Starting phenix.real_space_refine on Sat Jul 4 12:33:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ss3_40742/07_2026/8ss3_40742.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ss3_40742/07_2026/8ss3_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ss3_40742/07_2026/8ss3_40742.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ss3_40742/07_2026/8ss3_40742.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8ss3_40742/07_2026/8ss3_40742.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ss3_40742/07_2026/8ss3_40742.cif" model { file = "/net/cci-nas-00/data/ceres_data/8ss3_40742/07_2026/8ss3_40742.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ss3_40742/07_2026/8ss3_40742.cif" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 187 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: 167 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: 178 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: 164 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: 127 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: 127 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: 4.17, per 1000 atoms: 0.21 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: 1.96 Conformation dependent library (CDL) restraints added in 844.1 milliseconds 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: 0.54 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: 3.05 Time building geometry restraints manager: 2.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 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 - 35.79: 11351 35.79 - 71.58: 356 71.58 - 107.37: 28 107.37 - 143.16: 9 143.16 - 178.95: 15 Dihedral angle restraints: 11759 sinusoidal: 5177 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 11756 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: 6.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.470 Find NCS groups from input model: 0.400 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 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 : 17.854 178.946 7533 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 are 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/Z covalent geometry : bond 0.04733 / 2.35 (20308) covalent geometry : angle 1.89900 / 0.85 (27264) SS BOND : bond 0.01022 / 0.53 ( 6) SS BOND : angle 2.17489 / 1.34 ( 12) hydrogen bonds : bond 0.30028 / 19.34 ( 960) hydrogen bonds : angle 10.45065 / 7.06 ( 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 : 0.675 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: 0.1518 time to fit residues: 118.9150 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 : 0.711 ------------------------------------------------------------------------------- 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... A 412 HIS 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 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: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.172038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.126979 restraints weight = 22008.159| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.01 r_work: 0.3077 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20314 Z= 0.177 Angle : 1.326 31.283 27276 Z= 0.524 Chirality : 0.154 2.418 2961 Planarity : 0.006 0.063 3162 Dihedral : 21.018 177.463 3405 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.88 % Favored : 92.77 % Rotamer: Outliers : 2.84 % Allowed : 8.87 % Favored : 88.30 % 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 are not related in a simple way. whole: -3.22 (0.15), residues: 2240 helix: -1.30 (0.12), residues: 1306 sheet: -2.72 (0.32), residues: 194 loop : -3.33 (0.18), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 684 TYR 0.019 0.002 TYR C 702 PHE 0.023 0.002 PHE D 541 TRP 0.014 0.001 TRP D 766 HIS 0.008 0.001 HIS C 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.18 (20308) covalent geometry : angle 1.32612 / 0.52 (27264) SS BOND : bond 0.00353 / 0.18 ( 6) SS BOND : angle 1.20696 / 0.84 ( 12) hydrogen bonds : bond 0.05192 / 3.39 ( 960) hydrogen bonds : angle 4.72425 / 3.22 ( 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 382 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 327 time to evaluate : 0.875 Fit side-chains revert: symmetry clash REVERT: A 663 LYS cc_start: 0.8934 (mptp) cc_final: 0.8590 (mttt) REVERT: A 669 LYS cc_start: 0.7833 (ttmt) cc_final: 0.7176 (mtpt) REVERT: A 860 TYR cc_start: 0.8241 (m-80) cc_final: 0.7920 (m-80) REVERT: A 891 PHE cc_start: 0.7658 (m-80) cc_final: 0.7420 (m-80) REVERT: A 897 ARG cc_start: 0.7057 (OUTLIER) cc_final: 0.6852 (mtm-85) REVERT: B 439 LYS cc_start: 0.8532 (mtpm) cc_final: 0.8315 (mtmm) REVERT: B 695 LYS cc_start: 0.7167 (OUTLIER) cc_final: 0.6180 (mptt) REVERT: C 860 TYR cc_start: 0.8330 (m-80) cc_final: 0.7987 (m-80) REVERT: C 879 LYS cc_start: 0.8659 (ttmt) cc_final: 0.8192 (mtpp) REVERT: C 998 TYR cc_start: 0.7602 (p90) cc_final: 0.7340 (p90) REVERT: D 397 VAL cc_start: 0.8382 (OUTLIER) cc_final: 0.8170 (m) REVERT: D 695 LYS cc_start: 0.6553 (OUTLIER) cc_final: 0.5548 (mptt) REVERT: D 715 ARG cc_start: 0.7852 (tpp-160) cc_final: 0.7615 (mmt-90) REVERT: D 770 LYS cc_start: 0.7945 (mmtp) cc_final: 0.7574 (tttp) REVERT: D 817 LYS cc_start: 0.7649 (tppt) cc_final: 0.7320 (ttpt) outliers start: 55 outliers final: 23 residues processed: 363 average time/residue: 0.1416 time to fit residues: 79.6468 Evaluate side-chains 309 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 282 time to evaluate : 0.695 ------------------------------------------------------------------------------- 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 A residue 897 ARG 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 773 CYS 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 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: 0.6980 chunk 96 optimal weight: 0.7980 chunk 206 optimal weight: 4.9990 chunk 91 optimal weight: 0.5980 chunk 145 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 40 optimal weight: 9.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 985 ASN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.170141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.124486 restraints weight = 22080.021| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.05 r_work: 0.3025 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20314 Z= 0.187 Angle : 1.265 32.403 27276 Z= 0.493 Chirality : 0.150 2.395 2961 Planarity : 0.005 0.051 3162 Dihedral : 19.790 179.408 3405 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.10 % Favored : 92.54 % Rotamer: Outliers : 3.81 % Allowed : 10.31 % Favored : 85.88 % 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 are not related in a simple way. whole: -1.57 (0.17), residues: 2240 helix: 0.33 (0.14), residues: 1308 sheet: -2.76 (0.31), residues: 198 loop : -3.06 (0.19), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 684 TYR 0.022 0.002 TYR D 673 PHE 0.020 0.002 PHE C 999 TRP 0.014 0.002 TRP C 861 HIS 0.012 0.002 HIS C 883 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.19 (20308) covalent geometry : angle 1.26552 / 0.49 (27264) SS BOND : bond 0.00342 / 0.18 ( 6) SS BOND : angle 1.03689 / 0.71 ( 12) hydrogen bonds : bond 0.04315 / 2.84 ( 960) hydrogen bonds : angle 4.17750 / 2.85 ( 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: 74 poor density : 290 time to evaluate : 0.742 Fit side-chains revert: symmetry clash REVERT: A 511 LYS cc_start: 0.8424 (mmmt) cc_final: 0.8041 (tptp) REVERT: A 587 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.6818 (mm-40) REVERT: A 663 LYS cc_start: 0.8943 (mptp) cc_final: 0.8616 (mttt) REVERT: A 669 LYS cc_start: 0.7911 (ttmt) cc_final: 0.7361 (mtpt) REVERT: A 697 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8277 (pttp) REVERT: A 952 ARG cc_start: 0.6836 (ptp-170) cc_final: 0.6533 (ptp-170) REVERT: B 415 LEU cc_start: 0.7911 (mt) cc_final: 0.7628 (mt) REVERT: B 439 LYS cc_start: 0.8590 (mtpm) cc_final: 0.8343 (mtmm) REVERT: B 461 ASN cc_start: 0.7608 (t0) cc_final: 0.7038 (t0) REVERT: B 695 LYS cc_start: 0.7364 (OUTLIER) cc_final: 0.6354 (mptt) REVERT: C 585 MET cc_start: 0.9021 (OUTLIER) cc_final: 0.8284 (mmt) REVERT: C 697 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8030 (pttp) REVERT: C 860 TYR cc_start: 0.8398 (m-80) cc_final: 0.8064 (m-80) REVERT: C 877 GLU cc_start: 0.8074 (tt0) cc_final: 0.7850 (tt0) REVERT: C 879 LYS cc_start: 0.8654 (ttmt) cc_final: 0.8209 (mtpp) REVERT: C 985 ASN cc_start: 0.8148 (m-40) cc_final: 0.7934 (m110) REVERT: C 998 TYR cc_start: 0.8000 (p90) cc_final: 0.7762 (p90) REVERT: D 414 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.8142 (ptp) REVERT: D 461 ASN cc_start: 0.7743 (t0) cc_final: 0.7168 (t0) REVERT: D 635 SER cc_start: 0.8728 (t) cc_final: 0.8247 (p) REVERT: D 695 LYS cc_start: 0.7298 (OUTLIER) cc_final: 0.6222 (mptt) REVERT: D 764 ASN cc_start: 0.8407 (m110) cc_final: 0.7961 (m-40) REVERT: D 770 LYS cc_start: 0.8018 (mmtp) cc_final: 0.7791 (tttp) REVERT: D 817 LYS cc_start: 0.7727 (tppt) cc_final: 0.7401 (ttpt) REVERT: E 148 TYR cc_start: 0.8213 (t80) cc_final: 0.7771 (t80) outliers start: 74 outliers final: 35 residues processed: 344 average time/residue: 0.1402 time to fit residues: 75.2213 Evaluate side-chains 317 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 275 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 697 LYS 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 697 LYS 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 414 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 476 ILE 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 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: 0.5980 chunk 121 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 185 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 196 optimal weight: 0.9980 chunk 96 optimal weight: 0.6980 chunk 77 optimal weight: 0.0770 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 985 ASN ** 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 = 0.3890 r_free = 0.3890 target = 0.171411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.126252 restraints weight = 22010.491| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.05 r_work: 0.3051 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20314 Z= 0.142 Angle : 1.225 32.043 27276 Z= 0.470 Chirality : 0.148 2.300 2961 Planarity : 0.004 0.044 3162 Dihedral : 19.126 179.970 3405 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.70 % Favored : 92.95 % Rotamer: Outliers : 3.20 % Allowed : 11.86 % Favored : 84.95 % 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 are not related in a simple way. whole: -0.74 (0.18), residues: 2240 helix: 1.09 (0.14), residues: 1314 sheet: -2.58 (0.32), residues: 198 loop : -2.89 (0.20), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 684 TYR 0.018 0.002 TYR F 155 PHE 0.017 0.001 PHE B 438 TRP 0.009 0.001 TRP D 766 HIS 0.009 0.002 HIS C 883 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (20308) covalent geometry : angle 1.22465 / 0.47 (27264) SS BOND : bond 0.00959 / 0.49 ( 6) SS BOND : angle 1.82176 / 1.03 ( 12) hydrogen bonds : bond 0.03723 / 2.44 ( 960) hydrogen bonds : angle 3.93003 / 2.68 ( 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: 62 poor density : 291 time to evaluate : 0.469 Fit side-chains REVERT: A 511 LYS cc_start: 0.8369 (mmmt) cc_final: 0.8006 (tptp) REVERT: A 647 TYR cc_start: 0.8613 (OUTLIER) cc_final: 0.7972 (m-80) REVERT: A 663 LYS cc_start: 0.8975 (mptp) cc_final: 0.8621 (mttt) REVERT: A 669 LYS cc_start: 0.7942 (ttmt) cc_final: 0.7396 (mtpt) REVERT: A 697 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8152 (pttp) REVERT: A 952 ARG cc_start: 0.6858 (ptp-170) cc_final: 0.6558 (ptp-170) REVERT: A 957 ILE cc_start: 0.7691 (mp) cc_final: 0.7333 (tp) REVERT: A 985 ASN cc_start: 0.8172 (m-40) cc_final: 0.7883 (m-40) REVERT: B 415 LEU cc_start: 0.7953 (mt) cc_final: 0.7703 (mt) REVERT: B 439 LYS cc_start: 0.8582 (mtpm) cc_final: 0.8305 (mtmm) REVERT: B 461 ASN cc_start: 0.7566 (t0) cc_final: 0.7016 (t0) REVERT: B 695 LYS cc_start: 0.7490 (OUTLIER) cc_final: 0.6468 (mptt) REVERT: B 764 ASN cc_start: 0.8375 (m110) cc_final: 0.7906 (m-40) REVERT: C 585 MET cc_start: 0.8966 (OUTLIER) cc_final: 0.8296 (mmt) REVERT: C 663 LYS cc_start: 0.9029 (mttp) cc_final: 0.8619 (mttt) REVERT: C 721 MET cc_start: 0.8795 (ptt) cc_final: 0.8584 (ptt) REVERT: C 860 TYR cc_start: 0.8353 (m-80) cc_final: 0.8089 (m-80) REVERT: C 879 LYS cc_start: 0.8662 (ttmt) cc_final: 0.8279 (mtpt) REVERT: C 985 ASN cc_start: 0.8093 (m-40) cc_final: 0.7768 (m110) REVERT: D 414 MET cc_start: 0.8541 (OUTLIER) cc_final: 0.8142 (ptp) REVERT: D 415 LEU cc_start: 0.8040 (mt) cc_final: 0.7778 (mt) REVERT: D 443 THR cc_start: 0.8210 (m) cc_final: 0.7995 (m) REVERT: D 461 ASN cc_start: 0.7741 (t0) cc_final: 0.7182 (t0) REVERT: D 635 SER cc_start: 0.8572 (t) cc_final: 0.8100 (p) REVERT: D 695 LYS cc_start: 0.7102 (OUTLIER) cc_final: 0.6115 (mptt) REVERT: D 719 ASP cc_start: 0.7723 (t0) cc_final: 0.7286 (t0) REVERT: D 770 LYS cc_start: 0.8077 (mmtp) cc_final: 0.7840 (tttp) REVERT: D 817 LYS cc_start: 0.7756 (tppt) cc_final: 0.7445 (ttpt) outliers start: 62 outliers final: 33 residues processed: 334 average time/residue: 0.1294 time to fit residues: 68.5856 Evaluate side-chains 311 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 272 time to evaluate : 0.565 ------------------------------------------------------------------------------- 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 627 GLU Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 697 LYS 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 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 664 ILE Chi-restraints excluded: chain B residue 695 LYS Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 503 MET 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 654 SER Chi-restraints excluded: chain C residue 719 ASP Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 856 VAL 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 16 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 chunk 160 optimal weight: 9.9990 chunk 14 optimal weight: 0.6980 chunk 115 optimal weight: 2.9990 chunk 206 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 173 optimal weight: 0.7980 chunk 190 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 412 HIS A 764 ASN ** A 950 HIS ** 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** F 75 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.167326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.122140 restraints weight = 21929.143| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.95 r_work: 0.2993 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 20314 Z= 0.232 Angle : 1.262 32.229 27276 Z= 0.492 Chirality : 0.147 2.316 2961 Planarity : 0.004 0.050 3162 Dihedral : 18.900 177.923 3405 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.28 % Favored : 92.37 % Rotamer: Outliers : 4.07 % Allowed : 11.96 % Favored : 83.97 % 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 are not related in a simple way. whole: -0.57 (0.18), residues: 2240 helix: 1.23 (0.14), residues: 1302 sheet: -2.72 (0.32), residues: 190 loop : -2.71 (0.20), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 684 TYR 0.018 0.002 TYR B 816 PHE 0.019 0.002 PHE C 495 TRP 0.016 0.002 TRP D 766 HIS 0.009 0.002 HIS C 883 Details of bonding type rmsd/Z covalent geometry : bond 0.00565 / 0.23 (20308) covalent geometry : angle 1.26199 / 0.49 (27264) SS BOND : bond 0.00267 / 0.14 ( 6) SS BOND : angle 2.09734 / 1.07 ( 12) hydrogen bonds : bond 0.04171 / 2.75 ( 960) hydrogen bonds : angle 4.00732 / 2.73 ( 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 357 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 278 time to evaluate : 0.745 Fit side-chains REVERT: A 585 MET cc_start: 0.9103 (OUTLIER) cc_final: 0.8526 (mmt) REVERT: A 587 GLN cc_start: 0.8922 (OUTLIER) cc_final: 0.7061 (mm-40) REVERT: A 663 LYS cc_start: 0.9008 (mptp) cc_final: 0.8657 (mttt) REVERT: A 669 LYS cc_start: 0.8001 (ttmt) cc_final: 0.7348 (mtpt) REVERT: A 684 ARG cc_start: 0.8713 (ttm110) cc_final: 0.8505 (ttm110) REVERT: A 697 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8300 (pttp) REVERT: A 880 MET cc_start: 0.7798 (tpp) cc_final: 0.7549 (tpp) REVERT: A 952 ARG cc_start: 0.6906 (ptp-170) cc_final: 0.6548 (ptp-170) REVERT: A 957 ILE cc_start: 0.7729 (mp) cc_final: 0.7362 (tp) REVERT: A 985 ASN cc_start: 0.8154 (m-40) cc_final: 0.7852 (m110) REVERT: A 987 GLU cc_start: 0.7313 (tp30) cc_final: 0.7052 (tp30) REVERT: B 415 LEU cc_start: 0.8054 (mt) cc_final: 0.7811 (mt) REVERT: B 439 LYS cc_start: 0.8599 (mtpm) cc_final: 0.8229 (mtmm) REVERT: B 461 ASN cc_start: 0.7653 (t0) cc_final: 0.7097 (t0) REVERT: B 515 PHE cc_start: 0.9167 (m-80) cc_final: 0.8945 (m-10) REVERT: B 635 SER cc_start: 0.8668 (t) cc_final: 0.8148 (p) REVERT: B 695 LYS cc_start: 0.7791 (OUTLIER) cc_final: 0.6757 (mptt) REVERT: B 764 ASN cc_start: 0.8438 (m110) cc_final: 0.7989 (m-40) REVERT: C 585 MET cc_start: 0.9086 (OUTLIER) cc_final: 0.8325 (mmt) REVERT: C 663 LYS cc_start: 0.9037 (mttp) cc_final: 0.8640 (mttt) REVERT: C 669 LYS cc_start: 0.7962 (ttmt) cc_final: 0.7369 (mtpt) REVERT: C 697 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8226 (pttp) REVERT: C 789 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8793 (tt) REVERT: C 860 TYR cc_start: 0.8395 (m-80) cc_final: 0.7882 (m-80) REVERT: C 879 LYS cc_start: 0.8621 (ttmt) cc_final: 0.8228 (mtpt) REVERT: C 985 ASN cc_start: 0.8122 (m-40) cc_final: 0.7861 (m110) REVERT: C 987 GLU cc_start: 0.7450 (tp30) cc_final: 0.7206 (tp30) REVERT: D 414 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.8095 (ptp) REVERT: D 415 LEU cc_start: 0.8051 (mt) cc_final: 0.7744 (mt) REVERT: D 461 ASN cc_start: 0.7761 (t0) cc_final: 0.7207 (t0) REVERT: D 635 SER cc_start: 0.8644 (t) cc_final: 0.8192 (p) REVERT: D 695 LYS cc_start: 0.7517 (OUTLIER) cc_final: 0.6429 (mptt) REVERT: D 719 ASP cc_start: 0.7783 (t0) cc_final: 0.7377 (t0) REVERT: D 770 LYS cc_start: 0.8234 (mmtp) cc_final: 0.7903 (tttp) REVERT: D 817 LYS cc_start: 0.7771 (tppt) cc_final: 0.7375 (ttmt) REVERT: E 148 TYR cc_start: 0.8260 (t80) cc_final: 0.7741 (t80) outliers start: 79 outliers final: 50 residues processed: 335 average time/residue: 0.1404 time to fit residues: 72.7845 Evaluate side-chains 326 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 267 time to evaluate : 0.636 ------------------------------------------------------------------------------- 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 666 VAL Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain A residue 719 ASP Chi-restraints excluded: chain A residue 736 THR 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 524 GLU Chi-restraints excluded: chain B residue 631 SER 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 704 LEU Chi-restraints excluded: chain B residue 729 SER 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 498 LEU Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 508 GLN 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 652 SER Chi-restraints excluded: chain C residue 654 SER 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 736 THR Chi-restraints excluded: chain C residue 789 LEU 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 72 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 195 optimal weight: 0.5980 chunk 170 optimal weight: 0.5980 chunk 214 optimal weight: 0.8980 chunk 139 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 chunk 140 optimal weight: 1.9990 chunk 156 optimal weight: 0.5980 chunk 177 optimal weight: 0.5980 chunk 60 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 764 ASN ** 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 = 0.3921 r_free = 0.3921 target = 0.172499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.124330 restraints weight = 22172.928| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.19 r_work: 0.3043 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20314 Z= 0.136 Angle : 1.222 32.062 27276 Z= 0.469 Chirality : 0.147 2.275 2961 Planarity : 0.004 0.044 3162 Dihedral : 18.566 177.181 3405 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.79 % Favored : 92.86 % Rotamer: Outliers : 3.25 % Allowed : 13.56 % Favored : 83.20 % 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 are not related in a simple way. whole: -0.24 (0.18), residues: 2240 helix: 1.53 (0.15), residues: 1314 sheet: -2.60 (0.32), residues: 190 loop : -2.69 (0.20), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 684 TYR 0.022 0.001 TYR E 155 PHE 0.017 0.001 PHE B 438 TRP 0.014 0.001 TRP D 766 HIS 0.023 0.002 HIS C 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (20308) covalent geometry : angle 1.22035 / 0.47 (27264) SS BOND : bond 0.00212 / 0.12 ( 6) SS BOND : angle 3.35554 / 1.80 ( 12) hydrogen bonds : bond 0.03652 / 2.40 ( 960) hydrogen bonds : angle 3.82450 / 2.61 ( 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 350 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 287 time to evaluate : 0.751 Fit side-chains REVERT: A 511 LYS cc_start: 0.8435 (mmmt) cc_final: 0.8105 (tptp) REVERT: A 587 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.6761 (mm-40) REVERT: A 647 TYR cc_start: 0.8495 (OUTLIER) cc_final: 0.7846 (m-80) REVERT: A 651 ASP cc_start: 0.7265 (t70) cc_final: 0.6976 (p0) REVERT: A 663 LYS cc_start: 0.8942 (mptp) cc_final: 0.8596 (mttt) REVERT: A 669 LYS cc_start: 0.7877 (ttmt) cc_final: 0.7254 (mtpt) REVERT: A 697 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8234 (pttp) REVERT: A 858 THR cc_start: 0.9066 (t) cc_final: 0.8803 (p) REVERT: A 952 ARG cc_start: 0.6937 (ptp-170) cc_final: 0.6588 (ptp-170) REVERT: A 957 ILE cc_start: 0.7668 (mp) cc_final: 0.7309 (tp) REVERT: A 985 ASN cc_start: 0.8054 (m-40) cc_final: 0.7752 (m110) REVERT: A 987 GLU cc_start: 0.7220 (tp30) cc_final: 0.6973 (tp30) REVERT: B 415 LEU cc_start: 0.7999 (mt) cc_final: 0.7797 (mt) REVERT: B 461 ASN cc_start: 0.7439 (t0) cc_final: 0.6986 (t0) REVERT: B 635 SER cc_start: 0.8522 (t) cc_final: 0.8039 (p) REVERT: B 695 LYS cc_start: 0.7527 (OUTLIER) cc_final: 0.6542 (mptt) REVERT: B 764 ASN cc_start: 0.8379 (m110) cc_final: 0.7893 (m-40) REVERT: C 585 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8102 (mmt) REVERT: C 634 GLU cc_start: 0.8037 (pt0) cc_final: 0.7602 (pm20) REVERT: C 663 LYS cc_start: 0.8996 (mttp) cc_final: 0.8592 (mttt) REVERT: C 669 LYS cc_start: 0.7866 (ttmt) cc_final: 0.7283 (mtpt) REVERT: C 860 TYR cc_start: 0.8306 (m-80) cc_final: 0.7872 (m-80) REVERT: C 879 LYS cc_start: 0.8691 (ttmt) cc_final: 0.8332 (mtpt) REVERT: C 957 ILE cc_start: 0.7694 (mp) cc_final: 0.7379 (tp) REVERT: C 985 ASN cc_start: 0.8020 (m-40) cc_final: 0.7766 (m110) REVERT: C 987 GLU cc_start: 0.7373 (tp30) cc_final: 0.7111 (tp30) REVERT: D 414 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.8022 (ptp) REVERT: D 461 ASN cc_start: 0.7511 (t0) cc_final: 0.7099 (t0) REVERT: D 635 SER cc_start: 0.8489 (t) cc_final: 0.8066 (p) REVERT: D 695 LYS cc_start: 0.7381 (OUTLIER) cc_final: 0.6374 (mptt) REVERT: D 719 ASP cc_start: 0.7508 (t0) cc_final: 0.7081 (t0) REVERT: D 770 LYS cc_start: 0.8121 (mmtp) cc_final: 0.7852 (tttp) REVERT: D 817 LYS cc_start: 0.7785 (tppt) cc_final: 0.7480 (ttmt) REVERT: E 100 TYR cc_start: 0.7928 (t80) cc_final: 0.7726 (t80) REVERT: E 148 TYR cc_start: 0.8212 (t80) cc_final: 0.7799 (t80) outliers start: 63 outliers final: 41 residues processed: 331 average time/residue: 0.1477 time to fit residues: 77.2639 Evaluate side-chains 321 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 273 time to evaluate : 0.725 ------------------------------------------------------------------------------- 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 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 719 ASP 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 524 GLU Chi-restraints excluded: chain B residue 644 GLU 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 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 503 MET 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 719 ASP Chi-restraints excluded: chain C residue 736 THR 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 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 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 729 SER Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 790 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 181 optimal weight: 4.9990 chunk 224 optimal weight: 1.9990 chunk 12 optimal weight: 0.0870 chunk 177 optimal weight: 0.5980 chunk 167 optimal weight: 0.9990 chunk 208 optimal weight: 9.9990 chunk 92 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 45 optimal weight: 4.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 412 HIS ** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 HIS 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 = 0.3925 r_free = 0.3925 target = 0.172995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.124779 restraints weight = 22211.626| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.23 r_work: 0.3069 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 20314 Z= 0.139 Angle : 1.219 31.725 27276 Z= 0.466 Chirality : 0.146 2.246 2961 Planarity : 0.004 0.040 3162 Dihedral : 18.259 177.404 3405 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.79 % Favored : 92.86 % Rotamer: Outliers : 3.56 % Allowed : 13.61 % 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 are not related in a simple way. whole: 0.00 (0.18), residues: 2240 helix: 1.71 (0.15), residues: 1312 sheet: -2.47 (0.32), residues: 190 loop : -2.58 (0.21), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 684 TYR 0.027 0.001 TYR C 980 PHE 0.021 0.001 PHE B 438 TRP 0.012 0.001 TRP B 766 HIS 0.009 0.001 HIS A 883 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (20308) covalent geometry : angle 1.21642 / 0.46 (27264) SS BOND : bond 0.00523 / 0.27 ( 6) SS BOND : angle 3.68301 / 1.95 ( 12) hydrogen bonds : bond 0.03558 / 2.35 ( 960) hydrogen bonds : angle 3.75696 / 2.56 ( 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 362 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 293 time to evaluate : 0.687 Fit side-chains REVERT: A 511 LYS cc_start: 0.8427 (mmmt) cc_final: 0.8118 (tptp) REVERT: A 585 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.8255 (mmt) REVERT: A 587 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.6802 (mm-40) REVERT: A 647 TYR cc_start: 0.8477 (OUTLIER) cc_final: 0.7882 (m-80) REVERT: A 663 LYS cc_start: 0.8950 (mptp) cc_final: 0.8637 (mttt) REVERT: A 669 LYS cc_start: 0.7975 (ttmt) cc_final: 0.7379 (mtpt) REVERT: A 697 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8179 (pttp) REVERT: A 858 THR cc_start: 0.9128 (t) cc_final: 0.8900 (p) REVERT: A 952 ARG cc_start: 0.7056 (ptp-170) cc_final: 0.6702 (ptp-170) REVERT: A 957 ILE cc_start: 0.7731 (mp) cc_final: 0.7391 (tp) REVERT: A 987 GLU cc_start: 0.7287 (tp30) cc_final: 0.7038 (tp30) REVERT: B 461 ASN cc_start: 0.7451 (t0) cc_final: 0.7089 (t0) REVERT: B 635 SER cc_start: 0.8547 (t) cc_final: 0.8129 (p) REVERT: B 695 LYS cc_start: 0.7759 (OUTLIER) cc_final: 0.6851 (mptt) REVERT: B 764 ASN cc_start: 0.8498 (m110) cc_final: 0.8065 (m-40) REVERT: C 585 MET cc_start: 0.8849 (OUTLIER) cc_final: 0.8087 (mmt) REVERT: C 634 GLU cc_start: 0.8018 (pt0) cc_final: 0.7641 (pm20) REVERT: C 663 LYS cc_start: 0.8975 (mttp) cc_final: 0.8601 (mttt) REVERT: C 669 LYS cc_start: 0.7957 (ttmt) cc_final: 0.7370 (mtpt) REVERT: C 697 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8165 (pttp) REVERT: C 879 LYS cc_start: 0.8557 (ttmt) cc_final: 0.8121 (mtpt) REVERT: C 901 PHE cc_start: 0.7260 (m-10) cc_final: 0.6984 (m-10) REVERT: C 952 ARG cc_start: 0.7029 (ptp-170) cc_final: 0.6712 (ptp-170) REVERT: C 957 ILE cc_start: 0.7735 (mp) cc_final: 0.7428 (tp) REVERT: C 985 ASN cc_start: 0.8028 (m-40) cc_final: 0.7760 (m110) REVERT: D 461 ASN cc_start: 0.7488 (t0) cc_final: 0.7179 (t0) REVERT: D 635 SER cc_start: 0.8434 (t) cc_final: 0.8063 (p) REVERT: D 695 LYS cc_start: 0.7507 (OUTLIER) cc_final: 0.6555 (mptt) REVERT: D 719 ASP cc_start: 0.7562 (t0) cc_final: 0.7138 (t0) REVERT: D 817 LYS cc_start: 0.7834 (tppt) cc_final: 0.7575 (ttmt) REVERT: E 148 TYR cc_start: 0.8333 (t80) cc_final: 0.7927 (t80) REVERT: F 98 LEU cc_start: 0.7382 (tp) cc_final: 0.7125 (tt) outliers start: 69 outliers final: 43 residues processed: 337 average time/residue: 0.1517 time to fit residues: 80.3899 Evaluate side-chains 335 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 284 time to evaluate : 0.848 ------------------------------------------------------------------------------- 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 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 719 ASP Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 1027 LEU 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 644 GLU 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 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 412 HIS Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 503 MET 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 652 SER Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 719 ASP Chi-restraints excluded: chain C residue 736 THR 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 729 SER Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 790 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 107 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 147 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 26 optimal weight: 4.9990 chunk 31 optimal weight: 0.2980 chunk 223 optimal weight: 9.9990 chunk 184 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 985 ASN ** 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 = 0.3917 r_free = 0.3917 target = 0.172106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.125037 restraints weight = 22016.070| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.26 r_work: 0.3116 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20314 Z= 0.146 Angle : 1.229 31.586 27276 Z= 0.472 Chirality : 0.146 2.240 2961 Planarity : 0.004 0.057 3162 Dihedral : 18.132 178.368 3405 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.01 % Favored : 92.63 % Rotamer: Outliers : 2.89 % Allowed : 14.33 % 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 are not related in a simple way. whole: 0.07 (0.18), residues: 2240 helix: 1.76 (0.15), residues: 1314 sheet: -2.39 (0.33), residues: 190 loop : -2.56 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 684 TYR 0.027 0.002 TYR C 980 PHE 0.040 0.001 PHE B 515 TRP 0.014 0.001 TRP B 766 HIS 0.015 0.002 HIS C 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (20308) covalent geometry : angle 1.22378 / 0.47 (27264) SS BOND : bond 0.00751 / 0.39 ( 6) SS BOND : angle 5.72992 / 3.09 ( 12) hydrogen bonds : bond 0.03576 / 2.35 ( 960) hydrogen bonds : angle 3.74171 / 2.55 ( 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 340 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 284 time to evaluate : 0.721 Fit side-chains REVERT: A 511 LYS cc_start: 0.8402 (mmmt) cc_final: 0.8034 (tptp) REVERT: A 585 MET cc_start: 0.8888 (OUTLIER) cc_final: 0.8253 (mmt) REVERT: A 587 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.6776 (mm-40) REVERT: A 647 TYR cc_start: 0.8489 (OUTLIER) cc_final: 0.7844 (m-10) REVERT: A 651 ASP cc_start: 0.6930 (p0) cc_final: 0.6729 (p0) REVERT: A 663 LYS cc_start: 0.8957 (mptp) cc_final: 0.8647 (mttt) REVERT: A 669 LYS cc_start: 0.8005 (ttmt) cc_final: 0.7413 (mtpt) REVERT: A 697 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.8180 (pttp) REVERT: A 952 ARG cc_start: 0.7139 (ptp-170) cc_final: 0.6782 (ptp-170) REVERT: A 957 ILE cc_start: 0.7750 (mp) cc_final: 0.7419 (tp) REVERT: A 985 ASN cc_start: 0.8064 (m-40) cc_final: 0.7863 (m110) REVERT: A 987 GLU cc_start: 0.7307 (tp30) cc_final: 0.7062 (tp30) REVERT: B 461 ASN cc_start: 0.7415 (t0) cc_final: 0.7133 (t0) REVERT: B 515 PHE cc_start: 0.9056 (m-10) cc_final: 0.8851 (m-10) REVERT: B 635 SER cc_start: 0.8552 (t) cc_final: 0.8154 (p) REVERT: B 695 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.6921 (mptt) REVERT: B 764 ASN cc_start: 0.8517 (m110) cc_final: 0.8091 (m-40) REVERT: C 585 MET cc_start: 0.8874 (OUTLIER) cc_final: 0.8124 (mmt) REVERT: C 634 GLU cc_start: 0.8033 (pt0) cc_final: 0.7813 (pm20) REVERT: C 663 LYS cc_start: 0.8980 (mttp) cc_final: 0.8614 (mttt) REVERT: C 669 LYS cc_start: 0.7996 (ttmt) cc_final: 0.7367 (mtpt) REVERT: C 697 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8159 (pttp) REVERT: C 860 TYR cc_start: 0.8448 (m-80) cc_final: 0.7995 (m-80) REVERT: C 879 LYS cc_start: 0.8660 (ttmt) cc_final: 0.8313 (ttmm) REVERT: C 901 PHE cc_start: 0.7297 (m-10) cc_final: 0.6987 (m-10) REVERT: C 952 ARG cc_start: 0.7117 (ptp-170) cc_final: 0.6774 (ptp-170) REVERT: C 957 ILE cc_start: 0.7730 (mp) cc_final: 0.7426 (tp) REVERT: C 985 ASN cc_start: 0.8057 (m-40) cc_final: 0.7797 (m110) REVERT: D 461 ASN cc_start: 0.7526 (t0) cc_final: 0.7233 (t0) REVERT: D 635 SER cc_start: 0.8458 (t) cc_final: 0.8108 (p) REVERT: D 695 LYS cc_start: 0.7596 (OUTLIER) cc_final: 0.6695 (mptt) REVERT: D 719 ASP cc_start: 0.7587 (t0) cc_final: 0.7172 (t0) REVERT: D 817 LYS cc_start: 0.7818 (tppt) cc_final: 0.7571 (ttmt) REVERT: E 148 TYR cc_start: 0.8350 (t80) cc_final: 0.7950 (t80) REVERT: F 98 LEU cc_start: 0.7395 (tp) cc_final: 0.7142 (tt) outliers start: 56 outliers final: 38 residues processed: 322 average time/residue: 0.1450 time to fit residues: 73.5318 Evaluate side-chains 317 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 271 time to evaluate : 0.668 ------------------------------------------------------------------------------- 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 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 719 ASP Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 839 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 591 ILE Chi-restraints excluded: chain B residue 644 GLU 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 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 547 SER Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 719 ASP Chi-restraints excluded: chain C residue 736 THR 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 729 SER Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 790 SER 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: 0.6980 chunk 187 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 216 optimal weight: 10.0000 chunk 177 optimal weight: 0.9980 chunk 171 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 100 optimal weight: 0.0170 chunk 224 optimal weight: 0.6980 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3927 r_free = 0.3927 target = 0.173217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.124275 restraints weight = 22039.588| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.21 r_work: 0.3123 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.4072 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= 0.140 Angle : 1.222 31.517 27276 Z= 0.468 Chirality : 0.146 2.228 2961 Planarity : 0.004 0.057 3162 Dihedral : 17.865 179.579 3405 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.79 % Favored : 92.86 % Rotamer: Outliers : 2.99 % Allowed : 14.12 % Favored : 82.89 % 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 are not related in a simple way. whole: 0.16 (0.18), residues: 2240 helix: 1.81 (0.15), residues: 1318 sheet: -2.27 (0.33), residues: 190 loop : -2.51 (0.21), residues: 732 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 0.027 0.001 PHE B 515 TRP 0.016 0.001 TRP D 766 HIS 0.009 0.001 HIS A 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (20308) covalent geometry : angle 1.22068 / 0.47 (27264) SS BOND : bond 0.00266 / 0.14 ( 6) SS BOND : angle 3.23801 / 1.72 ( 12) hydrogen bonds : bond 0.03528 / 2.33 ( 960) hydrogen bonds : angle 3.71695 / 2.53 ( 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 332 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 274 time to evaluate : 0.723 Fit side-chains REVERT: A 511 LYS cc_start: 0.8400 (mmmt) cc_final: 0.8026 (tptp) REVERT: A 585 MET cc_start: 0.8880 (OUTLIER) cc_final: 0.8236 (mmt) REVERT: A 587 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.6780 (mm-40) REVERT: A 647 TYR cc_start: 0.8486 (OUTLIER) cc_final: 0.7858 (m-10) REVERT: A 663 LYS cc_start: 0.8950 (mptp) cc_final: 0.8641 (mttt) REVERT: A 669 LYS cc_start: 0.8000 (ttmt) cc_final: 0.7406 (mtpt) REVERT: A 697 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8184 (pttp) REVERT: A 952 ARG cc_start: 0.7116 (ptp-170) cc_final: 0.6754 (ptp-170) REVERT: A 957 ILE cc_start: 0.7765 (mp) cc_final: 0.7426 (tp) REVERT: A 985 ASN cc_start: 0.8131 (m-40) cc_final: 0.7814 (m-40) REVERT: B 461 ASN cc_start: 0.7401 (t0) cc_final: 0.7143 (t0) REVERT: B 515 PHE cc_start: 0.9052 (m-10) cc_final: 0.8850 (m-10) REVERT: B 635 SER cc_start: 0.8452 (t) cc_final: 0.8074 (p) REVERT: B 695 LYS cc_start: 0.7790 (OUTLIER) cc_final: 0.6951 (mptt) REVERT: B 764 ASN cc_start: 0.8499 (m110) cc_final: 0.8072 (m-40) REVERT: C 585 MET cc_start: 0.8855 (OUTLIER) cc_final: 0.8105 (mmt) REVERT: C 634 GLU cc_start: 0.8073 (pt0) cc_final: 0.7835 (pm20) REVERT: C 663 LYS cc_start: 0.8990 (mttp) cc_final: 0.8626 (mttt) REVERT: C 669 LYS cc_start: 0.8013 (ttmt) cc_final: 0.7373 (mtpt) REVERT: C 673 TYR cc_start: 0.8473 (t80) cc_final: 0.8224 (t80) REVERT: C 697 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8162 (pttp) REVERT: C 860 TYR cc_start: 0.8440 (m-80) cc_final: 0.7993 (m-80) REVERT: C 879 LYS cc_start: 0.8556 (ttmt) cc_final: 0.8219 (ttmm) REVERT: C 901 PHE cc_start: 0.7298 (m-10) cc_final: 0.7016 (m-10) REVERT: C 952 ARG cc_start: 0.7055 (ptp-170) cc_final: 0.6704 (ptp-170) REVERT: C 957 ILE cc_start: 0.7724 (mp) cc_final: 0.7425 (tp) REVERT: C 985 ASN cc_start: 0.8074 (m-40) cc_final: 0.7854 (m110) REVERT: D 461 ASN cc_start: 0.7499 (t0) cc_final: 0.7224 (t0) REVERT: D 635 SER cc_start: 0.8374 (t) cc_final: 0.8056 (p) REVERT: D 695 LYS cc_start: 0.7657 (OUTLIER) cc_final: 0.6792 (mptt) REVERT: D 719 ASP cc_start: 0.7565 (t0) cc_final: 0.7136 (t0) REVERT: D 817 LYS cc_start: 0.7792 (tppt) cc_final: 0.7553 (ttmt) REVERT: E 148 TYR cc_start: 0.8331 (t80) cc_final: 0.7947 (t80) REVERT: F 98 LEU cc_start: 0.7394 (tp) cc_final: 0.7135 (tt) outliers start: 58 outliers final: 43 residues processed: 314 average time/residue: 0.1431 time to fit residues: 71.1369 Evaluate side-chains 320 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 269 time to evaluate : 0.736 ------------------------------------------------------------------------------- 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 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 719 ASP Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 1027 LEU 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 644 GLU 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 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 547 SER 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 697 LYS Chi-restraints excluded: chain C residue 719 ASP Chi-restraints excluded: chain C residue 736 THR 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 729 SER Chi-restraints excluded: chain D residue 746 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 2 optimal weight: 2.9990 chunk 147 optimal weight: 9.9990 chunk 182 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 5 optimal weight: 0.5980 chunk 127 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 192 optimal weight: 0.9980 chunk 203 optimal weight: 5.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3902 r_free = 0.3902 target = 0.170860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.121680 restraints weight = 22269.139| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.29 r_work: 0.3050 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 20314 Z= 0.220 Angle : 1.254 31.699 27276 Z= 0.486 Chirality : 0.146 2.255 2961 Planarity : 0.004 0.067 3162 Dihedral : 17.886 177.558 3405 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.88 % Favored : 92.81 % Rotamer: Outliers : 2.84 % Allowed : 14.74 % Favored : 82.42 % 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 are not related in a simple way. whole: -0.01 (0.18), residues: 2240 helix: 1.65 (0.14), residues: 1316 sheet: -2.36 (0.32), residues: 190 loop : -2.54 (0.21), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 684 TYR 0.026 0.002 TYR C 980 PHE 0.026 0.002 PHE B 515 TRP 0.020 0.002 TRP D 766 HIS 0.021 0.002 HIS A 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.22 (20308) covalent geometry : angle 1.25216 / 0.49 (27264) SS BOND : bond 0.00268 / 0.12 ( 6) SS BOND : angle 3.25410 / 1.71 ( 12) hydrogen bonds : bond 0.03907 / 2.58 ( 960) hydrogen bonds : angle 3.83827 / 2.62 ( 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 327 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 272 time to evaluate : 0.781 Fit side-chains revert: symmetry clash REVERT: A 585 MET cc_start: 0.8933 (OUTLIER) cc_final: 0.8283 (mmt) REVERT: A 587 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.6923 (mm-40) REVERT: A 629 MET cc_start: 0.8352 (mmm) cc_final: 0.8068 (mtt) REVERT: A 647 TYR cc_start: 0.8560 (OUTLIER) cc_final: 0.8100 (m-80) REVERT: A 663 LYS cc_start: 0.8968 (mptp) cc_final: 0.8648 (mttt) REVERT: A 669 LYS cc_start: 0.8017 (ttmt) cc_final: 0.7378 (mtpt) REVERT: A 697 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8267 (pttp) REVERT: A 952 ARG cc_start: 0.7184 (ptp-170) cc_final: 0.6834 (ptp-170) REVERT: A 957 ILE cc_start: 0.7786 (mp) cc_final: 0.7432 (tp) REVERT: A 985 ASN cc_start: 0.8138 (m-40) cc_final: 0.7774 (m-40) REVERT: A 987 GLU cc_start: 0.7140 (tp30) cc_final: 0.6875 (tp30) REVERT: A 1027 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8322 (tt) REVERT: B 461 ASN cc_start: 0.7472 (t0) cc_final: 0.7209 (t0) REVERT: B 515 PHE cc_start: 0.9091 (m-10) cc_final: 0.8886 (m-10) REVERT: B 635 SER cc_start: 0.8513 (t) cc_final: 0.8139 (p) REVERT: B 695 LYS cc_start: 0.7960 (OUTLIER) cc_final: 0.7068 (mptt) REVERT: B 721 MET cc_start: 0.8436 (ttm) cc_final: 0.8223 (ttp) REVERT: B 764 ASN cc_start: 0.8506 (m110) cc_final: 0.8077 (m-40) REVERT: C 585 MET cc_start: 0.8926 (OUTLIER) cc_final: 0.8162 (mmt) REVERT: C 634 GLU cc_start: 0.8124 (pt0) cc_final: 0.7860 (pm20) REVERT: C 651 ASP cc_start: 0.7620 (t70) cc_final: 0.7409 (p0) REVERT: C 663 LYS cc_start: 0.8982 (mttp) cc_final: 0.8615 (mttt) REVERT: C 669 LYS cc_start: 0.8021 (ttmt) cc_final: 0.7388 (mtpt) REVERT: C 697 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8166 (pttp) REVERT: C 709 ASN cc_start: 0.9131 (t0) cc_final: 0.8873 (t0) REVERT: C 860 TYR cc_start: 0.8435 (m-80) cc_final: 0.8229 (m-80) REVERT: C 879 LYS cc_start: 0.8573 (ttmt) cc_final: 0.8234 (ttmm) REVERT: C 901 PHE cc_start: 0.7295 (m-10) cc_final: 0.7036 (m-10) REVERT: C 952 ARG cc_start: 0.7058 (ptp-170) cc_final: 0.6697 (ptp-170) REVERT: C 957 ILE cc_start: 0.7754 (mp) cc_final: 0.7419 (tp) REVERT: C 985 ASN cc_start: 0.8107 (m-40) cc_final: 0.7857 (m110) REVERT: C 1027 LEU cc_start: 0.8611 (tt) cc_final: 0.8373 (tt) REVERT: D 461 ASN cc_start: 0.7518 (t0) cc_final: 0.7235 (t0) REVERT: D 635 SER cc_start: 0.8337 (t) cc_final: 0.8001 (p) REVERT: D 695 LYS cc_start: 0.7800 (OUTLIER) cc_final: 0.6850 (mptt) REVERT: D 719 ASP cc_start: 0.7577 (t0) cc_final: 0.7151 (t0) REVERT: D 817 LYS cc_start: 0.7780 (tppt) cc_final: 0.7522 (ttmt) REVERT: E 148 TYR cc_start: 0.8326 (t80) cc_final: 0.7855 (t80) outliers start: 55 outliers final: 42 residues processed: 314 average time/residue: 0.1525 time to fit residues: 74.8597 Evaluate side-chains 315 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 264 time to evaluate : 0.706 ------------------------------------------------------------------------------- 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 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 736 THR Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 1027 LEU 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 664 ILE 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 399 THR Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 498 LEU 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 652 SER Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 719 ASP Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 742 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 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 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 Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain F residue 122 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 36 optimal weight: 4.9990 chunk 218 optimal weight: 0.7980 chunk 181 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 178 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 150 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 117 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 204 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3922 r_free = 0.3922 target = 0.172749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.124904 restraints weight = 22108.440| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.33 r_work: 0.3043 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.4164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 20314 Z= 0.147 Angle : 1.230 31.594 27276 Z= 0.472 Chirality : 0.146 2.237 2961 Planarity : 0.004 0.060 3162 Dihedral : 17.692 176.938 3405 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.23 % Favored : 92.46 % Rotamer: Outliers : 2.73 % Allowed : 14.90 % Favored : 82.37 % 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 are not related in a simple way. whole: 0.15 (0.18), residues: 2240 helix: 1.77 (0.15), residues: 1314 sheet: -2.25 (0.33), residues: 190 loop : -2.46 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 684 TYR 0.026 0.002 TYR C 980 PHE 0.022 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/Z covalent geometry : bond 0.00348 / 0.15 (20308) covalent geometry : angle 1.22805 / 0.47 (27264) SS BOND : bond 0.00253 / 0.13 ( 6) SS BOND : angle 3.19878 / 1.74 ( 12) hydrogen bonds : bond 0.03604 / 2.38 ( 960) hydrogen bonds : angle 3.75854 / 2.57 ( 2808) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5027.99 seconds wall clock time: 87 minutes 1.99 seconds (5221.99 seconds total)