 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 HIS ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.168481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.122388 restraints weight = 22076.459| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.96 r_work: 0.3016 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 20314 Z= 0.196 Angle : 1.252 33.014 27276 Z= 0.485 Chirality : 0.143 2.306 2961 Planarity : 0.004 0.041 3162 Dihedral : 26.496 179.823 4619 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.88 % Favored : 92.77 % Rotamer: Outliers : 3.56 % Allowed : 11.29 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.41 % 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: -0.87 (0.18), residues: 2240 helix: 0.99 (0.14), residues: 1302 sheet: -2.76 (0.31), residues: 200 loop : -2.85 (0.20), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 684 TYR 0.019 0.002 TYR F 155 PHE 0.018 0.002 PHE B 438 TRP 0.009 0.001 TRP B 766 HIS 0.009 0.002 HIS C 883 Details of bonding type rmsd covalent geometry : bond 0.00467 (20308) covalent geometry : angle 1.25151 (27264) SS BOND : bond 0.00372 ( 6) SS BOND : angle 1.73321 ( 12) hydrogen bonds : bond 0.04019 ( 960) hydrogen bonds : angle 4.03030 ( 2808) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 284 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 511 LYS cc_start: 0.8432 (mmmt) cc_final: 0.8085 (tptp) REVERT: A 647 TYR cc_start: 0.8614 (OUTLIER) cc_final: 0.7927 (m-80) REVERT: A 663 LYS cc_start: 0.8976 (mptp) cc_final: 0.8639 (mttt) REVERT: A 669 LYS cc_start: 0.7976 (ttmt) cc_final: 0.7351 (mtpt) REVERT: A 697 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8304 (pttp) REVERT: A 858 THR cc_start: 0.9018 (t) cc_final: 0.8738 (p) REVERT: A 952 ARG cc_start: 0.6871 (ptp-170) cc_final: 0.6583 (ptp-170) REVERT: A 957 ILE cc_start: 0.7759 (mp) cc_final: 0.7394 (tp) REVERT: A 987 GLU cc_start: 0.7282 (tp30) cc_final: 0.7000 (tp30) REVERT: B 415 LEU cc_start: 0.8033 (mt) cc_final: 0.7768 (mt) REVERT: B 461 ASN cc_start: 0.7620 (t0) cc_final: 0.7100 (t0) REVERT: B 695 LYS cc_start: 0.7646 (OUTLIER) cc_final: 0.6628 (mptt) REVERT: B 764 ASN cc_start: 0.8420 (m110) cc_final: 0.7977 (m-40) REVERT: C 585 MET cc_start: 0.9048 (OUTLIER) cc_final: 0.8358 (mmt) REVERT: C 860 TYR cc_start: 0.8391 (m-80) cc_final: 0.7943 (m-80) REVERT: C 879 LYS cc_start: 0.8695 (ttmt) cc_final: 0.8236 (mtpp) REVERT: C 880 MET cc_start: 0.7745 (tpp) cc_final: 0.7513 (tpp) REVERT: C 985 ASN cc_start: 0.8111 (m-40) cc_final: 0.7892 (m110) REVERT: D 414 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.8116 (ptp) REVERT: D 415 LEU cc_start: 0.8056 (mt) cc_final: 0.7811 (mt) REVERT: D 461 ASN cc_start: 0.7749 (t0) cc_final: 0.7213 (t0) REVERT: D 635 SER cc_start: 0.8685 (t) cc_final: 0.8208 (p) REVERT: D 695 LYS cc_start: 0.7307 (OUTLIER) cc_final: 0.6259 (mptt) REVERT: D 719 ASP cc_start: 0.7736 (t0) cc_final: 0.7311 (t0) REVERT: D 770 LYS cc_start: 0.8186 (mmtp) cc_final: 0.7879 (tttp) REVERT: D 817 LYS cc_start: 0.7746 (tppt) cc_final: 0.7310 (ttmt) REVERT: E 148 TYR cc_start: 0.8245 (t80) cc_final: 0.7815 (t80) outliers start: 69 outliers final: 42 residues processed: 334 average time/residue: 0.1453 time to fit residues: 75.9055 Evaluate side-chains 315 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 267 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 719 ASP Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 695 LYS Chi-restraints excluded: chain B residue 696 SER Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 729 SER Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 652 SER Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 856 VAL Chi-restraints excluded: chain C residue 925 ILE Chi-restraints excluded: chain C residue 962 SER Chi-restraints excluded: chain C residue 964 ILE Chi-restraints excluded: chain C residue 1013 SER Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 729 SER Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain D residue 790 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 16 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 160 optimal weight: 10.0000 chunk 14 optimal weight: 0.5980 chunk 115 optimal weight: 0.6980 chunk 206 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 173 optimal weight: 2.9990 chunk 190 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 764 ASN ** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 985 ASN C 764 ASN ** C 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.168737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.123842 restraints weight = 21900.347| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.05 r_work: 0.3009 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20314 Z= 0.177 Angle : 1.241 33.141 27276 Z= 0.479 Chirality : 0.142 2.290 2961 Planarity : 0.004 0.039 3162 Dihedral : 26.159 179.785 4619 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.88 % Favored : 92.77 % Rotamer: Outliers : 3.97 % Allowed : 11.96 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.41 % 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: -0.49 (0.18), residues: 2240 helix: 1.32 (0.14), residues: 1302 sheet: -2.67 (0.32), residues: 190 loop : -2.72 (0.20), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 684 TYR 0.017 0.002 TYR F 155 PHE 0.018 0.001 PHE B 438 TRP 0.008 0.001 TRP D 766 HIS 0.024 0.002 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00420 (20308) covalent geometry : angle 1.24010 (27264) SS BOND : bond 0.00465 ( 6) SS BOND : angle 2.28527 ( 12) hydrogen bonds : bond 0.03875 ( 960) hydrogen bonds : angle 3.92844 ( 2808) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 276 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 585 MET cc_start: 0.9045 (OUTLIER) cc_final: 0.8680 (mmt) REVERT: A 587 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.6896 (mm-40) REVERT: A 663 LYS cc_start: 0.8997 (mptp) cc_final: 0.8646 (mttt) REVERT: A 669 LYS cc_start: 0.7986 (ttmt) cc_final: 0.7342 (mtpt) REVERT: A 697 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8307 (pttp) REVERT: A 858 THR cc_start: 0.9053 (t) cc_final: 0.8781 (p) REVERT: A 952 ARG cc_start: 0.6875 (ptp-170) cc_final: 0.6528 (ptp-170) REVERT: A 957 ILE cc_start: 0.7709 (mp) cc_final: 0.7373 (tp) REVERT: A 987 GLU cc_start: 0.7234 (tp30) cc_final: 0.6973 (tp30) REVERT: B 415 LEU cc_start: 0.8018 (mt) cc_final: 0.7766 (mt) REVERT: B 461 ASN cc_start: 0.7638 (t0) cc_final: 0.7069 (t0) REVERT: B 695 LYS cc_start: 0.7687 (OUTLIER) cc_final: 0.6652 (mptt) REVERT: B 764 ASN cc_start: 0.8440 (m110) cc_final: 0.7961 (m-40) REVERT: C 503 MET cc_start: 0.8954 (ttp) cc_final: 0.8720 (ttm) REVERT: C 585 MET cc_start: 0.9051 (OUTLIER) cc_final: 0.8368 (mmt) REVERT: C 663 LYS cc_start: 0.9042 (mttp) cc_final: 0.8644 (mttt) REVERT: C 669 LYS cc_start: 0.7953 (ttmt) cc_final: 0.7392 (mtpt) REVERT: C 860 TYR cc_start: 0.8369 (m-80) cc_final: 0.7901 (m-80) REVERT: C 879 LYS cc_start: 0.8612 (ttmt) cc_final: 0.8150 (mtpp) REVERT: C 985 ASN cc_start: 0.8082 (m-40) cc_final: 0.7812 (m110) REVERT: C 987 GLU cc_start: 0.7439 (tp30) cc_final: 0.7182 (tp30) REVERT: D 415 LEU cc_start: 0.8050 (mt) cc_final: 0.7816 (mt) REVERT: D 461 ASN cc_start: 0.7707 (t0) cc_final: 0.7139 (t0) REVERT: D 635 SER cc_start: 0.8620 (t) cc_final: 0.8159 (p) REVERT: D 695 LYS cc_start: 0.7375 (OUTLIER) cc_final: 0.6300 (mptt) REVERT: D 719 ASP cc_start: 0.7736 (t0) cc_final: 0.7342 (t0) REVERT: D 770 LYS cc_start: 0.8236 (mmtp) cc_final: 0.7907 (tttp) REVERT: D 817 LYS cc_start: 0.7768 (tppt) cc_final: 0.7367 (ttmt) REVERT: E 148 TYR cc_start: 0.8234 (t80) cc_final: 0.7801 (t80) outliers start: 77 outliers final: 51 residues processed: 332 average time/residue: 0.1353 time to fit residues: 70.0899 Evaluate side-chains 324 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 267 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 719 ASP Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 902 THR Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 695 LYS Chi-restraints excluded: chain B residue 696 SER Chi-restraints excluded: chain B residue 729 SER Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 508 GLN Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 652 SER Chi-restraints excluded: chain C residue 661 ARG Chi-restraints excluded: chain C residue 719 ASP Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 962 SER Chi-restraints excluded: chain C residue 1013 SER Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 631 SER Chi-restraints excluded: chain D residue 644 GLU Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 729 SER Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain D residue 790 SER Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain F residue 123 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 72 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 195 optimal weight: 0.6980 chunk 170 optimal weight: 0.8980 chunk 214 optimal weight: 5.9990 chunk 139 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 156 optimal weight: 0.7980 chunk 177 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 950 HIS ** 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 = 0.3918 r_free = 0.3918 target = 0.172202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.124263 restraints weight = 22166.212| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.14 r_work: 0.3058 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20314 Z= 0.154 Angle : 1.228 32.957 27276 Z= 0.471 Chirality : 0.142 2.248 2961 Planarity : 0.004 0.036 3162 Dihedral : 25.738 179.940 4619 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.74 % Favored : 92.90 % Rotamer: Outliers : 3.56 % Allowed : 13.04 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.41 % 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 (0.18), residues: 2240 helix: 1.53 (0.14), residues: 1314 sheet: -2.59 (0.32), residues: 190 loop : -2.66 (0.20), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 684 TYR 0.019 0.001 TYR F 155 PHE 0.018 0.001 PHE B 438 TRP 0.007 0.001 TRP B 460 HIS 0.009 0.001 HIS C 883 Details of bonding type rmsd covalent geometry : bond 0.00360 (20308) covalent geometry : angle 1.22668 (27264) SS BOND : bond 0.00535 ( 6) SS BOND : angle 2.89486 ( 12) hydrogen bonds : bond 0.03671 ( 960) hydrogen bonds : angle 3.82401 ( 2808) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 285 time to evaluate : 0.746 Fit side-chains revert: symmetry clash REVERT: A 511 LYS cc_start: 0.8448 (mmmt) cc_final: 0.8123 (tptp) REVERT: A 585 MET cc_start: 0.8877 (OUTLIER) cc_final: 0.8472 (mmt) REVERT: A 587 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.6833 (mm-40) REVERT: A 647 TYR cc_start: 0.8495 (OUTLIER) cc_final: 0.7778 (m-80) REVERT: A 651 ASP cc_start: 0.7419 (t70) cc_final: 0.7160 (p0) REVERT: A 663 LYS cc_start: 0.8937 (mptp) cc_final: 0.8612 (mttt) REVERT: A 669 LYS cc_start: 0.7925 (ttmt) cc_final: 0.7305 (mtpt) REVERT: A 697 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8253 (pttp) REVERT: A 858 THR cc_start: 0.9077 (t) cc_final: 0.8851 (p) REVERT: A 952 ARG cc_start: 0.6987 (ptp-170) cc_final: 0.6647 (ptp-170) REVERT: A 957 ILE cc_start: 0.7674 (mp) cc_final: 0.7323 (tp) REVERT: A 987 GLU cc_start: 0.7199 (tp30) cc_final: 0.6953 (tp30) REVERT: B 461 ASN cc_start: 0.7482 (t0) cc_final: 0.7085 (t0) REVERT: B 635 SER cc_start: 0.8559 (t) cc_final: 0.8087 (p) REVERT: B 695 LYS cc_start: 0.7607 (OUTLIER) cc_final: 0.6608 (mptt) REVERT: B 764 ASN cc_start: 0.8455 (m110) cc_final: 0.8009 (m-40) REVERT: C 585 MET cc_start: 0.8884 (OUTLIER) cc_final: 0.8126 (mmt) REVERT: C 663 LYS cc_start: 0.8990 (mttp) cc_final: 0.8596 (mttt) REVERT: C 669 LYS cc_start: 0.7914 (ttmt) cc_final: 0.7321 (mtpt) REVERT: C 860 TYR cc_start: 0.8327 (m-80) cc_final: 0.7853 (m-80) REVERT: C 879 LYS cc_start: 0.8693 (ttmt) cc_final: 0.8318 (mtpt) REVERT: C 957 ILE cc_start: 0.7693 (mp) cc_final: 0.7381 (tp) REVERT: C 985 ASN cc_start: 0.7986 (m-40) cc_final: 0.7660 (m110) REVERT: D 415 LEU cc_start: 0.8032 (mt) cc_final: 0.7832 (mt) REVERT: D 461 ASN cc_start: 0.7565 (t0) cc_final: 0.7199 (t0) REVERT: D 635 SER cc_start: 0.8484 (t) cc_final: 0.8066 (p) REVERT: D 695 LYS cc_start: 0.7474 (OUTLIER) cc_final: 0.6433 (mptt) REVERT: D 719 ASP cc_start: 0.7495 (t0) cc_final: 0.7177 (t0) REVERT: D 770 LYS cc_start: 0.8204 (mmtp) cc_final: 0.7933 (tttp) REVERT: D 817 LYS cc_start: 0.7806 (tppt) cc_final: 0.7488 (ttmt) REVERT: E 148 TYR cc_start: 0.8223 (t80) cc_final: 0.7816 (t80) outliers start: 69 outliers final: 43 residues processed: 332 average time/residue: 0.1544 time to fit residues: 80.0917 Evaluate side-chains 322 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 272 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 902 THR Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 695 LYS Chi-restraints excluded: chain B residue 696 SER Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 705 GLU Chi-restraints excluded: chain B residue 729 SER Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 719 ASP Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 962 SER Chi-restraints excluded: chain C residue 1013 SER Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 644 GLU Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 729 SER Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain D residue 790 SER Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain F residue 123 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 181 optimal weight: 3.9990 chunk 224 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 177 optimal weight: 0.5980 chunk 167 optimal weight: 0.9980 chunk 208 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 8 optimal weight: 0.0000 chunk 45 optimal weight: 4.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS ** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 586 GLN ** C 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.173035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.125385 restraints weight = 22201.478| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.11 r_work: 0.3059 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.3911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20314 Z= 0.140 Angle : 1.219 32.783 27276 Z= 0.466 Chirality : 0.142 2.216 2961 Planarity : 0.004 0.037 3162 Dihedral : 25.342 179.576 4619 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.88 % Favored : 92.77 % Rotamer: Outliers : 3.81 % Allowed : 12.78 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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: 0.03 (0.18), residues: 2240 helix: 1.72 (0.15), residues: 1316 sheet: -2.48 (0.32), residues: 190 loop : -2.55 (0.21), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 684 TYR 0.016 0.001 TYR F 155 PHE 0.020 0.001 PHE B 438 TRP 0.014 0.001 TRP D 766 HIS 0.009 0.001 HIS A 883 Details of bonding type rmsd covalent geometry : bond 0.00321 (20308) covalent geometry : angle 1.21664 (27264) SS BOND : bond 0.00285 ( 6) SS BOND : angle 3.70147 ( 12) hydrogen bonds : bond 0.03545 ( 960) hydrogen bonds : angle 3.74480 ( 2808) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 295 time to evaluate : 0.786 Fit side-chains REVERT: A 511 LYS cc_start: 0.8398 (mmmt) cc_final: 0.7996 (tptp) REVERT: A 585 MET cc_start: 0.8979 (OUTLIER) cc_final: 0.8608 (mmt) REVERT: A 587 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.6805 (mm-40) REVERT: A 634 GLU cc_start: 0.8419 (pt0) cc_final: 0.7763 (pm20) REVERT: A 647 TYR cc_start: 0.8577 (OUTLIER) cc_final: 0.7882 (m-80) REVERT: A 651 ASP cc_start: 0.7549 (t70) cc_final: 0.7253 (p0) REVERT: A 663 LYS cc_start: 0.8994 (mptp) cc_final: 0.8633 (mttt) REVERT: A 669 LYS cc_start: 0.7978 (ttmt) cc_final: 0.7340 (mtpt) REVERT: A 697 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8255 (pttp) REVERT: A 952 ARG cc_start: 0.6916 (ptp-170) cc_final: 0.6552 (ptp-170) REVERT: A 957 ILE cc_start: 0.7640 (mp) cc_final: 0.7274 (tp) REVERT: A 987 GLU cc_start: 0.7371 (tp30) cc_final: 0.7132 (tp30) REVERT: B 459 ILE cc_start: 0.9107 (OUTLIER) cc_final: 0.8906 (mp) REVERT: B 461 ASN cc_start: 0.7597 (t0) cc_final: 0.7165 (t0) REVERT: B 635 SER cc_start: 0.8532 (t) cc_final: 0.8053 (p) REVERT: B 695 LYS cc_start: 0.7624 (OUTLIER) cc_final: 0.6660 (mptt) REVERT: B 764 ASN cc_start: 0.8491 (m110) cc_final: 0.8029 (m-40) REVERT: C 585 MET cc_start: 0.9006 (OUTLIER) cc_final: 0.8317 (mmt) REVERT: C 634 GLU cc_start: 0.8294 (pt0) cc_final: 0.7747 (pm20) REVERT: C 663 LYS cc_start: 0.9024 (mttp) cc_final: 0.8632 (mttt) REVERT: C 669 LYS cc_start: 0.7966 (ttmt) cc_final: 0.7335 (mtpt) REVERT: C 860 TYR cc_start: 0.8364 (m-80) cc_final: 0.7853 (m-80) REVERT: C 879 LYS cc_start: 0.8698 (ttmt) cc_final: 0.8371 (mtpt) REVERT: C 901 PHE cc_start: 0.7242 (m-10) cc_final: 0.6927 (m-10) REVERT: C 952 ARG cc_start: 0.6915 (ptp-170) cc_final: 0.6521 (ptp-170) REVERT: C 957 ILE cc_start: 0.7637 (mp) cc_final: 0.7309 (tp) REVERT: C 985 ASN cc_start: 0.8134 (m-40) cc_final: 0.7821 (m110) REVERT: D 415 LEU cc_start: 0.8051 (mt) cc_final: 0.7843 (mt) REVERT: D 461 ASN cc_start: 0.7660 (t0) cc_final: 0.7235 (t0) REVERT: D 635 SER cc_start: 0.8425 (t) cc_final: 0.7974 (p) REVERT: D 695 LYS cc_start: 0.7411 (OUTLIER) cc_final: 0.6437 (mptt) REVERT: D 719 ASP cc_start: 0.7701 (t0) cc_final: 0.7362 (t0) REVERT: D 721 MET cc_start: 0.8472 (ttm) cc_final: 0.8261 (ttp) REVERT: D 770 LYS cc_start: 0.8210 (mmtp) cc_final: 0.7893 (tttp) REVERT: D 817 LYS cc_start: 0.7819 (tppt) cc_final: 0.7485 (ttmt) REVERT: E 148 TYR cc_start: 0.8314 (t80) cc_final: 0.7894 (t80) REVERT: F 98 LEU cc_start: 0.7301 (tp) cc_final: 0.7041 (tt) outliers start: 74 outliers final: 50 residues processed: 343 average time/residue: 0.1527 time to fit residues: 82.4679 Evaluate side-chains 334 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 276 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 719 ASP Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 695 LYS Chi-restraints excluded: chain B residue 696 SER Chi-restraints excluded: chain B residue 705 GLU Chi-restraints excluded: chain B residue 729 SER Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 652 SER Chi-restraints excluded: chain C residue 661 ARG Chi-restraints excluded: chain C residue 719 ASP Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 962 SER Chi-restraints excluded: chain C residue 1013 SER Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 644 GLU Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain D residue 729 SER Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 790 SER Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain F residue 123 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 107 optimal weight: 0.2980 chunk 19 optimal weight: 0.9980 chunk 147 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 chunk 109 optimal weight: 0.0170 chunk 4 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 223 optimal weight: 9.9990 chunk 184 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 950 HIS ** 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 = 0.3928 r_free = 0.3928 target = 0.173049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.126167 restraints weight = 21967.171| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.14 r_work: 0.3093 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20314 Z= 0.124 Angle : 1.220 32.627 27276 Z= 0.466 Chirality : 0.142 2.196 2961 Planarity : 0.004 0.058 3162 Dihedral : 25.177 179.448 4619 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.74 % Favored : 92.90 % Rotamer: Outliers : 2.99 % Allowed : 13.76 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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: 0.18 (0.18), residues: 2240 helix: 1.82 (0.15), residues: 1318 sheet: -2.31 (0.34), residues: 190 loop : -2.48 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 684 TYR 0.014 0.001 TYR F 155 PHE 0.022 0.001 PHE B 438 TRP 0.014 0.001 TRP D 766 HIS 0.020 0.002 HIS A 412 Details of bonding type rmsd covalent geometry : bond 0.00278 (20308) covalent geometry : angle 1.21492 (27264) SS BOND : bond 0.00339 ( 6) SS BOND : angle 5.19963 ( 12) hydrogen bonds : bond 0.03466 ( 960) hydrogen bonds : angle 3.69902 ( 2808) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 293 time to evaluate : 0.792 Fit side-chains revert: symmetry clash REVERT: A 511 LYS cc_start: 0.8353 (mmmt) cc_final: 0.7978 (tptp) REVERT: A 585 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.8406 (mmt) REVERT: A 587 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.6785 (mm-40) REVERT: A 647 TYR cc_start: 0.8458 (OUTLIER) cc_final: 0.7825 (m-80) REVERT: A 663 LYS cc_start: 0.8935 (mptp) cc_final: 0.8607 (mttt) REVERT: A 669 LYS cc_start: 0.7955 (ttmt) cc_final: 0.7368 (mtpt) REVERT: A 697 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.8238 (pttp) REVERT: A 952 ARG cc_start: 0.7056 (ptp-170) cc_final: 0.6698 (ptp-170) REVERT: A 957 ILE cc_start: 0.7680 (mp) cc_final: 0.7345 (tp) REVERT: B 461 ASN cc_start: 0.7384 (t0) cc_final: 0.7098 (t0) REVERT: B 635 SER cc_start: 0.8405 (t) cc_final: 0.7995 (p) REVERT: B 695 LYS cc_start: 0.7693 (OUTLIER) cc_final: 0.6833 (mptt) REVERT: B 764 ASN cc_start: 0.8472 (m110) cc_final: 0.8017 (m-40) REVERT: C 585 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.8120 (mmt) REVERT: C 634 GLU cc_start: 0.8022 (pt0) cc_final: 0.7606 (pm20) REVERT: C 663 LYS cc_start: 0.8962 (mttp) cc_final: 0.8587 (mttt) REVERT: C 669 LYS cc_start: 0.7950 (ttmt) cc_final: 0.7313 (mtpt) REVERT: C 673 TYR cc_start: 0.8484 (t80) cc_final: 0.8271 (t80) REVERT: C 860 TYR cc_start: 0.8363 (m-80) cc_final: 0.7881 (m-80) REVERT: C 879 LYS cc_start: 0.8701 (ttmt) cc_final: 0.8283 (mtpt) REVERT: C 901 PHE cc_start: 0.7224 (m-10) cc_final: 0.6922 (m-10) REVERT: C 952 ARG cc_start: 0.7038 (ptp-170) cc_final: 0.6707 (ptp-170) REVERT: C 957 ILE cc_start: 0.7690 (mp) cc_final: 0.7376 (tp) REVERT: C 985 ASN cc_start: 0.7992 (m-40) cc_final: 0.7720 (m110) REVERT: D 415 LEU cc_start: 0.8019 (mt) cc_final: 0.7801 (mt) REVERT: D 461 ASN cc_start: 0.7459 (t0) cc_final: 0.7160 (t0) REVERT: D 635 SER cc_start: 0.8324 (t) cc_final: 0.7946 (p) REVERT: D 695 LYS cc_start: 0.7495 (OUTLIER) cc_final: 0.6609 (mptt) REVERT: D 719 ASP cc_start: 0.7460 (t0) cc_final: 0.7112 (t0) REVERT: D 770 LYS cc_start: 0.8181 (mmtp) cc_final: 0.7955 (tttp) REVERT: D 817 LYS cc_start: 0.7757 (tppt) cc_final: 0.7510 (ttmt) REVERT: F 98 LEU cc_start: 0.7375 (tp) cc_final: 0.7131 (tt) outliers start: 58 outliers final: 40 residues processed: 333 average time/residue: 0.1540 time to fit residues: 80.4957 Evaluate side-chains 327 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 280 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 719 ASP Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 695 LYS Chi-restraints excluded: chain B residue 696 SER Chi-restraints excluded: chain B residue 705 GLU Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 661 ARG Chi-restraints excluded: chain C residue 719 ASP Chi-restraints excluded: chain C residue 962 SER Chi-restraints excluded: chain C residue 1013 SER Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 644 GLU Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 790 SER Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain F residue 123 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 149 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 187 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 216 optimal weight: 10.0000 chunk 177 optimal weight: 0.8980 chunk 171 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 100 optimal weight: 0.0980 chunk 224 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS ** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN ** C 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.172776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.125015 restraints weight = 22053.970| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.03 r_work: 0.3078 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20314 Z= 0.145 Angle : 1.226 32.586 27276 Z= 0.468 Chirality : 0.141 2.190 2961 Planarity : 0.004 0.065 3162 Dihedral : 25.064 179.850 4619 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.79 % Favored : 92.86 % Rotamer: Outliers : 3.09 % Allowed : 13.92 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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: 0.24 (0.18), residues: 2240 helix: 1.85 (0.15), residues: 1316 sheet: -2.20 (0.34), residues: 190 loop : -2.46 (0.21), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 684 TYR 0.028 0.001 TYR A 980 PHE 0.022 0.001 PHE B 438 TRP 0.016 0.001 TRP D 766 HIS 0.011 0.002 HIS A 412 Details of bonding type rmsd covalent geometry : bond 0.00336 (20308) covalent geometry : angle 1.22413 (27264) SS BOND : bond 0.00221 ( 6) SS BOND : angle 3.69278 ( 12) hydrogen bonds : bond 0.03555 ( 960) hydrogen bonds : angle 3.70683 ( 2808) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 283 time to evaluate : 0.708 Fit side-chains REVERT: A 511 LYS cc_start: 0.8358 (mmmt) cc_final: 0.7979 (tptp) REVERT: A 585 MET cc_start: 0.8981 (OUTLIER) cc_final: 0.8602 (mmt) REVERT: A 587 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.6811 (mm-40) REVERT: A 647 TYR cc_start: 0.8592 (OUTLIER) cc_final: 0.7807 (m-10) REVERT: A 663 LYS cc_start: 0.8994 (mptp) cc_final: 0.8632 (mttt) REVERT: A 669 LYS cc_start: 0.7989 (ttmt) cc_final: 0.7350 (mtpt) REVERT: A 697 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8252 (pttp) REVERT: A 952 ARG cc_start: 0.7041 (ptp-170) cc_final: 0.6688 (ptp-170) REVERT: A 957 ILE cc_start: 0.7678 (mp) cc_final: 0.7302 (tp) REVERT: B 461 ASN cc_start: 0.7524 (t0) cc_final: 0.7098 (t0) REVERT: B 635 SER cc_start: 0.8388 (t) cc_final: 0.7947 (p) REVERT: B 695 LYS cc_start: 0.7685 (OUTLIER) cc_final: 0.6784 (mptt) REVERT: B 764 ASN cc_start: 0.8471 (m110) cc_final: 0.8015 (m-40) REVERT: C 585 MET cc_start: 0.9009 (OUTLIER) cc_final: 0.8313 (mmt) REVERT: C 634 GLU cc_start: 0.8294 (pt0) cc_final: 0.7878 (pm20) REVERT: C 651 ASP cc_start: 0.7685 (t70) cc_final: 0.7391 (p0) REVERT: C 663 LYS cc_start: 0.9039 (mttp) cc_final: 0.8637 (mttt) REVERT: C 669 LYS cc_start: 0.7991 (ttmt) cc_final: 0.7313 (mtpt) REVERT: C 673 TYR cc_start: 0.8420 (t80) cc_final: 0.8216 (t80) REVERT: C 860 TYR cc_start: 0.8387 (m-80) cc_final: 0.7883 (m-80) REVERT: C 879 LYS cc_start: 0.8683 (ttmt) cc_final: 0.8357 (ttmm) REVERT: C 891 PHE cc_start: 0.7768 (m-80) cc_final: 0.7430 (m-80) REVERT: C 952 ARG cc_start: 0.6965 (ptp-170) cc_final: 0.6602 (ptp-170) REVERT: C 957 ILE cc_start: 0.7600 (mp) cc_final: 0.7237 (tp) REVERT: C 985 ASN cc_start: 0.8038 (m-40) cc_final: 0.7750 (m110) REVERT: D 415 LEU cc_start: 0.8041 (mt) cc_final: 0.7840 (mt) REVERT: D 461 ASN cc_start: 0.7641 (t0) cc_final: 0.7269 (t0) REVERT: D 635 SER cc_start: 0.8248 (t) cc_final: 0.7831 (p) REVERT: D 695 LYS cc_start: 0.7493 (OUTLIER) cc_final: 0.6556 (mptt) REVERT: D 719 ASP cc_start: 0.7690 (t0) cc_final: 0.7290 (t0) REVERT: D 721 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.8268 (ttp) REVERT: D 817 LYS cc_start: 0.7834 (tppt) cc_final: 0.7529 (ttmt) REVERT: E 148 TYR cc_start: 0.8285 (t80) cc_final: 0.7866 (t80) REVERT: F 98 LEU cc_start: 0.7298 (tp) cc_final: 0.7017 (tt) outliers start: 60 outliers final: 45 residues processed: 325 average time/residue: 0.1563 time to fit residues: 79.7828 Evaluate side-chains 325 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 272 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 695 LYS Chi-restraints excluded: chain B residue 696 SER Chi-restraints excluded: chain B residue 705 GLU Chi-restraints excluded: chain B residue 729 SER Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 661 ARG Chi-restraints excluded: chain C residue 719 ASP Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 962 SER Chi-restraints excluded: chain C residue 1013 SER Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 644 GLU Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 729 SER Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 790 SER Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain F residue 123 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 2 optimal weight: 3.9990 chunk 147 optimal weight: 10.0000 chunk 182 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 5 optimal weight: 0.1980 chunk 127 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 192 optimal weight: 0.9980 chunk 203 optimal weight: 5.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.170600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.122317 restraints weight = 22266.861| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.01 r_work: 0.3077 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 20314 Z= 0.216 Angle : 1.260 32.886 27276 Z= 0.489 Chirality : 0.141 2.223 2961 Planarity : 0.004 0.062 3162 Dihedral : 25.110 179.999 4619 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.05 % Favored : 92.63 % Rotamer: Outliers : 2.78 % Allowed : 14.38 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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: 0.06 (0.18), residues: 2240 helix: 1.69 (0.14), residues: 1318 sheet: -2.27 (0.33), residues: 190 loop : -2.50 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 684 TYR 0.026 0.002 TYR A 980 PHE 0.031 0.002 PHE B 515 TRP 0.021 0.002 TRP D 766 HIS 0.015 0.002 HIS A 412 Details of bonding type rmsd covalent geometry : bond 0.00523 (20308) covalent geometry : angle 1.25729 (27264) SS BOND : bond 0.00442 ( 6) SS BOND : angle 4.38946 ( 12) hydrogen bonds : bond 0.03924 ( 960) hydrogen bonds : angle 3.82188 ( 2808) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 277 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 585 MET cc_start: 0.8925 (OUTLIER) cc_final: 0.8498 (mmt) REVERT: A 587 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.6864 (mm-40) REVERT: A 647 TYR cc_start: 0.8540 (OUTLIER) cc_final: 0.8122 (m-80) REVERT: A 663 LYS cc_start: 0.8955 (mptp) cc_final: 0.8622 (mttt) REVERT: A 669 LYS cc_start: 0.7979 (ttmt) cc_final: 0.7328 (mtpt) REVERT: A 697 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8258 (pttp) REVERT: A 952 ARG cc_start: 0.7146 (ptp-170) cc_final: 0.6807 (ptp-170) REVERT: A 957 ILE cc_start: 0.7732 (mp) cc_final: 0.7365 (tp) REVERT: B 461 ASN cc_start: 0.7433 (t0) cc_final: 0.7142 (t0) REVERT: B 515 PHE cc_start: 0.9088 (m-10) cc_final: 0.8802 (m-10) REVERT: B 635 SER cc_start: 0.8475 (t) cc_final: 0.8093 (p) REVERT: B 695 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.6967 (mptt) REVERT: B 764 ASN cc_start: 0.8464 (m110) cc_final: 0.8002 (m-40) REVERT: C 585 MET cc_start: 0.8942 (OUTLIER) cc_final: 0.8138 (mmt) REVERT: C 651 ASP cc_start: 0.7605 (t70) cc_final: 0.7375 (p0) REVERT: C 663 LYS cc_start: 0.8974 (mttp) cc_final: 0.8588 (mttt) REVERT: C 669 LYS cc_start: 0.7972 (ttmt) cc_final: 0.7305 (mtpt) REVERT: C 673 TYR cc_start: 0.8473 (t80) cc_final: 0.8256 (t80) REVERT: C 860 TYR cc_start: 0.8371 (m-80) cc_final: 0.7855 (m-80) REVERT: C 879 LYS cc_start: 0.8609 (ttmt) cc_final: 0.8324 (ttmt) REVERT: C 952 ARG cc_start: 0.7024 (ptp-170) cc_final: 0.6660 (ptp-170) REVERT: C 957 ILE cc_start: 0.7635 (mp) cc_final: 0.7288 (tp) REVERT: C 985 ASN cc_start: 0.8020 (m-40) cc_final: 0.7756 (m110) REVERT: D 415 LEU cc_start: 0.8035 (mt) cc_final: 0.7829 (mt) REVERT: D 461 ASN cc_start: 0.7486 (t0) cc_final: 0.7183 (t0) REVERT: D 635 SER cc_start: 0.8351 (t) cc_final: 0.7980 (p) REVERT: D 695 LYS cc_start: 0.7778 (OUTLIER) cc_final: 0.6855 (mptt) REVERT: D 719 ASP cc_start: 0.7528 (t0) cc_final: 0.7186 (t0) REVERT: D 721 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.8153 (ttp) REVERT: D 817 LYS cc_start: 0.7812 (tppt) cc_final: 0.7593 (ttmt) REVERT: E 148 TYR cc_start: 0.8240 (t80) cc_final: 0.7780 (t80) outliers start: 54 outliers final: 44 residues processed: 314 average time/residue: 0.1566 time to fit residues: 76.0964 Evaluate side-chains 321 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 269 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 695 LYS Chi-restraints excluded: chain B residue 696 SER Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 705 GLU Chi-restraints excluded: chain B residue 729 SER Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 661 ARG Chi-restraints excluded: chain C residue 719 ASP Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 962 SER Chi-restraints excluded: chain C residue 1013 SER Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 644 GLU Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 729 SER Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 790 SER Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 123 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 36 optimal weight: 1.9990 chunk 218 optimal weight: 0.0030 chunk 181 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 178 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 150 optimal weight: 5.9990 chunk 44 optimal weight: 0.6980 chunk 117 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 204 optimal weight: 0.9980 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS ** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 950 HIS ** 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 = 0.173050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.124155 restraints weight = 22141.371| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.26 r_work: 0.3079 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20314 Z= 0.143 Angle : 1.229 32.833 27276 Z= 0.471 Chirality : 0.141 2.214 2961 Planarity : 0.004 0.057 3162 Dihedral : 24.941 179.275 4619 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.10 % Favored : 92.59 % Rotamer: Outliers : 2.53 % Allowed : 14.69 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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 (0.18), residues: 2240 helix: 1.84 (0.14), residues: 1318 sheet: -2.14 (0.34), residues: 190 loop : -2.42 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 684 TYR 0.027 0.001 TYR A 980 PHE 0.027 0.001 PHE B 515 TRP 0.018 0.001 TRP D 766 HIS 0.010 0.002 HIS C 883 Details of bonding type rmsd covalent geometry : bond 0.00331 (20308) covalent geometry : angle 1.22778 (27264) SS BOND : bond 0.00194 ( 6) SS BOND : angle 3.25850 ( 12) hydrogen bonds : bond 0.03575 ( 960) hydrogen bonds : angle 3.71266 ( 2808) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5450.16 seconds wall clock time: 94 minutes 16.73 seconds (5656.73 seconds total)