Starting phenix.real_space_refine on Wed Jun 18 06:20:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ss3_40742/06_2025/8ss3_40742.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ss3_40742/06_2025/8ss3_40742.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ss3_40742/06_2025/8ss3_40742.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ss3_40742/06_2025/8ss3_40742.map" model { file = "/net/cci-nas-00/data/ceres_data/8ss3_40742/06_2025/8ss3_40742.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ss3_40742/06_2025/8ss3_40742.cif" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 19887 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4671 Classifications: {'peptide': 596} Link IDs: {'PCIS': 3, 'PTRANS': 14, 'TRANS': 578} Chain breaks: 4 Chain: "B" Number of atoms: 3156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3156 Classifications: {'peptide': 404} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 390} Chain breaks: 2 Chain: "C" Number of atoms: 4671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4671 Classifications: {'peptide': 596} Link IDs: {'PCIS': 3, 'PTRANS': 14, 'TRANS': 578} Chain breaks: 4 Chain: "D" Number of atoms: 3156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3156 Classifications: {'peptide': 404} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 390} Chain breaks: 2 Chain: "E" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1166 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain breaks: 1 Chain: "F" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1166 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain breaks: 1 Chain: "A" Number of atoms: 613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 613 Unusual residues: {'AJP': 3, 'CLR': 2, 'PCW': 12, 'SPD': 1, 'ZK1': 1} Classifications: {'undetermined': 19} Link IDs: {None: 18} Unresolved non-hydrogen bonds: 395 Unresolved non-hydrogen angles: 512 Unresolved non-hydrogen dihedrals: 543 Unresolved non-hydrogen chiralities: 65 Planarities with less than four sites: {'PCW:plan-1': 5, 'PCW:plan-2': 2, 'PCW:plan-3': 5, 'PCW:plan-4': 5} Unresolved non-hydrogen planarities: 63 Chain: "B" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 358 Unusual residues: {'PCW': 10, 'ZK1': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 209 Unresolved non-hydrogen angles: 236 Unresolved non-hydrogen dihedrals: 197 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PCW:plan-1': 3, 'PCW:plan-2': 3, 'PCW:plan-3': 3, 'PCW:plan-4': 4} Unresolved non-hydrogen planarities: 47 Chain: "C" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 449 Unusual residues: {'AJP': 3, 'CLR': 2, 'PCW': 9, 'ZK1': 1} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 387 Unresolved non-hydrogen angles: 505 Unresolved non-hydrogen dihedrals: 538 Unresolved non-hydrogen chiralities: 66 Planarities with less than four sites: {'PCW:plan-1': 5, 'PCW:plan-2': 2, 'PCW:plan-3': 5, 'PCW:plan-4': 5} Unresolved non-hydrogen planarities: 63 Chain: "D" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 307 Unusual residues: {'PCW': 9, 'ZK1': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 206 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 194 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PCW:plan-1': 3, 'PCW:plan-2': 3, 'PCW:plan-3': 3, 'PCW:plan-4': 4} Unresolved non-hydrogen planarities: 47 Chain: "E" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 87 Unusual residues: {'PCW': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 183 Unresolved non-hydrogen angles: 219 Unresolved non-hydrogen dihedrals: 167 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PCW:plan-1': 4, 'PCW:plan-2': 1, 'PCW:plan-3': 4, 'PCW:plan-4': 4} Unresolved non-hydrogen planarities: 49 Chain: "F" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 87 Unusual residues: {'PCW': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 183 Unresolved non-hydrogen angles: 219 Unresolved non-hydrogen dihedrals: 167 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PCW:plan-1': 4, 'PCW:plan-2': 1, 'PCW:plan-3': 4, 'PCW:plan-4': 4} Unresolved non-hydrogen planarities: 49 Time building chain proxies: 12.65, per 1000 atoms: 0.64 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: 4.76 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 1.83 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: 6.04 Time building geometry restraints manager: 5.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.02 - 0.46: 5 0.46 - 0.90: 6 0.90 - 1.34: 5363 1.34 - 1.78: 14681 1.78 - 2.22: 253 Warning: very small bond lengths. Bond restraints: 20308 Sorted by residual: bond pdb=" C27 AJP C1110 " pdb=" O78 AJP C1110 " ideal model delta sigma weight residual 1.406 0.016 1.390 2.00e-02 2.50e+03 4.83e+03 bond pdb=" C27 AJP A1111 " pdb=" O78 AJP A1111 " ideal model delta sigma weight residual 1.406 0.048 1.358 2.00e-02 2.50e+03 4.61e+03 bond pdb=" C27 AJP C1114 " pdb=" O78 AJP C1114 " ideal model delta sigma weight residual 1.406 0.058 1.348 2.00e-02 2.50e+03 4.54e+03 bond pdb=" C27 AJP A1110 " pdb=" O78 AJP A1110 " ideal model delta sigma weight residual 1.406 0.070 1.336 2.00e-02 2.50e+03 4.46e+03 bond pdb=" C27 AJP A1116 " pdb=" O78 AJP A1116 " ideal model delta sigma weight residual 1.406 0.088 1.318 2.00e-02 2.50e+03 4.34e+03 ... (remaining 20303 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.71: 26292 4.71 - 9.41: 799 9.41 - 14.12: 152 14.12 - 18.82: 15 18.82 - 23.53: 6 Bond angle restraints: 27264 Sorted by residual: angle pdb=" C17 CLR A1107 " pdb=" C13 CLR A1107 " pdb=" C18 CLR A1107 " ideal model delta sigma weight residual 110.18 86.65 23.53 3.00e+00 1.11e-01 6.15e+01 angle pdb=" C17 CLR C1106 " pdb=" C13 CLR C1106 " pdb=" C18 CLR C1106 " ideal model delta sigma weight residual 110.18 86.77 23.41 3.00e+00 1.11e-01 6.09e+01 angle pdb=" C17 CLR A1112 " pdb=" C13 CLR A1112 " pdb=" C18 CLR A1112 " ideal model delta sigma weight residual 110.18 88.52 21.66 3.00e+00 1.11e-01 5.21e+01 angle pdb=" N VAL B 514 " pdb=" CA VAL B 514 " pdb=" C VAL B 514 " ideal model delta sigma weight residual 112.83 105.74 7.09 9.90e-01 1.02e+00 5.14e+01 angle pdb=" N VAL D 514 " pdb=" CA VAL D 514 " pdb=" C VAL D 514 " ideal model delta sigma weight residual 112.83 105.74 7.09 9.90e-01 1.02e+00 5.13e+01 ... (remaining 27259 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 12006 35.97 - 71.94: 635 71.94 - 107.91: 187 107.91 - 143.88: 97 143.88 - 179.85: 48 Dihedral angle restraints: 12973 sinusoidal: 6391 harmonic: 6582 Sorted by residual: dihedral pdb=" CA PRO F 109 " pdb=" C PRO F 109 " pdb=" N ALA F 110 " pdb=" CA ALA F 110 " ideal model delta harmonic sigma weight residual -180.00 -118.55 -61.45 0 5.00e+00 4.00e-02 1.51e+02 dihedral pdb=" CA PRO E 109 " pdb=" C PRO E 109 " pdb=" N ALA E 110 " pdb=" CA ALA E 110 " ideal model delta harmonic sigma weight residual -180.00 -118.58 -61.42 0 5.00e+00 4.00e-02 1.51e+02 dihedral pdb=" CA MET E 116 " pdb=" C MET E 116 " pdb=" N TYR E 117 " pdb=" CA TYR E 117 " ideal model delta harmonic sigma weight residual 180.00 120.86 59.14 0 5.00e+00 4.00e-02 1.40e+02 ... (remaining 12970 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.098: 2878 1.098 - 2.196: 14 2.196 - 3.294: 11 3.294 - 4.392: 16 4.392 - 5.489: 42 Chirality restraints: 2961 Sorted by residual: chirality pdb=" C15 AJP A1110 " pdb=" C14 AJP A1110 " pdb=" C16 AJP A1110 " pdb=" C20 AJP A1110 " both_signs ideal model delta sigma weight residual False -2.42 3.07 -5.49 2.00e-01 2.50e+01 7.53e+02 chirality pdb=" C15 AJP C1109 " pdb=" C14 AJP C1109 " pdb=" C16 AJP C1109 " pdb=" C20 AJP C1109 " both_signs ideal model delta sigma weight residual False -2.42 3.07 -5.49 2.00e-01 2.50e+01 7.53e+02 chirality pdb=" C02 AJP A1110 " pdb=" C01 AJP A1110 " pdb=" C03 AJP A1110 " pdb=" C85 AJP A1110 " both_signs ideal model delta sigma weight residual False 2.60 -2.84 5.44 2.00e-01 2.50e+01 7.40e+02 ... (remaining 2958 not shown) Planarity restraints: 3162 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET E 116 " 0.014 2.00e-02 2.50e+03 2.77e-02 7.69e+00 pdb=" C MET E 116 " -0.048 2.00e-02 2.50e+03 pdb=" O MET E 116 " 0.018 2.00e-02 2.50e+03 pdb=" N TYR E 117 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET F 116 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.64e+00 pdb=" C MET F 116 " 0.048 2.00e-02 2.50e+03 pdb=" O MET F 116 " -0.018 2.00e-02 2.50e+03 pdb=" N TYR F 117 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 406 " -0.013 2.00e-02 2.50e+03 2.57e-02 6.61e+00 pdb=" C VAL D 406 " 0.044 2.00e-02 2.50e+03 pdb=" O VAL D 406 " -0.017 2.00e-02 2.50e+03 pdb=" N MET D 407 " -0.015 2.00e-02 2.50e+03 ... (remaining 3159 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 530 2.68 - 3.23: 17707 3.23 - 3.79: 29684 3.79 - 4.34: 41312 4.34 - 4.90: 68155 Nonbonded interactions: 157388 Sorted by model distance: nonbonded pdb=" OE2 GLU C 705 " pdb=" OH TYR C 732 " model vdw 2.123 3.040 nonbonded pdb=" OE2 GLU A 705 " pdb=" OH TYR A 732 " model vdw 2.123 3.040 nonbonded pdb=" O25 AJP A1111 " pdb=" O79 AJP A1111 " model vdw 2.172 2.432 nonbonded pdb=" O25 AJP C1110 " pdb=" O79 AJP C1110 " model vdw 2.176 2.432 nonbonded pdb=" O31 AJP A1110 " pdb=" O78 AJP A1110 " model vdw 2.196 2.432 ... (remaining 157383 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 392 through 1035 or resid 1101 through 1104 or (resid 1105 \ and (name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or na \ me C19 or name C20 or name C21 or name C22 or name C23)) or resid 1108 or resid \ 1110 or (resid 1113 and (name C13 or name C14 or name C15 or name C16 or name C1 \ 7 or name C18 or name C19 or name C20 or name C21 or name C22 or name C23)) or r \ esid 1115)) selection = (chain 'C' and (resid 392 through 1035 or resid 1101 through 1105 or resid 1108 \ or resid 1110 or resid 1113 or resid 1115)) } ncs_group { reference = (chain 'B' and (resid 392 through 820 or resid 1101 through 1109 or (resid 1110 \ and (name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or nam \ e C19 or name C20 or name C21 or name C22 or name C23)))) selection = (chain 'D' and (resid 392 through 820 or resid 1101 through 1108 or (resid 1109 \ through 1110 and (name C13 or name C14 or name C15 or name C16 or name C17 or na \ me 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 159 or resid 201 or (resid 202 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 resid 204 through 205)) selection = (chain 'F' and (resid 2 through 159 or resid 201 or (resid 202 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 resid 204 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: 5.320 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: 0.780 Check model and map are aligned: 0.140 Set scattering table: 0.150 Process input model: 43.020 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.090 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:3.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.047 1.390 20314 Z= 2.351 Angle : 1.899 23.526 27276 Z= 0.849 Chirality : 0.688 5.489 2961 Planarity : 0.007 0.062 3162 Dihedral : 28.238 179.849 8747 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 11.20 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.017 0.003 TRP C 861 HIS 0.007 0.002 HIS E 27 PHE 0.033 0.003 PHE A 574 TYR 0.033 0.003 TYR C 702 ARG 0.006 0.001 ARG C 485 Details of bonding type rmsd hydrogen bonds : bond 0.30028 ( 960) hydrogen bonds : angle 10.45065 ( 2808) SS BOND : bond 0.01022 ( 6) SS BOND : angle 2.17489 ( 12) covalent geometry : bond 0.04733 (20308) covalent geometry : angle 1.89900 (27264) *********************** 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 : 1.882 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: 0.3466 time to fit residues: 267.6160 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 : 2.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 190 optimal weight: 0.9990 chunk 171 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 115 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 chunk 177 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 107 optimal weight: 0.7980 chunk 131 optimal weight: 0.0980 chunk 205 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3919 r_free = 0.3919 target = 0.173620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.129469 restraints weight = 22069.818| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.04 r_work: 0.3122 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20314 Z= 0.172 Angle : 1.319 32.116 27276 Z= 0.520 Chirality : 0.152 2.461 2961 Planarity : 0.006 0.063 3162 Dihedral : 28.226 179.309 4619 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.61 % Favored : 93.04 % Rotamer: Outliers : 2.68 % Allowed : 8.97 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.64 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.26 (0.15), residues: 2240 helix: -1.33 (0.12), residues: 1320 sheet: -2.71 (0.32), residues: 194 loop : -3.40 (0.18), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 766 HIS 0.008 0.001 HIS C 412 PHE 0.022 0.002 PHE D 541 TYR 0.018 0.002 TYR C 702 ARG 0.007 0.000 ARG C 684 Details of bonding type rmsd hydrogen bonds : bond 0.05219 ( 960) hydrogen bonds : angle 4.72263 ( 2808) SS BOND : bond 0.00368 ( 6) SS BOND : angle 1.26459 ( 12) covalent geometry : bond 0.00362 (20308) covalent geometry : angle 1.31914 (27264) *********************** 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 379 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 327 time to evaluate : 1.879 Fit side-chains revert: symmetry clash REVERT: A 663 LYS cc_start: 0.8945 (mptp) cc_final: 0.8608 (mttt) REVERT: A 669 LYS cc_start: 0.7852 (ttmt) cc_final: 0.7255 (mtpt) REVERT: A 860 TYR cc_start: 0.8279 (m-80) cc_final: 0.7960 (m-80) REVERT: A 891 PHE cc_start: 0.7653 (m-80) cc_final: 0.7319 (m-80) REVERT: A 985 ASN cc_start: 0.8352 (m-40) cc_final: 0.8148 (m-40) REVERT: B 695 LYS cc_start: 0.7127 (OUTLIER) cc_final: 0.6136 (mptt) REVERT: C 860 TYR cc_start: 0.8339 (m-80) cc_final: 0.8019 (m-80) REVERT: C 879 LYS cc_start: 0.8658 (ttmt) cc_final: 0.8196 (mtpp) REVERT: C 998 TYR cc_start: 0.7593 (p90) cc_final: 0.7345 (p90) REVERT: D 397 VAL cc_start: 0.8422 (OUTLIER) cc_final: 0.8218 (m) REVERT: D 439 LYS cc_start: 0.8628 (mtmm) cc_final: 0.8325 (mmtm) REVERT: D 695 LYS cc_start: 0.6464 (OUTLIER) cc_final: 0.5396 (mptt) REVERT: D 715 ARG cc_start: 0.7878 (tpp-160) cc_final: 0.7662 (mmt-90) REVERT: D 770 LYS cc_start: 0.7962 (mmtp) cc_final: 0.7611 (tttp) REVERT: D 817 LYS cc_start: 0.7682 (tppt) cc_final: 0.7379 (ttpt) outliers start: 52 outliers final: 21 residues processed: 361 average time/residue: 0.3174 time to fit residues: 176.0074 Evaluate side-chains 305 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 281 time to evaluate : 3.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 631 SER Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 695 LYS Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 729 SER Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 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 161 optimal weight: 0.6980 chunk 96 optimal weight: 0.9990 chunk 187 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 208 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 167 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 587 GLN C 412 HIS 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.171668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.127278 restraints weight = 21803.530| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.99 r_work: 0.3053 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20314 Z= 0.170 Angle : 1.260 33.566 27276 Z= 0.490 Chirality : 0.145 2.388 2961 Planarity : 0.004 0.052 3162 Dihedral : 27.055 179.996 4619 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.96 % Favored : 92.68 % Rotamer: Outliers : 3.20 % Allowed : 10.62 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.41 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.17), residues: 2240 helix: 0.28 (0.14), residues: 1310 sheet: -2.72 (0.32), residues: 198 loop : -3.08 (0.19), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 861 HIS 0.015 0.002 HIS C 883 PHE 0.018 0.002 PHE C 999 TYR 0.019 0.002 TYR F 155 ARG 0.009 0.001 ARG C 684 Details of bonding type rmsd hydrogen bonds : bond 0.04230 ( 960) hydrogen bonds : angle 4.18167 ( 2808) SS BOND : bond 0.00335 ( 6) SS BOND : angle 1.26773 ( 12) covalent geometry : bond 0.00387 (20308) covalent geometry : angle 1.25997 (27264) *********************** 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 360 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 298 time to evaluate : 1.918 Fit side-chains revert: symmetry clash REVERT: A 663 LYS cc_start: 0.8924 (mptp) cc_final: 0.8609 (mttt) REVERT: A 669 LYS cc_start: 0.7926 (ttmt) cc_final: 0.7397 (mtpt) REVERT: A 697 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.8292 (pttp) REVERT: A 952 ARG cc_start: 0.6805 (ptp-170) cc_final: 0.6500 (ptp-170) REVERT: B 415 LEU cc_start: 0.7920 (mt) cc_final: 0.7627 (mt) REVERT: B 695 LYS cc_start: 0.7371 (OUTLIER) cc_final: 0.6319 (mptt) REVERT: B 696 SER cc_start: 0.8422 (OUTLIER) cc_final: 0.8125 (t) REVERT: C 585 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8318 (mmt) REVERT: C 697 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8135 (pttp) REVERT: C 860 TYR cc_start: 0.8432 (m-80) cc_final: 0.8106 (m-80) REVERT: C 877 GLU cc_start: 0.8088 (tt0) cc_final: 0.7864 (tt0) REVERT: C 879 LYS cc_start: 0.8645 (ttmt) cc_final: 0.8194 (mtpp) REVERT: C 985 ASN cc_start: 0.8176 (m-40) cc_final: 0.7975 (m110) REVERT: C 998 TYR cc_start: 0.7990 (p90) cc_final: 0.7689 (p90) REVERT: D 414 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.8175 (ptp) REVERT: D 635 SER cc_start: 0.8679 (t) cc_final: 0.8183 (p) REVERT: D 695 LYS cc_start: 0.7167 (OUTLIER) cc_final: 0.6152 (mptt) REVERT: D 770 LYS cc_start: 0.8065 (mmtp) cc_final: 0.7794 (tttp) REVERT: D 817 LYS cc_start: 0.7780 (tppt) cc_final: 0.7480 (ttpt) REVERT: E 148 TYR cc_start: 0.8229 (t80) cc_final: 0.7834 (t80) outliers start: 62 outliers final: 33 residues processed: 336 average time/residue: 0.3251 time to fit residues: 172.1318 Evaluate side-chains 320 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 280 time to evaluate : 2.129 ------------------------------------------------------------------------------- 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 666 VAL Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 695 LYS Chi-restraints excluded: chain B residue 696 SER Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 729 SER Chi-restraints excluded: chain 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 666 VAL Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 719 ASP Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 962 SER Chi-restraints excluded: chain C residue 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 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 721 MET Chi-restraints excluded: chain D residue 729 SER Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 790 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 207 optimal weight: 9.9990 chunk 202 optimal weight: 9.9990 chunk 115 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 131 optimal weight: 0.9990 chunk 197 optimal weight: 5.9990 chunk 192 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 80 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 985 ASN C 412 HIS ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.168750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.122667 restraints weight = 22181.533| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.77 r_work: 0.3054 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20314 Z= 0.160 Angle : 1.239 32.870 27276 Z= 0.478 Chirality : 0.143 2.298 2961 Planarity : 0.004 0.045 3162 Dihedral : 26.445 179.487 4619 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.83 % Favored : 92.81 % Rotamer: Outliers : 3.61 % Allowed : 11.24 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.41 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.18), residues: 2240 helix: 0.99 (0.14), residues: 1318 sheet: -2.59 (0.32), residues: 198 loop : -2.95 (0.20), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 766 HIS 0.010 0.002 HIS C 883 PHE 0.019 0.002 PHE C 999 TYR 0.016 0.002 TYR F 155 ARG 0.003 0.000 ARG F 65 Details of bonding type rmsd hydrogen bonds : bond 0.03881 ( 960) hydrogen bonds : angle 3.97455 ( 2808) SS BOND : bond 0.00441 ( 6) SS BOND : angle 1.72181 ( 12) covalent geometry : bond 0.00367 (20308) covalent geometry : angle 1.23845 (27264) *********************** 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 367 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 297 time to evaluate : 2.043 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 585 MET cc_start: 0.9036 (OUTLIER) cc_final: 0.8660 (mmt) REVERT: A 587 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.6925 (mm-40) REVERT: A 663 LYS cc_start: 0.8959 (mptp) cc_final: 0.8668 (mttt) REVERT: A 669 LYS cc_start: 0.8131 (ttmt) cc_final: 0.7620 (mtpt) REVERT: A 952 ARG cc_start: 0.7017 (ptp-170) cc_final: 0.6711 (ptp-170) REVERT: A 957 ILE cc_start: 0.7848 (mp) cc_final: 0.7534 (tp) REVERT: B 415 LEU cc_start: 0.8079 (mt) cc_final: 0.7830 (mt) REVERT: B 461 ASN cc_start: 0.7672 (t0) cc_final: 0.7210 (t0) REVERT: B 695 LYS cc_start: 0.7729 (OUTLIER) cc_final: 0.6706 (mptt) REVERT: B 764 ASN cc_start: 0.8508 (m110) cc_final: 0.8088 (m-40) REVERT: C 503 MET cc_start: 0.8882 (ttp) cc_final: 0.8665 (ttm) REVERT: C 585 MET cc_start: 0.9004 (OUTLIER) cc_final: 0.8385 (mmt) REVERT: C 663 LYS cc_start: 0.9023 (mttp) cc_final: 0.8656 (mttt) REVERT: C 860 TYR cc_start: 0.8551 (m-80) cc_final: 0.8295 (m-80) REVERT: C 879 LYS cc_start: 0.8681 (ttmt) cc_final: 0.8238 (mtpp) REVERT: C 985 ASN cc_start: 0.8247 (m-40) cc_final: 0.7992 (m110) REVERT: D 414 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.8099 (ptp) REVERT: D 415 LEU cc_start: 0.8150 (mt) cc_final: 0.7910 (mt) REVERT: D 461 ASN cc_start: 0.7874 (t0) cc_final: 0.7379 (t0) REVERT: D 635 SER cc_start: 0.8670 (t) cc_final: 0.8234 (p) REVERT: D 695 LYS cc_start: 0.7481 (OUTLIER) cc_final: 0.6447 (mptt) REVERT: D 764 ASN cc_start: 0.8606 (m110) cc_final: 0.8246 (m-40) REVERT: D 817 LYS cc_start: 0.7835 (tppt) cc_final: 0.7570 (ttpt) REVERT: E 148 TYR cc_start: 0.8426 (t80) cc_final: 0.8027 (t80) outliers start: 70 outliers final: 40 residues processed: 343 average time/residue: 0.2947 time to fit residues: 159.7781 Evaluate side-chains 319 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 273 time to evaluate : 2.019 ------------------------------------------------------------------------------- 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 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 719 ASP Chi-restraints excluded: chain A residue 741 SER 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 B residue 773 CYS Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 741 SER 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 664 ILE Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 729 SER Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain D residue 790 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 37 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 186 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 chunk 120 optimal weight: 0.8980 chunk 203 optimal weight: 0.8980 chunk 221 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 207 optimal weight: 0.0870 chunk 14 optimal weight: 0.9980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS A 764 ASN ** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 985 ASN C 412 HIS ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.171663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.126928 restraints weight = 22021.446| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.06 r_work: 0.3059 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.3539 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= 0.140 Angle : 1.224 32.760 27276 Z= 0.468 Chirality : 0.142 2.255 2961 Planarity : 0.004 0.048 3162 Dihedral : 25.952 179.908 4619 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.14 % Favored : 92.50 % Rotamer: Outliers : 3.71 % Allowed : 11.91 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.41 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.18), residues: 2240 helix: 1.37 (0.15), residues: 1318 sheet: -2.56 (0.32), residues: 198 loop : -2.80 (0.20), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 766 HIS 0.009 0.002 HIS C 883 PHE 0.017 0.001 PHE B 438 TYR 0.022 0.001 TYR E 155 ARG 0.005 0.000 ARG A 684 Details of bonding type rmsd hydrogen bonds : bond 0.03655 ( 960) hydrogen bonds : angle 3.84146 ( 2808) SS BOND : bond 0.00346 ( 6) SS BOND : angle 2.29917 ( 12) covalent geometry : bond 0.00322 (20308) covalent geometry : angle 1.22297 (27264) *********************** 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 366 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 294 time to evaluate : 1.973 Fit side-chains revert: symmetry clash REVERT: A 585 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.8594 (mmt) REVERT: A 587 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.6867 (mm-40) REVERT: A 634 GLU cc_start: 0.8306 (pt0) cc_final: 0.7671 (pm20) REVERT: A 663 LYS cc_start: 0.8941 (mptp) cc_final: 0.8600 (mttt) REVERT: A 669 LYS cc_start: 0.7937 (ttmt) cc_final: 0.7395 (mtpt) REVERT: A 880 MET cc_start: 0.7747 (tpp) cc_final: 0.7528 (tpp) REVERT: A 952 ARG cc_start: 0.6871 (ptp-170) cc_final: 0.6506 (ptp-170) REVERT: A 957 ILE cc_start: 0.7705 (mp) cc_final: 0.7347 (tp) REVERT: A 985 ASN cc_start: 0.8136 (m-40) cc_final: 0.7933 (m110) REVERT: B 415 LEU cc_start: 0.7969 (mt) cc_final: 0.7729 (mt) REVERT: B 461 ASN cc_start: 0.7531 (t0) cc_final: 0.6949 (t0) REVERT: B 695 LYS cc_start: 0.7605 (OUTLIER) cc_final: 0.6590 (mptt) REVERT: B 696 SER cc_start: 0.8450 (t) cc_final: 0.8138 (t) REVERT: B 721 MET cc_start: 0.8549 (ttp) cc_final: 0.8341 (ttm) REVERT: B 764 ASN cc_start: 0.8392 (m110) cc_final: 0.7949 (m-40) REVERT: C 585 MET cc_start: 0.8970 (OUTLIER) cc_final: 0.8297 (mmt) REVERT: C 663 LYS cc_start: 0.8997 (mttp) cc_final: 0.8585 (mttt) REVERT: C 669 LYS cc_start: 0.7890 (ttmt) cc_final: 0.7412 (mtpt) REVERT: C 860 TYR cc_start: 0.8373 (m-80) cc_final: 0.8135 (m-80) REVERT: C 879 LYS cc_start: 0.8659 (ttmt) cc_final: 0.8343 (mtpt) REVERT: C 880 MET cc_start: 0.7735 (tpp) cc_final: 0.7390 (tpp) REVERT: C 985 ASN cc_start: 0.7992 (m-40) cc_final: 0.7705 (m110) REVERT: C 987 GLU cc_start: 0.7416 (tp30) cc_final: 0.7149 (tp30) REVERT: D 414 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.8116 (ptp) REVERT: D 415 LEU cc_start: 0.8024 (mt) cc_final: 0.7741 (mt) REVERT: D 443 THR cc_start: 0.8181 (m) cc_final: 0.7947 (m) REVERT: D 461 ASN cc_start: 0.7646 (t0) cc_final: 0.7072 (t0) REVERT: D 635 SER cc_start: 0.8555 (t) cc_final: 0.8099 (p) REVERT: D 695 LYS cc_start: 0.7321 (OUTLIER) cc_final: 0.6283 (mptt) REVERT: D 817 LYS cc_start: 0.7774 (tppt) cc_final: 0.7430 (ttmt) REVERT: F 123 MET cc_start: 0.5572 (mmm) cc_final: 0.5218 (mmm) outliers start: 72 outliers final: 45 residues processed: 342 average time/residue: 0.3146 time to fit residues: 170.6920 Evaluate side-chains 324 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 273 time to evaluate : 1.930 ------------------------------------------------------------------------------- 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 473 ASP 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 666 VAL Chi-restraints excluded: chain A residue 719 ASP Chi-restraints excluded: chain A residue 741 SER 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 445 VAL Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 591 ILE 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 729 SER Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 652 SER Chi-restraints excluded: chain C residue 719 ASP Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 925 ILE 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 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 Chi-restraints excluded: chain E residue 123 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 154 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 179 optimal weight: 0.5980 chunk 79 optimal weight: 0.6980 chunk 166 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 82 optimal weight: 3.9990 chunk 169 optimal weight: 0.0870 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS ** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.170941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.122945 restraints weight = 21934.541| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.92 r_work: 0.3029 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20314 Z= 0.153 Angle : 1.227 32.706 27276 Z= 0.470 Chirality : 0.141 2.225 2961 Planarity : 0.004 0.050 3162 Dihedral : 25.624 179.836 4619 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.92 % Favored : 92.72 % Rotamer: Outliers : 3.81 % Allowed : 12.16 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.18), residues: 2240 helix: 1.56 (0.15), residues: 1314 sheet: -2.53 (0.33), residues: 190 loop : -2.67 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 766 HIS 0.008 0.001 HIS C 412 PHE 0.017 0.001 PHE B 438 TYR 0.014 0.001 TYR E 155 ARG 0.006 0.000 ARG C 684 Details of bonding type rmsd hydrogen bonds : bond 0.03645 ( 960) hydrogen bonds : angle 3.80060 ( 2808) SS BOND : bond 0.00600 ( 6) SS BOND : angle 2.98397 ( 12) covalent geometry : bond 0.00354 (20308) covalent geometry : angle 1.22574 (27264) *********************** 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 370 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 296 time to evaluate : 1.982 Fit side-chains REVERT: A 585 MET cc_start: 0.8998 (OUTLIER) cc_final: 0.8593 (mmt) REVERT: A 587 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.6792 (mm-40) REVERT: A 647 TYR cc_start: 0.8575 (OUTLIER) cc_final: 0.7843 (m-80) REVERT: A 663 LYS cc_start: 0.8955 (mptp) cc_final: 0.8603 (mttt) REVERT: A 669 LYS cc_start: 0.7897 (ttmt) cc_final: 0.7291 (mtpt) REVERT: A 858 THR cc_start: 0.9072 (t) cc_final: 0.8790 (p) REVERT: A 879 LYS cc_start: 0.8606 (ttmt) cc_final: 0.8387 (ttmt) REVERT: A 952 ARG cc_start: 0.6813 (ptp-170) cc_final: 0.6449 (ptp-170) REVERT: A 957 ILE cc_start: 0.7636 (mp) cc_final: 0.7262 (tp) REVERT: A 985 ASN cc_start: 0.8096 (m-40) cc_final: 0.7792 (m110) REVERT: A 987 GLU cc_start: 0.7199 (tp30) cc_final: 0.6927 (tp30) REVERT: B 415 LEU cc_start: 0.7980 (mt) cc_final: 0.7735 (mt) REVERT: B 461 ASN cc_start: 0.7562 (t0) cc_final: 0.7018 (t0) REVERT: B 635 SER cc_start: 0.8498 (t) cc_final: 0.7955 (p) REVERT: B 695 LYS cc_start: 0.7549 (OUTLIER) cc_final: 0.6570 (mptt) REVERT: B 764 ASN cc_start: 0.8360 (m110) cc_final: 0.7911 (m-40) REVERT: C 585 MET cc_start: 0.8998 (OUTLIER) cc_final: 0.8316 (mmt) REVERT: C 634 GLU cc_start: 0.8253 (pt0) cc_final: 0.7710 (pm20) REVERT: C 661 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.8155 (ptt180) REVERT: C 663 LYS cc_start: 0.9020 (mttp) cc_final: 0.8607 (mttt) REVERT: C 669 LYS cc_start: 0.7860 (ttmt) cc_final: 0.7315 (mtpt) REVERT: C 860 TYR cc_start: 0.8311 (m-80) cc_final: 0.8049 (m-80) REVERT: C 879 LYS cc_start: 0.8710 (ttmt) cc_final: 0.8368 (mtpt) REVERT: C 880 MET cc_start: 0.7819 (tpp) cc_final: 0.7453 (tpp) REVERT: C 952 ARG cc_start: 0.6789 (ptp-170) cc_final: 0.6513 (ptp-170) REVERT: C 957 ILE cc_start: 0.7640 (mp) cc_final: 0.7318 (tp) REVERT: C 985 ASN cc_start: 0.7948 (m-40) cc_final: 0.7625 (m110) REVERT: C 987 GLU cc_start: 0.7320 (tp30) cc_final: 0.7064 (tp30) REVERT: D 414 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.8089 (ptp) REVERT: D 415 LEU cc_start: 0.7997 (mt) cc_final: 0.7700 (mt) REVERT: D 461 ASN cc_start: 0.7612 (t0) cc_final: 0.7159 (t0) REVERT: D 635 SER cc_start: 0.8529 (t) cc_final: 0.8043 (p) REVERT: D 695 LYS cc_start: 0.7253 (OUTLIER) cc_final: 0.6255 (mptt) REVERT: D 817 LYS cc_start: 0.7802 (tppt) cc_final: 0.7444 (ttmt) REVERT: E 142 TYR cc_start: 0.7705 (m-10) cc_final: 0.7472 (m-10) REVERT: E 148 TYR cc_start: 0.8181 (t80) cc_final: 0.7771 (t80) outliers start: 74 outliers final: 43 residues processed: 348 average time/residue: 0.3023 time to fit residues: 164.9952 Evaluate side-chains 331 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 280 time to evaluate : 1.902 ------------------------------------------------------------------------------- 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 511 LYS Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 719 ASP Chi-restraints excluded: chain A residue 741 SER 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 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 399 THR Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 661 ARG Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 719 ASP Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 741 SER 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 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 123 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 22 optimal weight: 4.9990 chunk 208 optimal weight: 7.9990 chunk 140 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 89 optimal weight: 0.2980 chunk 36 optimal weight: 0.1980 chunk 145 optimal weight: 1.9990 chunk 220 optimal weight: 3.9990 chunk 222 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS ** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 HIS ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.169386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.121091 restraints weight = 21812.170| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.92 r_work: 0.3009 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20314 Z= 0.180 Angle : 1.240 32.910 27276 Z= 0.477 Chirality : 0.141 2.228 2961 Planarity : 0.004 0.047 3162 Dihedral : 25.468 179.878 4619 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.92 % Favored : 92.72 % Rotamer: Outliers : 3.76 % Allowed : 12.99 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.18), residues: 2240 helix: 1.57 (0.14), residues: 1316 sheet: -2.53 (0.32), residues: 190 loop : -2.59 (0.21), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 766 HIS 0.009 0.002 HIS A 883 PHE 0.019 0.002 PHE B 438 TYR 0.027 0.002 TYR A 980 ARG 0.006 0.000 ARG C 684 Details of bonding type rmsd hydrogen bonds : bond 0.03784 ( 960) hydrogen bonds : angle 3.83199 ( 2808) SS BOND : bond 0.00550 ( 6) SS BOND : angle 3.94026 ( 12) covalent geometry : bond 0.00429 (20308) covalent geometry : angle 1.23706 (27264) *********************** 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 361 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 288 time to evaluate : 1.898 Fit side-chains REVERT: A 585 MET cc_start: 0.9031 (OUTLIER) cc_final: 0.8637 (mmt) REVERT: A 587 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.6812 (mm-40) REVERT: A 647 TYR cc_start: 0.8569 (OUTLIER) cc_final: 0.7837 (m-80) REVERT: A 663 LYS cc_start: 0.8978 (mptp) cc_final: 0.8636 (mttt) REVERT: A 669 LYS cc_start: 0.7920 (ttmt) cc_final: 0.7300 (mtpt) REVERT: A 858 THR cc_start: 0.9071 (t) cc_final: 0.8817 (p) REVERT: A 952 ARG cc_start: 0.6879 (ptp-170) cc_final: 0.6514 (ptp-170) REVERT: A 957 ILE cc_start: 0.7631 (mp) cc_final: 0.7254 (tp) REVERT: A 985 ASN cc_start: 0.8022 (m-40) cc_final: 0.7688 (m110) REVERT: A 987 GLU cc_start: 0.7202 (tp30) cc_final: 0.6925 (tp30) REVERT: B 415 LEU cc_start: 0.8000 (mt) cc_final: 0.7765 (mt) REVERT: B 461 ASN cc_start: 0.7601 (t0) cc_final: 0.7106 (t0) REVERT: B 635 SER cc_start: 0.8542 (t) cc_final: 0.8027 (p) REVERT: B 695 LYS cc_start: 0.7675 (OUTLIER) cc_final: 0.6688 (mptt) REVERT: B 764 ASN cc_start: 0.8456 (m110) cc_final: 0.7990 (m-40) REVERT: C 585 MET cc_start: 0.9030 (OUTLIER) cc_final: 0.8333 (mmt) REVERT: C 634 GLU cc_start: 0.8290 (pt0) cc_final: 0.7841 (pm20) REVERT: C 663 LYS cc_start: 0.9009 (mttp) cc_final: 0.8593 (mttt) REVERT: C 669 LYS cc_start: 0.7910 (ttmt) cc_final: 0.7250 (mtpt) REVERT: C 860 TYR cc_start: 0.8349 (m-80) cc_final: 0.8097 (m-80) REVERT: C 879 LYS cc_start: 0.8697 (ttmt) cc_final: 0.8216 (mtpt) REVERT: C 952 ARG cc_start: 0.6820 (ptp-170) cc_final: 0.6482 (ptp-170) REVERT: C 957 ILE cc_start: 0.7586 (mp) cc_final: 0.7248 (tp) REVERT: C 985 ASN cc_start: 0.7946 (m-40) cc_final: 0.7642 (m110) REVERT: C 987 GLU cc_start: 0.7348 (tp30) cc_final: 0.7084 (tp30) REVERT: D 415 LEU cc_start: 0.7987 (mt) cc_final: 0.7770 (mt) REVERT: D 461 ASN cc_start: 0.7626 (t0) cc_final: 0.7151 (t0) REVERT: D 635 SER cc_start: 0.8563 (t) cc_final: 0.8087 (p) REVERT: D 695 LYS cc_start: 0.7480 (OUTLIER) cc_final: 0.6487 (mptt) REVERT: D 817 LYS cc_start: 0.7790 (tppt) cc_final: 0.7437 (ttmt) REVERT: E 100 TYR cc_start: 0.8202 (t80) cc_final: 0.7935 (t80) REVERT: E 142 TYR cc_start: 0.7741 (m-10) cc_final: 0.7503 (m-10) REVERT: E 148 TYR cc_start: 0.8187 (t80) cc_final: 0.7765 (t80) outliers start: 73 outliers final: 55 residues processed: 339 average time/residue: 0.3156 time to fit residues: 167.9317 Evaluate side-chains 340 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 279 time to evaluate : 1.988 ------------------------------------------------------------------------------- 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 666 VAL 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 741 SER Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 631 SER 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 392 GLN Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 629 MET Chi-restraints excluded: chain C residue 652 SER Chi-restraints excluded: chain C residue 661 ARG Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 719 ASP Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 741 SER Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 962 SER Chi-restraints excluded: chain C residue 1013 SER Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 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 123 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 186 optimal weight: 3.9990 chunk 95 optimal weight: 0.2980 chunk 124 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 106 optimal weight: 0.5980 chunk 47 optimal weight: 5.9990 chunk 158 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 193 optimal weight: 0.5980 chunk 97 optimal weight: 0.6980 chunk 157 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 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 = 0.3921 r_free = 0.3921 target = 0.172486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.123482 restraints weight = 22282.430| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.23 r_work: 0.3059 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20314 Z= 0.157 Angle : 1.240 32.897 27276 Z= 0.476 Chirality : 0.141 2.223 2961 Planarity : 0.004 0.045 3162 Dihedral : 25.303 179.893 4619 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.92 % Favored : 92.72 % Rotamer: Outliers : 3.40 % Allowed : 13.56 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.18), residues: 2240 helix: 1.68 (0.14), residues: 1316 sheet: -2.48 (0.32), residues: 190 loop : -2.52 (0.21), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 766 HIS 0.019 0.002 HIS C 412 PHE 0.022 0.001 PHE A 999 TYR 0.025 0.002 TYR A 980 ARG 0.007 0.000 ARG C 684 Details of bonding type rmsd hydrogen bonds : bond 0.03652 ( 960) hydrogen bonds : angle 3.77753 ( 2808) SS BOND : bond 0.00772 ( 6) SS BOND : angle 4.90462 ( 12) covalent geometry : bond 0.00369 (20308) covalent geometry : angle 1.23588 (27264) *********************** 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 349 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 283 time to evaluate : 2.067 Fit side-chains revert: symmetry clash REVERT: A 585 MET cc_start: 0.8878 (OUTLIER) cc_final: 0.8406 (mmt) REVERT: A 587 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.6828 (mm-40) REVERT: A 647 TYR cc_start: 0.8474 (OUTLIER) cc_final: 0.7823 (m-10) REVERT: A 663 LYS cc_start: 0.8925 (mptp) cc_final: 0.8622 (mttt) REVERT: A 669 LYS cc_start: 0.7934 (ttmt) cc_final: 0.7297 (mtpt) REVERT: A 858 THR cc_start: 0.9085 (t) cc_final: 0.8856 (p) REVERT: A 952 ARG cc_start: 0.7049 (ptp-170) cc_final: 0.6688 (ptp-170) REVERT: A 957 ILE cc_start: 0.7714 (mp) cc_final: 0.7357 (tp) REVERT: A 987 GLU cc_start: 0.7235 (tp30) cc_final: 0.6956 (tp30) REVERT: B 461 ASN cc_start: 0.7412 (t0) cc_final: 0.7067 (t0) REVERT: B 635 SER cc_start: 0.8521 (t) cc_final: 0.8092 (p) REVERT: B 695 LYS cc_start: 0.7718 (OUTLIER) cc_final: 0.6805 (mptt) REVERT: B 764 ASN cc_start: 0.8466 (m110) cc_final: 0.7998 (m-40) REVERT: C 585 MET cc_start: 0.8899 (OUTLIER) cc_final: 0.8149 (mmt) REVERT: C 634 GLU cc_start: 0.8103 (pt0) cc_final: 0.7788 (pm20) REVERT: C 663 LYS cc_start: 0.8969 (mttp) cc_final: 0.8574 (mttt) REVERT: C 669 LYS cc_start: 0.7910 (ttmt) cc_final: 0.7267 (mtpt) REVERT: C 860 TYR cc_start: 0.8356 (m-80) cc_final: 0.7846 (m-80) REVERT: C 879 LYS cc_start: 0.8640 (ttmt) cc_final: 0.8272 (mtpt) REVERT: C 881 SER cc_start: 0.8459 (t) cc_final: 0.7821 (m) REVERT: C 952 ARG cc_start: 0.7028 (ptp-170) cc_final: 0.6698 (ptp-170) REVERT: C 957 ILE cc_start: 0.7671 (mp) cc_final: 0.7343 (tp) REVERT: C 985 ASN cc_start: 0.7935 (m-40) cc_final: 0.7639 (m110) REVERT: D 415 LEU cc_start: 0.8048 (mt) cc_final: 0.7837 (mt) REVERT: D 461 ASN cc_start: 0.7464 (t0) cc_final: 0.7114 (t0) REVERT: D 635 SER cc_start: 0.8527 (t) cc_final: 0.8118 (p) REVERT: D 695 LYS cc_start: 0.7530 (OUTLIER) cc_final: 0.6592 (mptt) REVERT: D 817 LYS cc_start: 0.7790 (tppt) cc_final: 0.7518 (ttmt) REVERT: E 142 TYR cc_start: 0.7820 (m-10) cc_final: 0.7607 (m-10) REVERT: E 148 TYR cc_start: 0.8260 (t80) cc_final: 0.7876 (t80) outliers start: 66 outliers final: 48 residues processed: 327 average time/residue: 0.3139 time to fit residues: 158.5662 Evaluate side-chains 329 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 275 time to evaluate : 2.000 ------------------------------------------------------------------------------- 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 511 LYS Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 719 ASP Chi-restraints excluded: chain A residue 741 SER Chi-restraints excluded: chain A residue 795 VAL 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 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 664 ILE Chi-restraints excluded: chain B residue 695 LYS 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 581 LEU Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 629 MET Chi-restraints excluded: chain C residue 652 SER Chi-restraints excluded: chain C residue 661 ARG Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 719 ASP Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 741 SER Chi-restraints excluded: chain C residue 795 VAL 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 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 123 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 220 optimal weight: 0.9980 chunk 215 optimal weight: 0.6980 chunk 151 optimal weight: 0.6980 chunk 89 optimal weight: 0.0870 chunk 8 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS ** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 985 ASN C 412 HIS ** 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 = 0.3930 r_free = 0.3930 target = 0.173481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.124605 restraints weight = 22110.764| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.25 r_work: 0.3059 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.4080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20314 Z= 0.142 Angle : 1.225 32.776 27276 Z= 0.470 Chirality : 0.142 2.293 2961 Planarity : 0.004 0.045 3162 Dihedral : 25.077 179.552 4619 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.83 % Favored : 92.86 % Rotamer: Outliers : 3.35 % Allowed : 13.92 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.18), residues: 2240 helix: 1.78 (0.15), residues: 1320 sheet: -2.33 (0.33), residues: 190 loop : -2.49 (0.21), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 766 HIS 0.010 0.002 HIS C 412 PHE 0.030 0.001 PHE B 515 TYR 0.025 0.001 TYR E 155 ARG 0.008 0.000 ARG A 684 Details of bonding type rmsd hydrogen bonds : bond 0.03515 ( 960) hydrogen bonds : angle 3.72400 ( 2808) SS BOND : bond 0.00207 ( 6) SS BOND : angle 3.76290 ( 12) covalent geometry : bond 0.00330 (20308) covalent geometry : angle 1.22257 (27264) *********************** 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 347 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 282 time to evaluate : 1.985 Fit side-chains revert: symmetry clash REVERT: A 585 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.8386 (mmt) REVERT: A 587 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.6803 (mm-40) REVERT: A 647 TYR cc_start: 0.8455 (OUTLIER) cc_final: 0.7694 (m-10) REVERT: A 663 LYS cc_start: 0.8924 (mptp) cc_final: 0.8621 (mttt) REVERT: A 669 LYS cc_start: 0.7939 (ttmt) cc_final: 0.7313 (mtpt) REVERT: A 858 THR cc_start: 0.9093 (t) cc_final: 0.8886 (p) REVERT: A 952 ARG cc_start: 0.7075 (ptp-170) cc_final: 0.6720 (ptp-170) REVERT: A 957 ILE cc_start: 0.7694 (mp) cc_final: 0.7329 (tp) REVERT: B 461 ASN cc_start: 0.7384 (t0) cc_final: 0.7080 (t0) REVERT: B 635 SER cc_start: 0.8382 (t) cc_final: 0.7983 (p) REVERT: B 695 LYS cc_start: 0.7689 (OUTLIER) cc_final: 0.6824 (mptt) REVERT: B 764 ASN cc_start: 0.8453 (m110) cc_final: 0.7984 (m-40) REVERT: C 585 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.8134 (mmt) REVERT: C 634 GLU cc_start: 0.8072 (pt0) cc_final: 0.7774 (pm20) REVERT: C 651 ASP cc_start: 0.7538 (t70) cc_final: 0.7297 (p0) REVERT: C 663 LYS cc_start: 0.8957 (mttp) cc_final: 0.8569 (mttt) REVERT: C 669 LYS cc_start: 0.7944 (ttmt) cc_final: 0.7291 (mtpt) REVERT: C 673 TYR cc_start: 0.8455 (t80) cc_final: 0.8244 (t80) REVERT: C 860 TYR cc_start: 0.8363 (m-80) cc_final: 0.7855 (m-80) REVERT: C 879 LYS cc_start: 0.8541 (ttmt) cc_final: 0.8181 (mtpt) REVERT: C 880 MET cc_start: 0.7812 (tpp) cc_final: 0.7595 (tpp) REVERT: C 952 ARG cc_start: 0.7021 (ptp-170) cc_final: 0.6674 (ptp-170) REVERT: C 957 ILE cc_start: 0.7619 (mp) cc_final: 0.7279 (tp) REVERT: C 985 ASN cc_start: 0.8037 (m-40) cc_final: 0.7773 (m110) REVERT: D 461 ASN cc_start: 0.7456 (t0) cc_final: 0.7124 (t0) REVERT: D 635 SER cc_start: 0.8423 (t) cc_final: 0.8028 (p) REVERT: D 695 LYS cc_start: 0.7570 (OUTLIER) cc_final: 0.6663 (mptt) REVERT: D 817 LYS cc_start: 0.7772 (tppt) cc_final: 0.7512 (ttmt) REVERT: E 100 TYR cc_start: 0.8217 (t80) cc_final: 0.7873 (t80) REVERT: E 142 TYR cc_start: 0.7832 (m-10) cc_final: 0.7608 (m-10) REVERT: E 148 TYR cc_start: 0.8246 (t80) cc_final: 0.7857 (t80) outliers start: 65 outliers final: 49 residues processed: 324 average time/residue: 0.3049 time to fit residues: 153.8875 Evaluate side-chains 330 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 275 time to evaluate : 1.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 511 LYS 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 719 ASP Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 741 SER Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 884 SER 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 631 SER 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 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 412 HIS Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 629 MET Chi-restraints excluded: chain C residue 652 SER Chi-restraints excluded: chain C residue 661 ARG Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 719 ASP Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 741 SER Chi-restraints excluded: chain C residue 962 SER Chi-restraints excluded: chain C residue 1013 SER Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 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 E residue 123 MET 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 46 optimal weight: 2.9990 chunk 204 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 81 optimal weight: 0.0670 chunk 146 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 157 optimal weight: 4.9990 chunk 225 optimal weight: 0.9990 chunk 8 optimal weight: 0.4980 chunk 108 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS ** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 HIS ** C 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.173855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.125652 restraints weight = 22194.537| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.08 r_work: 0.3111 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.4140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20314 Z= 0.139 Angle : 1.224 32.699 27276 Z= 0.467 Chirality : 0.141 2.196 2961 Planarity : 0.004 0.044 3162 Dihedral : 24.967 179.500 4619 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.70 % Favored : 93.04 % Rotamer: Outliers : 2.89 % Allowed : 14.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.18), residues: 2240 helix: 1.82 (0.14), residues: 1320 sheet: -2.22 (0.33), residues: 190 loop : -2.49 (0.21), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 766 HIS 0.014 0.002 HIS C 412 PHE 0.031 0.001 PHE B 515 TYR 0.023 0.001 TYR A 980 ARG 0.008 0.000 ARG C 684 Details of bonding type rmsd hydrogen bonds : bond 0.03486 ( 960) hydrogen bonds : angle 3.71057 ( 2808) SS BOND : bond 0.00152 ( 6) SS BOND : angle 2.68180 ( 12) covalent geometry : bond 0.00323 (20308) covalent geometry : angle 1.22251 (27264) ********************** 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 339 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 283 time to evaluate : 2.020 Fit side-chains revert: symmetry clash REVERT: A 585 MET cc_start: 0.8848 (OUTLIER) cc_final: 0.8388 (mmt) REVERT: A 587 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.6776 (mm-40) REVERT: A 647 TYR cc_start: 0.8509 (OUTLIER) cc_final: 0.8130 (m-80) REVERT: A 663 LYS cc_start: 0.8932 (mptp) cc_final: 0.8615 (mttt) REVERT: A 669 LYS cc_start: 0.7959 (ttmt) cc_final: 0.7302 (mtpt) REVERT: A 952 ARG cc_start: 0.7074 (ptp-170) cc_final: 0.6712 (ptp-170) REVERT: A 957 ILE cc_start: 0.7703 (mp) cc_final: 0.7335 (tp) REVERT: B 461 ASN cc_start: 0.7422 (t0) cc_final: 0.7119 (t0) REVERT: B 515 PHE cc_start: 0.9022 (m-10) cc_final: 0.8747 (m-10) REVERT: B 635 SER cc_start: 0.8324 (t) cc_final: 0.7941 (p) REVERT: B 695 LYS cc_start: 0.7690 (OUTLIER) cc_final: 0.6859 (mptt) REVERT: B 764 ASN cc_start: 0.8458 (m110) cc_final: 0.7992 (m-40) REVERT: C 585 MET cc_start: 0.8872 (OUTLIER) cc_final: 0.8136 (mmt) REVERT: C 634 GLU cc_start: 0.8087 (pt0) cc_final: 0.7773 (pm20) REVERT: C 651 ASP cc_start: 0.7576 (t70) cc_final: 0.7340 (p0) REVERT: C 663 LYS cc_start: 0.8971 (mttp) cc_final: 0.8575 (mttt) REVERT: C 669 LYS cc_start: 0.7949 (ttmt) cc_final: 0.7299 (mtpt) REVERT: C 860 TYR cc_start: 0.8372 (m-80) cc_final: 0.7863 (m-80) REVERT: C 879 LYS cc_start: 0.8542 (ttmt) cc_final: 0.8144 (mtpt) REVERT: C 880 MET cc_start: 0.7765 (tpp) cc_final: 0.7549 (tpp) REVERT: C 952 ARG cc_start: 0.7017 (ptp-170) cc_final: 0.6669 (ptp-170) REVERT: C 957 ILE cc_start: 0.7633 (mp) cc_final: 0.7292 (tp) REVERT: C 985 ASN cc_start: 0.8019 (m-40) cc_final: 0.7722 (m110) REVERT: D 461 ASN cc_start: 0.7477 (t0) cc_final: 0.7159 (t0) REVERT: D 635 SER cc_start: 0.8364 (t) cc_final: 0.7983 (p) REVERT: D 695 LYS cc_start: 0.7580 (OUTLIER) cc_final: 0.6702 (mptt) REVERT: D 817 LYS cc_start: 0.7805 (tppt) cc_final: 0.7561 (ttmt) REVERT: E 142 TYR cc_start: 0.7819 (m-10) cc_final: 0.7604 (m-10) REVERT: E 148 TYR cc_start: 0.8224 (t80) cc_final: 0.7843 (t80) outliers start: 56 outliers final: 47 residues processed: 320 average time/residue: 0.3039 time to fit residues: 152.5048 Evaluate side-chains 327 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 274 time to evaluate : 1.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 511 LYS 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 719 ASP Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 741 SER Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 884 SER 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 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 412 HIS Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 629 MET Chi-restraints excluded: chain C residue 652 SER Chi-restraints excluded: chain C residue 661 ARG Chi-restraints excluded: chain C residue 719 ASP Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 741 SER Chi-restraints excluded: chain C residue 962 SER Chi-restraints excluded: chain C residue 1013 SER Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 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 E residue 123 MET 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 174 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 143 optimal weight: 8.9990 chunk 195 optimal weight: 0.5980 chunk 155 optimal weight: 2.9990 chunk 184 optimal weight: 0.8980 chunk 225 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 chunk 103 optimal weight: 0.4980 chunk 47 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS ** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 HIS ** C 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.174238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.125791 restraints weight = 22199.393| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.26 r_work: 0.3135 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.4200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20314 Z= 0.132 Angle : 1.219 32.607 27276 Z= 0.465 Chirality : 0.141 2.189 2961 Planarity : 0.004 0.064 3162 Dihedral : 24.864 179.362 4619 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.92 % Favored : 92.81 % Rotamer: Outliers : 2.73 % Allowed : 14.54 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.18), residues: 2240 helix: 1.87 (0.15), residues: 1320 sheet: -2.11 (0.34), residues: 190 loop : -2.44 (0.21), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 766 HIS 0.012 0.001 HIS C 412 PHE 0.027 0.001 PHE B 515 TYR 0.024 0.001 TYR E 155 ARG 0.008 0.000 ARG C 684 Details of bonding type rmsd hydrogen bonds : bond 0.03428 ( 960) hydrogen bonds : angle 3.68166 ( 2808) SS BOND : bond 0.00130 ( 6) SS BOND : angle 2.28822 ( 12) covalent geometry : bond 0.00303 (20308) covalent geometry : angle 1.21856 (27264) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11255.23 seconds wall clock time: 194 minutes 22.01 seconds (11662.01 seconds total)