Starting phenix.real_space_refine on Wed May 21 03:02:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ss3_40742/05_2025/8ss3_40742.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ss3_40742/05_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_40742/05_2025/8ss3_40742.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ss3_40742/05_2025/8ss3_40742.map" model { file = "/net/cci-nas-00/data/ceres_data/8ss3_40742/05_2025/8ss3_40742.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ss3_40742/05_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-5687/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: 11.20, per 1000 atoms: 0.56 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: 4.47 Conformation dependent library (CDL) restraints added in 2.2 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: 1.74 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: 5.84 Time building geometry restraints manager: 5.20 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: 3.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.690 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 39.910 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.300 ------------------------------------------------------------------------------- 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 : 2.152 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: 0.3390 time to fit residues: 262.2371 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 : 2.083 ------------------------------------------------------------------------------- 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 = 0.3911 r_free = 0.3911 target = 0.172944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.126452 restraints weight = 22084.299| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.13 r_work: 0.3124 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2351 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= 0.163 Angle : 1.320 31.650 27276 Z= 0.521 Chirality : 0.151 2.436 2961 Planarity : 0.006 0.062 3162 Dihedral : 28.284 179.176 4619 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.65 % Favored : 92.95 % 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: -3.27 (0.15), residues: 2240 helix: -1.32 (0.12), residues: 1320 sheet: -2.71 (0.32), residues: 194 loop : -3.41 (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 0.05229 ( 960) hydrogen bonds : angle 4.72935 ( 2808) SS BOND : bond 0.00349 ( 6) SS BOND : angle 1.22269 ( 12) covalent geometry : bond 0.00352 (20308) covalent geometry : angle 1.32038 (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 374 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 322 time to evaluate : 1.914 Fit side-chains revert: symmetry clash REVERT: A 663 LYS cc_start: 0.8932 (mptp) cc_final: 0.8591 (mttt) REVERT: A 669 LYS cc_start: 0.7843 (ttmt) cc_final: 0.7248 (mtpt) REVERT: A 860 TYR cc_start: 0.8219 (m-80) cc_final: 0.7913 (m-80) REVERT: A 880 MET cc_start: 0.7648 (tpp) cc_final: 0.7443 (tpp) REVERT: A 891 PHE cc_start: 0.7618 (m-80) cc_final: 0.7280 (m-80) REVERT: A 985 ASN cc_start: 0.8326 (m-40) cc_final: 0.8121 (m-40) REVERT: B 439 LYS cc_start: 0.8527 (mtpm) cc_final: 0.8324 (mtmm) REVERT: B 695 LYS cc_start: 0.7104 (OUTLIER) cc_final: 0.6112 (mptt) REVERT: C 860 TYR cc_start: 0.8309 (m-80) cc_final: 0.7990 (m-80) REVERT: C 879 LYS cc_start: 0.8655 (ttmt) cc_final: 0.8194 (mtpp) REVERT: C 998 TYR cc_start: 0.7564 (p90) cc_final: 0.7309 (p90) REVERT: D 397 VAL cc_start: 0.8373 (OUTLIER) cc_final: 0.8167 (m) REVERT: D 439 LYS cc_start: 0.8626 (mtmm) cc_final: 0.8321 (mmtm) REVERT: D 695 LYS cc_start: 0.6447 (OUTLIER) cc_final: 0.5393 (mptt) REVERT: D 715 ARG cc_start: 0.7838 (tpp-160) cc_final: 0.7625 (mmt-90) REVERT: D 770 LYS cc_start: 0.7941 (mmtp) cc_final: 0.7587 (tttp) REVERT: D 817 LYS cc_start: 0.7698 (tppt) cc_final: 0.7427 (ttpt) outliers start: 52 outliers final: 21 residues processed: 356 average time/residue: 0.3069 time to fit residues: 167.9992 Evaluate side-chains 306 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 282 time to evaluate : 2.099 ------------------------------------------------------------------------------- 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: 0.9990 chunk 96 optimal weight: 0.8980 chunk 187 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 208 optimal weight: 10.0000 chunk 46 optimal weight: 0.0040 chunk 42 optimal weight: 5.9990 chunk 167 optimal weight: 0.7980 overall best weight: 0.9396 ------------------------------------------------------------------------------- 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 = 0.3881 r_free = 0.3881 target = 0.170427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.124419 restraints weight = 21769.812| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.07 r_work: 0.3086 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 20314 Z= 0.177 Angle : 1.263 33.734 27276 Z= 0.492 Chirality : 0.146 2.411 2961 Planarity : 0.005 0.052 3162 Dihedral : 27.082 179.900 4619 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.05 % Favored : 92.59 % Rotamer: Outliers : 3.40 % Allowed : 10.46 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.41 % Rama-Z (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: -1.63 (0.17), residues: 2240 helix: 0.29 (0.14), residues: 1310 sheet: -2.80 (0.31), residues: 198 loop : -3.09 (0.19), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 861 HIS 0.016 0.002 HIS C 883 PHE 0.019 0.002 PHE D 515 TYR 0.016 0.002 TYR C 702 ARG 0.007 0.001 ARG C 684 Details of bonding type rmsd hydrogen bonds : bond 0.04287 ( 960) hydrogen bonds : angle 4.18572 ( 2808) SS BOND : bond 0.03018 ( 6) SS BOND : angle 1.60962 ( 12) covalent geometry : bond 0.00409 (20308) covalent geometry : angle 1.26318 (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 363 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 297 time to evaluate : 2.015 Fit side-chains revert: symmetry clash REVERT: A 587 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.6797 (mm-40) REVERT: A 663 LYS cc_start: 0.8913 (mptp) cc_final: 0.8583 (mttt) REVERT: A 669 LYS cc_start: 0.7855 (ttmt) cc_final: 0.7315 (mtpt) REVERT: A 697 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8240 (pttp) REVERT: A 952 ARG cc_start: 0.6755 (ptp-170) cc_final: 0.6457 (ptp-170) REVERT: B 415 LEU cc_start: 0.7873 (mt) cc_final: 0.7579 (mt) REVERT: B 439 LYS cc_start: 0.8570 (mtpm) cc_final: 0.8322 (mtmm) REVERT: B 695 LYS cc_start: 0.7294 (OUTLIER) cc_final: 0.6240 (mptt) REVERT: C 585 MET cc_start: 0.8989 (OUTLIER) cc_final: 0.8272 (mmt) REVERT: C 860 TYR cc_start: 0.8377 (m-80) cc_final: 0.8041 (m-80) REVERT: C 877 GLU cc_start: 0.8068 (tt0) cc_final: 0.7843 (tt0) REVERT: C 879 LYS cc_start: 0.8646 (ttmt) cc_final: 0.8196 (mtpp) REVERT: C 985 ASN cc_start: 0.8112 (m-40) cc_final: 0.7889 (m110) REVERT: C 998 TYR cc_start: 0.7920 (p90) cc_final: 0.7631 (p90) REVERT: D 414 MET cc_start: 0.8534 (OUTLIER) cc_final: 0.8137 (ptp) REVERT: D 635 SER cc_start: 0.8675 (t) cc_final: 0.8170 (p) REVERT: D 695 LYS cc_start: 0.7120 (OUTLIER) cc_final: 0.6092 (mptt) REVERT: D 770 LYS cc_start: 0.8012 (mmtp) cc_final: 0.7724 (tttp) REVERT: D 817 LYS cc_start: 0.7692 (tppt) cc_final: 0.7356 (ttpt) REVERT: E 148 TYR cc_start: 0.8152 (t80) cc_final: 0.7750 (t80) outliers start: 66 outliers final: 34 residues processed: 340 average time/residue: 0.2998 time to fit residues: 158.0394 Evaluate side-chains 316 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 276 time to evaluate : 1.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain A residue 719 ASP Chi-restraints excluded: chain A residue 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 C residue 392 GLN Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 661 ARG Chi-restraints excluded: chain C residue 666 VAL 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 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: 1.9990 chunk 58 optimal weight: 2.9990 chunk 131 optimal weight: 0.4980 chunk 197 optimal weight: 5.9990 chunk 192 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 80 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3878 r_free = 0.3878 target = 0.170310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.125887 restraints weight = 22020.881| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.05 r_work: 0.3040 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3315 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 : 1.242 32.899 27276 Z= 0.480 Chirality : 0.143 2.303 2961 Planarity : 0.004 0.045 3162 Dihedral : 26.440 179.912 4619 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.05 % Favored : 92.59 % Rotamer: Outliers : 3.71 % Allowed : 11.19 % Favored : 85.10 % 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: -0.87 (0.18), residues: 2240 helix: 0.99 (0.14), residues: 1314 sheet: -2.64 (0.32), residues: 198 loop : -2.95 (0.20), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 766 HIS 0.010 0.002 HIS A 883 PHE 0.019 0.002 PHE C 999 TYR 0.018 0.002 TYR F 155 ARG 0.009 0.001 ARG C 684 Details of bonding type rmsd hydrogen bonds : bond 0.03921 ( 960) hydrogen bonds : angle 3.99178 ( 2808) SS BOND : bond 0.00360 ( 6) SS BOND : angle 1.19379 ( 12) covalent geometry : bond 0.00400 (20308) covalent geometry : angle 1.24239 (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 364 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 292 time to evaluate : 2.146 Fit side-chains revert: symmetry clash REVERT: A 511 LYS cc_start: 0.8408 (mmmt) cc_final: 0.8043 (tptp) REVERT: A 585 MET cc_start: 0.9030 (OUTLIER) cc_final: 0.8645 (mmt) REVERT: A 647 TYR cc_start: 0.8635 (OUTLIER) cc_final: 0.8020 (m-80) REVERT: A 663 LYS cc_start: 0.8956 (mptp) cc_final: 0.8623 (mttt) REVERT: A 669 LYS cc_start: 0.7939 (ttmt) cc_final: 0.7345 (mtpt) REVERT: A 952 ARG cc_start: 0.6855 (ptp-170) cc_final: 0.6561 (ptp-170) REVERT: A 957 ILE cc_start: 0.7744 (mp) cc_final: 0.7383 (tp) REVERT: A 985 ASN cc_start: 0.8147 (m-40) cc_final: 0.7935 (m110) REVERT: B 415 LEU cc_start: 0.7970 (mt) cc_final: 0.7705 (mt) REVERT: B 439 LYS cc_start: 0.8576 (mtpm) cc_final: 0.8313 (mtmm) REVERT: B 461 ASN cc_start: 0.7587 (t0) cc_final: 0.7059 (t0) REVERT: B 695 LYS cc_start: 0.7650 (OUTLIER) cc_final: 0.6630 (mptt) REVERT: B 764 ASN cc_start: 0.8408 (m110) cc_final: 0.7951 (m-40) REVERT: C 585 MET cc_start: 0.9020 (OUTLIER) cc_final: 0.8337 (mmt) REVERT: C 642 GLN cc_start: 0.7447 (pp30) cc_final: 0.6008 (mp10) REVERT: C 663 LYS cc_start: 0.9004 (mttp) cc_final: 0.8598 (mttt) REVERT: C 669 LYS cc_start: 0.7897 (ttmt) cc_final: 0.7400 (mtpt) REVERT: C 721 MET cc_start: 0.8797 (ptt) cc_final: 0.8583 (ptt) REVERT: C 860 TYR cc_start: 0.8394 (m-80) cc_final: 0.8118 (m-80) REVERT: C 879 LYS cc_start: 0.8673 (ttmt) cc_final: 0.8211 (mtpp) REVERT: C 880 MET cc_start: 0.7713 (tpp) cc_final: 0.7407 (tpp) REVERT: C 985 ASN cc_start: 0.8079 (m-40) cc_final: 0.7768 (m110) REVERT: D 414 MET cc_start: 0.8541 (OUTLIER) cc_final: 0.8145 (ptp) REVERT: D 415 LEU cc_start: 0.8032 (mt) cc_final: 0.7762 (mt) REVERT: D 461 ASN cc_start: 0.7735 (t0) cc_final: 0.7173 (t0) REVERT: D 635 SER cc_start: 0.8609 (t) cc_final: 0.8129 (p) REVERT: D 695 LYS cc_start: 0.7179 (OUTLIER) cc_final: 0.6174 (mptt) REVERT: D 770 LYS cc_start: 0.8100 (mmtp) cc_final: 0.7865 (tttp) REVERT: D 817 LYS cc_start: 0.7739 (tppt) cc_final: 0.7310 (ttmt) REVERT: E 148 TYR cc_start: 0.8224 (t80) cc_final: 0.7805 (t80) outliers start: 72 outliers final: 40 residues processed: 341 average time/residue: 0.3024 time to fit residues: 163.0516 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 : 1.953 ------------------------------------------------------------------------------- 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 627 GLU Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 666 VAL 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 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 585 MET Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 719 ASP 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 925 ILE Chi-restraints excluded: chain C residue 962 SER Chi-restraints excluded: chain C residue 964 ILE Chi-restraints excluded: chain C residue 1013 SER Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 729 SER Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 790 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 37 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 186 optimal weight: 3.9990 chunk 157 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 203 optimal weight: 1.9990 chunk 221 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 207 optimal weight: 7.9990 chunk 14 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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** C 412 HIS C 764 ASN ** 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 = 0.3863 r_free = 0.3863 target = 0.168982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.123880 restraints weight = 22033.329| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.99 r_work: 0.3033 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20314 Z= 0.183 Angle : 1.245 33.120 27276 Z= 0.480 Chirality : 0.142 2.278 2961 Planarity : 0.004 0.040 3162 Dihedral : 26.036 179.720 4619 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.01 % Favored : 92.63 % Rotamer: Outliers : 3.97 % Allowed : 11.86 % Favored : 84.18 % 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: -0.54 (0.18), residues: 2240 helix: 1.28 (0.14), residues: 1312 sheet: -2.68 (0.32), residues: 190 loop : -2.82 (0.20), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 766 HIS 0.009 0.002 HIS C 883 PHE 0.018 0.002 PHE B 438 TYR 0.023 0.002 TYR E 155 ARG 0.006 0.000 ARG A 684 Details of bonding type rmsd hydrogen bonds : bond 0.03900 ( 960) hydrogen bonds : angle 3.91478 ( 2808) SS BOND : bond 0.00408 ( 6) SS BOND : angle 2.18211 ( 12) covalent geometry : bond 0.00435 (20308) covalent geometry : angle 1.24436 (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 359 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 282 time to evaluate : 1.908 Fit side-chains REVERT: A 511 LYS cc_start: 0.8442 (mmmt) cc_final: 0.8108 (tptp) REVERT: A 585 MET cc_start: 0.9059 (OUTLIER) cc_final: 0.8655 (mmt) REVERT: A 587 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.6852 (mm-40) REVERT: A 663 LYS cc_start: 0.8989 (mptp) cc_final: 0.8650 (mttt) REVERT: A 669 LYS cc_start: 0.7991 (ttmt) cc_final: 0.7371 (mtpt) REVERT: A 952 ARG cc_start: 0.6910 (ptp-170) cc_final: 0.6559 (ptp-170) REVERT: A 957 ILE cc_start: 0.7715 (mp) cc_final: 0.7355 (tp) REVERT: A 985 ASN cc_start: 0.8098 (m-40) cc_final: 0.7810 (m110) REVERT: B 415 LEU cc_start: 0.8018 (mt) cc_final: 0.7770 (mt) REVERT: B 439 LYS cc_start: 0.8608 (mtpm) cc_final: 0.8256 (mtmm) REVERT: B 461 ASN cc_start: 0.7607 (t0) cc_final: 0.7064 (t0) REVERT: B 695 LYS cc_start: 0.7640 (OUTLIER) cc_final: 0.6643 (mptt) REVERT: B 764 ASN cc_start: 0.8425 (m110) cc_final: 0.7980 (m-40) REVERT: C 503 MET cc_start: 0.8980 (ttp) cc_final: 0.8778 (ttm) REVERT: C 585 MET cc_start: 0.9061 (OUTLIER) cc_final: 0.8366 (mmt) REVERT: C 634 GLU cc_start: 0.8215 (pt0) cc_final: 0.7692 (pm20) REVERT: C 663 LYS cc_start: 0.9033 (mttp) cc_final: 0.8638 (mttt) REVERT: C 669 LYS cc_start: 0.7978 (ttmt) cc_final: 0.7429 (mtpt) REVERT: C 860 TYR cc_start: 0.8384 (m-80) cc_final: 0.7915 (m-80) REVERT: C 879 LYS cc_start: 0.8689 (ttmt) cc_final: 0.8277 (mtpt) REVERT: C 985 ASN cc_start: 0.8067 (m-40) cc_final: 0.7798 (m110) REVERT: C 987 GLU cc_start: 0.7406 (tp30) cc_final: 0.7143 (tp30) REVERT: D 414 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.8112 (ptp) REVERT: D 415 LEU cc_start: 0.8033 (mt) cc_final: 0.7728 (mt) REVERT: D 461 ASN cc_start: 0.7685 (t0) cc_final: 0.7114 (t0) REVERT: D 635 SER cc_start: 0.8643 (t) cc_final: 0.8180 (p) REVERT: D 695 LYS cc_start: 0.7406 (OUTLIER) cc_final: 0.6332 (mptt) REVERT: D 770 LYS cc_start: 0.8223 (mmtp) cc_final: 0.7899 (tttp) REVERT: D 817 LYS cc_start: 0.7796 (tppt) cc_final: 0.7410 (ttmt) REVERT: E 148 TYR cc_start: 0.8248 (t80) cc_final: 0.7816 (t80) outliers start: 77 outliers final: 50 residues processed: 336 average time/residue: 0.2976 time to fit residues: 154.6828 Evaluate side-chains 327 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 271 time to evaluate : 1.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 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 902 THR Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 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 695 LYS Chi-restraints excluded: chain B residue 729 SER Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 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 661 ARG Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 719 ASP 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 631 SER 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 Chi-restraints excluded: chain F residue 123 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 154 optimal weight: 7.9990 chunk 133 optimal weight: 0.9980 chunk 101 optimal weight: 0.0000 chunk 179 optimal weight: 0.9990 chunk 79 optimal weight: 0.5980 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: 0.9980 chunk 169 optimal weight: 1.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS ** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.170685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.126058 restraints weight = 21892.430| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.99 r_work: 0.3049 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20314 Z= 0.138 Angle : 1.226 32.918 27276 Z= 0.469 Chirality : 0.142 2.246 2961 Planarity : 0.004 0.038 3162 Dihedral : 25.742 179.864 4619 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.05 % Favored : 92.59 % Rotamer: Outliers : 3.92 % Allowed : 12.42 % Favored : 83.66 % 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: -0.21 (0.18), residues: 2240 helix: 1.55 (0.15), residues: 1314 sheet: -2.60 (0.32), residues: 190 loop : -2.68 (0.20), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 766 HIS 0.017 0.002 HIS C 412 PHE 0.019 0.001 PHE B 438 TYR 0.016 0.001 TYR B 816 ARG 0.005 0.000 ARG C 684 Details of bonding type rmsd hydrogen bonds : bond 0.03621 ( 960) hydrogen bonds : angle 3.80529 ( 2808) SS BOND : bond 0.00645 ( 6) SS BOND : angle 3.36234 ( 12) covalent geometry : bond 0.00314 (20308) covalent geometry : angle 1.22393 (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 367 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 291 time to evaluate : 1.877 Fit side-chains REVERT: A 511 LYS cc_start: 0.8414 (mmmt) cc_final: 0.8101 (tptp) REVERT: A 585 MET cc_start: 0.8995 (OUTLIER) cc_final: 0.8608 (mmt) REVERT: A 587 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.6798 (mm-40) REVERT: A 647 TYR cc_start: 0.8556 (OUTLIER) cc_final: 0.7828 (m-10) REVERT: A 651 ASP cc_start: 0.7314 (t70) cc_final: 0.6969 (p0) REVERT: A 663 LYS cc_start: 0.8958 (mptp) cc_final: 0.8627 (mttt) REVERT: A 669 LYS cc_start: 0.7957 (ttmt) cc_final: 0.7345 (mtpt) REVERT: A 697 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8233 (pttp) REVERT: A 858 THR cc_start: 0.9091 (t) cc_final: 0.8817 (p) REVERT: A 952 ARG cc_start: 0.6899 (ptp-170) cc_final: 0.6543 (ptp-170) REVERT: A 957 ILE cc_start: 0.7661 (mp) cc_final: 0.7300 (tp) REVERT: A 985 ASN cc_start: 0.8121 (m-40) cc_final: 0.7847 (m110) REVERT: A 987 GLU cc_start: 0.7251 (tp30) cc_final: 0.6980 (tp30) REVERT: B 415 LEU cc_start: 0.7994 (mt) cc_final: 0.7767 (mt) REVERT: B 439 LYS cc_start: 0.8556 (mtpm) cc_final: 0.8165 (mtmm) REVERT: B 461 ASN cc_start: 0.7574 (t0) cc_final: 0.7081 (t0) REVERT: B 635 SER cc_start: 0.8570 (t) cc_final: 0.8065 (p) REVERT: B 695 LYS cc_start: 0.7505 (OUTLIER) cc_final: 0.6511 (mptt) REVERT: B 764 ASN cc_start: 0.8412 (m110) cc_final: 0.7952 (m-40) REVERT: C 503 MET cc_start: 0.8988 (ttp) cc_final: 0.8756 (ttm) REVERT: C 585 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8288 (mmt) REVERT: C 634 GLU cc_start: 0.8219 (pt0) cc_final: 0.7685 (pm20) REVERT: C 663 LYS cc_start: 0.9013 (mttp) cc_final: 0.8612 (mttt) REVERT: C 669 LYS cc_start: 0.7933 (ttmt) cc_final: 0.7364 (mtpt) REVERT: C 860 TYR cc_start: 0.8353 (m-80) cc_final: 0.7870 (m-80) REVERT: C 879 LYS cc_start: 0.8704 (ttmt) cc_final: 0.8346 (mtpt) REVERT: C 985 ASN cc_start: 0.7980 (m-40) cc_final: 0.7683 (m110) REVERT: C 987 GLU cc_start: 0.7377 (tp30) cc_final: 0.7133 (tp30) REVERT: D 414 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.8081 (ptp) REVERT: D 415 LEU cc_start: 0.8036 (mt) cc_final: 0.7801 (mt) REVERT: D 461 ASN cc_start: 0.7657 (t0) cc_final: 0.7221 (t0) REVERT: D 635 SER cc_start: 0.8557 (t) cc_final: 0.8100 (p) REVERT: D 695 LYS cc_start: 0.7375 (OUTLIER) cc_final: 0.6360 (mptt) REVERT: D 770 LYS cc_start: 0.8150 (mmtp) cc_final: 0.7875 (tttp) REVERT: D 817 LYS cc_start: 0.7810 (tppt) cc_final: 0.7469 (ttmt) REVERT: E 148 TYR cc_start: 0.8220 (t80) cc_final: 0.7810 (t80) outliers start: 76 outliers final: 47 residues processed: 345 average time/residue: 0.2813 time to fit residues: 152.5045 Evaluate side-chains 332 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 277 time to evaluate : 1.956 ------------------------------------------------------------------------------- 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 647 TYR Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 719 ASP Chi-restraints excluded: chain A residue 741 SER Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 902 THR Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 695 LYS Chi-restraints excluded: chain B residue 705 GLU Chi-restraints excluded: chain B residue 729 SER Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 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 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 720 THR Chi-restraints excluded: chain D residue 729 SER Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 790 SER Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain F residue 123 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- 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: 0.8980 chunk 15 optimal weight: 1.9990 chunk 89 optimal weight: 0.0010 chunk 36 optimal weight: 0.0570 chunk 145 optimal weight: 1.9990 chunk 220 optimal weight: 4.9990 chunk 222 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 overall best weight: 0.9908 ------------------------------------------------------------------------------- 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 = 0.3868 r_free = 0.3868 target = 0.169478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.124035 restraints weight = 21815.174| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.08 r_work: 0.3029 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 20314 Z= 0.173 Angle : 1.236 32.946 27276 Z= 0.475 Chirality : 0.142 2.232 2961 Planarity : 0.004 0.038 3162 Dihedral : 25.457 179.949 4619 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.83 % Favored : 92.81 % Rotamer: Outliers : 3.56 % Allowed : 13.51 % Favored : 82.94 % 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: -0.12 (0.18), residues: 2240 helix: 1.60 (0.14), residues: 1314 sheet: -2.56 (0.32), residues: 190 loop : -2.60 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 766 HIS 0.009 0.002 HIS A 412 PHE 0.020 0.001 PHE B 438 TYR 0.028 0.002 TYR A 980 ARG 0.007 0.000 ARG C 684 Details of bonding type rmsd hydrogen bonds : bond 0.03723 ( 960) hydrogen bonds : angle 3.81402 ( 2808) SS BOND : bond 0.00520 ( 6) SS BOND : angle 3.78057 ( 12) covalent geometry : bond 0.00409 (20308) covalent geometry : angle 1.23346 (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 360 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 291 time to evaluate : 2.002 Fit side-chains REVERT: A 585 MET cc_start: 0.9041 (OUTLIER) cc_final: 0.8639 (mmt) REVERT: A 587 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.6870 (mm-40) REVERT: A 647 TYR cc_start: 0.8557 (OUTLIER) cc_final: 0.7882 (m-10) REVERT: A 651 ASP cc_start: 0.7428 (t70) cc_final: 0.7150 (p0) REVERT: A 663 LYS cc_start: 0.8978 (mptp) cc_final: 0.8655 (mttt) REVERT: A 669 LYS cc_start: 0.7989 (ttmt) cc_final: 0.7350 (mtpt) REVERT: A 684 ARG cc_start: 0.8758 (ttm110) cc_final: 0.8540 (ttm110) REVERT: A 697 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8227 (pttp) REVERT: A 858 THR cc_start: 0.9087 (t) cc_final: 0.8831 (p) REVERT: A 952 ARG cc_start: 0.6948 (ptp-170) cc_final: 0.6586 (ptp-170) REVERT: A 957 ILE cc_start: 0.7679 (mp) cc_final: 0.7309 (tp) REVERT: A 985 ASN cc_start: 0.8067 (m-40) cc_final: 0.7789 (m110) REVERT: A 987 GLU cc_start: 0.7309 (tp30) cc_final: 0.7045 (tp30) REVERT: B 415 LEU cc_start: 0.8016 (mt) cc_final: 0.7798 (mt) REVERT: B 461 ASN cc_start: 0.7624 (t0) cc_final: 0.7142 (t0) REVERT: B 635 SER cc_start: 0.8586 (t) cc_final: 0.8106 (p) REVERT: B 695 LYS cc_start: 0.7718 (OUTLIER) cc_final: 0.6750 (mptt) REVERT: B 764 ASN cc_start: 0.8486 (m110) cc_final: 0.8005 (m-40) REVERT: C 585 MET cc_start: 0.9035 (OUTLIER) cc_final: 0.8332 (mmt) REVERT: C 663 LYS cc_start: 0.9020 (mttp) cc_final: 0.8624 (mttt) REVERT: C 669 LYS cc_start: 0.7966 (ttmt) cc_final: 0.7346 (mtpt) REVERT: C 860 TYR cc_start: 0.8393 (m-80) cc_final: 0.8140 (m-80) REVERT: C 879 LYS cc_start: 0.8648 (ttmt) cc_final: 0.8248 (mtpt) REVERT: C 880 MET cc_start: 0.7818 (tpp) cc_final: 0.7615 (tpp) REVERT: C 952 ARG cc_start: 0.6915 (ptp-170) cc_final: 0.6571 (ptp-170) REVERT: C 985 ASN cc_start: 0.8010 (m-40) cc_final: 0.7719 (m110) REVERT: C 987 GLU cc_start: 0.7371 (tp30) cc_final: 0.7104 (tp30) REVERT: D 415 LEU cc_start: 0.8044 (mt) cc_final: 0.7769 (mt) REVERT: D 461 ASN cc_start: 0.7655 (t0) cc_final: 0.7216 (t0) REVERT: D 635 SER cc_start: 0.8538 (t) cc_final: 0.8091 (p) REVERT: D 695 LYS cc_start: 0.7484 (OUTLIER) cc_final: 0.6491 (mptt) REVERT: D 770 LYS cc_start: 0.8225 (mmtp) cc_final: 0.7885 (tttp) REVERT: D 817 LYS cc_start: 0.7782 (tppt) cc_final: 0.7433 (ttmt) REVERT: E 100 TYR cc_start: 0.8239 (t80) cc_final: 0.8031 (t80) REVERT: E 148 TYR cc_start: 0.8246 (t80) cc_final: 0.7822 (t80) outliers start: 69 outliers final: 50 residues processed: 336 average time/residue: 0.3083 time to fit residues: 161.1781 Evaluate side-chains 337 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 280 time to evaluate : 2.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 719 ASP Chi-restraints excluded: chain A residue 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 B residue 397 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 695 LYS Chi-restraints excluded: chain B residue 705 GLU Chi-restraints excluded: chain B residue 729 SER Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 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 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 445 VAL Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 644 GLU Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain D residue 729 SER Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 790 SER Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain F residue 123 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 186 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 106 optimal weight: 0.5980 chunk 47 optimal weight: 0.0030 chunk 158 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 193 optimal weight: 0.2980 chunk 97 optimal weight: 0.9980 chunk 157 optimal weight: 3.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.172142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.125203 restraints weight = 22257.795| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.10 r_work: 0.3087 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.3951 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= 0.135 Angle : 1.228 32.843 27276 Z= 0.471 Chirality : 0.142 2.216 2961 Planarity : 0.004 0.038 3162 Dihedral : 25.297 179.635 4619 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.92 % Favored : 92.72 % Rotamer: Outliers : 3.25 % Allowed : 13.76 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z (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: 0.06 (0.18), residues: 2240 helix: 1.76 (0.15), residues: 1314 sheet: -2.41 (0.33), residues: 190 loop : -2.57 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 766 HIS 0.013 0.002 HIS C 412 PHE 0.021 0.001 PHE B 438 TYR 0.026 0.001 TYR A 980 ARG 0.007 0.000 ARG C 684 Details of bonding type rmsd hydrogen bonds : bond 0.03535 ( 960) hydrogen bonds : angle 3.73975 ( 2808) SS BOND : bond 0.00713 ( 6) SS BOND : angle 5.84898 ( 12) covalent geometry : bond 0.00307 (20308) covalent geometry : angle 1.22254 (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 352 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 289 time to evaluate : 2.075 Fit side-chains REVERT: A 511 LYS cc_start: 0.8436 (mmmt) cc_final: 0.8079 (tptp) REVERT: A 585 MET cc_start: 0.8966 (OUTLIER) cc_final: 0.8553 (mmt) REVERT: A 587 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.6774 (mm-40) REVERT: A 647 TYR cc_start: 0.8588 (OUTLIER) cc_final: 0.7891 (m-10) REVERT: A 651 ASP cc_start: 0.7458 (t70) cc_final: 0.7187 (p0) REVERT: A 663 LYS cc_start: 0.8986 (mptp) cc_final: 0.8659 (mttt) REVERT: A 669 LYS cc_start: 0.8013 (ttmt) cc_final: 0.7384 (mtpt) REVERT: A 697 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8248 (pttp) REVERT: A 858 THR cc_start: 0.9112 (t) cc_final: 0.8879 (p) REVERT: A 952 ARG cc_start: 0.6984 (ptp-170) cc_final: 0.6616 (ptp-170) REVERT: A 957 ILE cc_start: 0.7665 (mp) cc_final: 0.7308 (tp) REVERT: A 985 ASN cc_start: 0.8087 (m-40) cc_final: 0.7839 (m110) REVERT: B 415 LEU cc_start: 0.8058 (mt) cc_final: 0.7850 (mt) REVERT: B 461 ASN cc_start: 0.7575 (t0) cc_final: 0.7155 (t0) REVERT: B 635 SER cc_start: 0.8547 (t) cc_final: 0.8096 (p) REVERT: B 695 LYS cc_start: 0.7674 (OUTLIER) cc_final: 0.6747 (mptt) REVERT: B 764 ASN cc_start: 0.8508 (m110) cc_final: 0.8066 (m-40) REVERT: C 503 MET cc_start: 0.9052 (ttp) cc_final: 0.8728 (ttm) REVERT: C 585 MET cc_start: 0.8992 (OUTLIER) cc_final: 0.8284 (mmt) REVERT: C 663 LYS cc_start: 0.9026 (mttp) cc_final: 0.8638 (mttt) REVERT: C 669 LYS cc_start: 0.7968 (ttmt) cc_final: 0.7327 (mtpt) REVERT: C 860 TYR cc_start: 0.8398 (m-80) cc_final: 0.7880 (m-80) REVERT: C 879 LYS cc_start: 0.8683 (ttmt) cc_final: 0.8226 (mtpt) REVERT: C 952 ARG cc_start: 0.6954 (ptp-170) cc_final: 0.6601 (ptp-170) REVERT: C 985 ASN cc_start: 0.8011 (m-40) cc_final: 0.7739 (m110) REVERT: C 987 GLU cc_start: 0.7363 (tp30) cc_final: 0.7102 (tp30) REVERT: D 415 LEU cc_start: 0.8086 (mt) cc_final: 0.7847 (mt) REVERT: D 461 ASN cc_start: 0.7667 (t0) cc_final: 0.7279 (t0) REVERT: D 635 SER cc_start: 0.8502 (t) cc_final: 0.8083 (p) REVERT: D 695 LYS cc_start: 0.7454 (OUTLIER) cc_final: 0.6493 (mptt) REVERT: D 770 LYS cc_start: 0.8190 (mmtp) cc_final: 0.7874 (tttp) REVERT: D 817 LYS cc_start: 0.7813 (tppt) cc_final: 0.7495 (ttmt) REVERT: E 148 TYR cc_start: 0.8342 (t80) cc_final: 0.7935 (t80) REVERT: F 98 LEU cc_start: 0.7336 (tp) cc_final: 0.7064 (tt) outliers start: 63 outliers final: 46 residues processed: 332 average time/residue: 0.3004 time to fit residues: 156.8760 Evaluate side-chains 330 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 277 time to evaluate : 1.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain A residue 719 ASP Chi-restraints excluded: chain A residue 741 SER 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 591 ILE Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 695 LYS Chi-restraints excluded: chain B residue 705 GLU Chi-restraints excluded: chain B residue 729 SER Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 652 SER Chi-restraints excluded: chain C residue 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 445 VAL Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 644 GLU Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain D residue 729 SER Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 790 SER Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain F residue 123 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 220 optimal weight: 4.9990 chunk 215 optimal weight: 0.0980 chunk 151 optimal weight: 3.9990 chunk 89 optimal weight: 0.0010 chunk 8 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 139 optimal weight: 0.0670 chunk 71 optimal weight: 0.2980 chunk 95 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 overall best weight: 0.2524 ------------------------------------------------------------------------------- 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 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 HIS C 586 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.175445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.127225 restraints weight = 22054.434| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.31 r_work: 0.3128 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20314 Z= 0.113 Angle : 1.213 32.371 27276 Z= 0.460 Chirality : 0.140 2.168 2961 Planarity : 0.004 0.059 3162 Dihedral : 24.911 179.840 4619 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.61 % Favored : 93.08 % Rotamer: Outliers : 2.63 % Allowed : 14.48 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z (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: 0.34 (0.18), residues: 2240 helix: 1.95 (0.15), residues: 1320 sheet: -2.08 (0.34), residues: 190 loop : -2.50 (0.21), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 766 HIS 0.010 0.001 HIS C 883 PHE 0.018 0.001 PHE B 438 TYR 0.026 0.001 TYR A 980 ARG 0.008 0.000 ARG A 684 Details of bonding type rmsd hydrogen bonds : bond 0.03239 ( 960) hydrogen bonds : angle 3.63282 ( 2808) SS BOND : bond 0.00442 ( 6) SS BOND : angle 3.28594 ( 12) covalent geometry : bond 0.00241 (20308) covalent geometry : angle 1.21083 (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 354 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 303 time to evaluate : 1.828 Fit side-chains REVERT: A 511 LYS cc_start: 0.8310 (mmmt) cc_final: 0.7896 (tptp) REVERT: A 585 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.8354 (mmt) REVERT: A 587 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.6733 (mm-40) REVERT: A 647 TYR cc_start: 0.8427 (OUTLIER) cc_final: 0.7824 (m-80) REVERT: A 663 LYS cc_start: 0.8921 (mptp) cc_final: 0.8643 (mttt) REVERT: A 669 LYS cc_start: 0.7952 (ttmt) cc_final: 0.7435 (mtpt) REVERT: A 697 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8219 (pttp) REVERT: A 952 ARG cc_start: 0.7078 (ptp-170) cc_final: 0.6710 (ptp-170) REVERT: A 957 ILE cc_start: 0.7733 (mp) cc_final: 0.7391 (tp) REVERT: A 985 ASN cc_start: 0.8137 (m-40) cc_final: 0.7905 (m110) REVERT: B 461 ASN cc_start: 0.7352 (t0) cc_final: 0.7080 (t0) REVERT: B 635 SER cc_start: 0.8286 (t) cc_final: 0.7906 (p) REVERT: B 695 LYS cc_start: 0.7594 (OUTLIER) cc_final: 0.6836 (mptt) REVERT: B 696 SER cc_start: 0.8517 (t) cc_final: 0.8123 (t) REVERT: B 764 ASN cc_start: 0.8479 (m110) cc_final: 0.8027 (m-40) REVERT: C 511 LYS cc_start: 0.8136 (mmmt) cc_final: 0.7855 (tptp) REVERT: C 585 MET cc_start: 0.8765 (OUTLIER) cc_final: 0.8045 (mmt) REVERT: C 663 LYS cc_start: 0.8959 (mttp) cc_final: 0.8590 (mttt) REVERT: C 669 LYS cc_start: 0.7950 (ttmt) cc_final: 0.7449 (mtpt) REVERT: C 860 TYR cc_start: 0.8410 (m-80) cc_final: 0.7929 (m-80) REVERT: C 879 LYS cc_start: 0.8642 (ttmt) cc_final: 0.8312 (ttmm) REVERT: C 952 ARG cc_start: 0.7029 (ptp-170) cc_final: 0.6698 (ptp-170) REVERT: D 635 SER cc_start: 0.8185 (t) cc_final: 0.7887 (p) REVERT: D 695 LYS cc_start: 0.7490 (OUTLIER) cc_final: 0.6706 (mptt) REVERT: D 696 SER cc_start: 0.8429 (t) cc_final: 0.8032 (t) REVERT: F 98 LEU cc_start: 0.7392 (tp) cc_final: 0.7140 (tt) outliers start: 51 outliers final: 35 residues processed: 336 average time/residue: 0.2926 time to fit residues: 155.1469 Evaluate side-chains 321 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 279 time to evaluate : 1.956 ------------------------------------------------------------------------------- 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 585 MET Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain A residue 719 ASP Chi-restraints excluded: chain A residue 741 SER Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 695 LYS Chi-restraints excluded: chain B residue 705 GLU Chi-restraints excluded: chain B residue 729 SER Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 719 ASP Chi-restraints excluded: chain C residue 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 445 VAL Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 644 GLU Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain D residue 729 SER Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain F residue 123 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 46 optimal weight: 4.9990 chunk 204 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 chunk 81 optimal weight: 0.7980 chunk 146 optimal weight: 9.9990 chunk 97 optimal weight: 0.9980 chunk 157 optimal weight: 4.9990 chunk 225 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 113 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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** C 412 HIS C 764 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.174141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.127559 restraints weight = 22227.639| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.03 r_work: 0.3101 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20314 Z= 0.148 Angle : 1.222 32.348 27276 Z= 0.466 Chirality : 0.140 2.171 2961 Planarity : 0.004 0.064 3162 Dihedral : 24.856 179.661 4619 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.70 % Favored : 93.04 % Rotamer: Outliers : 2.42 % Allowed : 15.00 % Favored : 82.58 % 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: 0.34 (0.18), residues: 2240 helix: 1.95 (0.14), residues: 1318 sheet: -2.01 (0.34), residues: 190 loop : -2.50 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 766 HIS 0.009 0.001 HIS A 412 PHE 0.018 0.001 PHE B 438 TYR 0.028 0.001 TYR A 980 ARG 0.008 0.000 ARG C 684 Details of bonding type rmsd hydrogen bonds : bond 0.03447 ( 960) hydrogen bonds : angle 3.68152 ( 2808) SS BOND : bond 0.00282 ( 6) SS BOND : angle 3.02054 ( 12) covalent geometry : bond 0.00345 (20308) covalent geometry : angle 1.22067 (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 319 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 272 time to evaluate : 1.989 Fit side-chains REVERT: A 511 LYS cc_start: 0.8284 (mmmt) cc_final: 0.7888 (tptp) REVERT: A 585 MET cc_start: 0.8965 (OUTLIER) cc_final: 0.8551 (mmt) REVERT: A 587 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.6785 (mm-40) REVERT: A 647 TYR cc_start: 0.8606 (OUTLIER) cc_final: 0.8070 (m-80) REVERT: A 663 LYS cc_start: 0.8955 (mptp) cc_final: 0.8633 (mttt) REVERT: A 669 LYS cc_start: 0.7934 (ttmt) cc_final: 0.7321 (mtpt) REVERT: A 697 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8248 (pttp) REVERT: A 952 ARG cc_start: 0.6987 (ptp-170) cc_final: 0.6624 (ptp-170) REVERT: A 957 ILE cc_start: 0.7674 (mp) cc_final: 0.7289 (tp) REVERT: A 985 ASN cc_start: 0.8127 (m-40) cc_final: 0.7908 (m110) REVERT: A 987 GLU cc_start: 0.7394 (tp30) cc_final: 0.7141 (tp30) REVERT: B 461 ASN cc_start: 0.7530 (t0) cc_final: 0.7186 (t0) REVERT: B 635 SER cc_start: 0.8289 (t) cc_final: 0.7846 (p) REVERT: B 695 LYS cc_start: 0.7639 (OUTLIER) cc_final: 0.6821 (mptt) REVERT: B 764 ASN cc_start: 0.8479 (m110) cc_final: 0.8009 (m-40) REVERT: C 511 LYS cc_start: 0.8068 (mmmt) cc_final: 0.7806 (tptp) REVERT: C 585 MET cc_start: 0.8957 (OUTLIER) cc_final: 0.8270 (mmt) REVERT: C 651 ASP cc_start: 0.7656 (t70) cc_final: 0.7376 (p0) REVERT: C 663 LYS cc_start: 0.9037 (mttp) cc_final: 0.8633 (mttt) REVERT: C 669 LYS cc_start: 0.7971 (ttmt) cc_final: 0.7329 (mtpt) REVERT: C 860 TYR cc_start: 0.8389 (m-80) cc_final: 0.8141 (m-80) REVERT: C 879 LYS cc_start: 0.8623 (ttmt) cc_final: 0.8372 (ttmt) REVERT: C 939 MET cc_start: 0.7119 (tpp) cc_final: 0.6742 (ttt) REVERT: C 952 ARG cc_start: 0.6892 (ptp-170) cc_final: 0.6539 (ptp-170) REVERT: D 635 SER cc_start: 0.8251 (t) cc_final: 0.7868 (p) REVERT: D 695 LYS cc_start: 0.7492 (OUTLIER) cc_final: 0.6641 (mptt) REVERT: D 817 LYS cc_start: 0.8309 (ttmt) cc_final: 0.8054 (ttmt) REVERT: F 98 LEU cc_start: 0.7268 (tp) cc_final: 0.6997 (tt) outliers start: 47 outliers final: 36 residues processed: 303 average time/residue: 0.2939 time to fit residues: 139.6146 Evaluate side-chains 312 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 269 time to evaluate : 1.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain A residue 741 SER Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 695 LYS Chi-restraints excluded: chain B residue 705 GLU Chi-restraints excluded: chain B residue 729 SER Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 719 ASP Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 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 695 LYS Chi-restraints excluded: chain D residue 729 SER Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 123 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 174 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 143 optimal weight: 0.8980 chunk 195 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 184 optimal weight: 0.5980 chunk 225 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 47 optimal weight: 9.9990 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 412 HIS ** 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 = 0.3929 r_free = 0.3929 target = 0.173431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.125752 restraints weight = 22207.251| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.07 r_work: 0.3061 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20314 Z= 0.154 Angle : 1.224 32.440 27276 Z= 0.468 Chirality : 0.140 2.181 2961 Planarity : 0.004 0.059 3162 Dihedral : 24.808 179.804 4619 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.96 % Favored : 92.77 % Rotamer: Outliers : 2.68 % Allowed : 14.85 % Favored : 82.47 % 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: 0.34 (0.18), residues: 2240 helix: 1.93 (0.14), residues: 1320 sheet: -2.00 (0.34), residues: 190 loop : -2.47 (0.21), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 766 HIS 0.014 0.001 HIS C 412 PHE 0.012 0.001 PHE A 495 TYR 0.027 0.001 TYR A 980 ARG 0.008 0.000 ARG A 684 Details of bonding type rmsd hydrogen bonds : bond 0.03514 ( 960) hydrogen bonds : angle 3.69212 ( 2808) SS BOND : bond 0.00147 ( 6) SS BOND : angle 2.47181 ( 12) covalent geometry : bond 0.00364 (20308) covalent geometry : angle 1.22355 (27264) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10911.73 seconds wall clock time: 189 minutes 39.13 seconds (11379.13 seconds total)