Starting phenix.real_space_refine on Fri Jun 5 04:09:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zko_74379/06_2026/9zko_74379.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zko_74379/06_2026/9zko_74379.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9zko_74379/06_2026/9zko_74379.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zko_74379/06_2026/9zko_74379.map" model { file = "/net/cci-nas-00/data/ceres_data/9zko_74379/06_2026/9zko_74379.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zko_74379/06_2026/9zko_74379.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 112 5.16 5 C 11400 2.51 5 N 2669 2.21 5 O 3006 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17195 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 2966 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 13, 'TRANS': 389} Chain breaks: 1 Unresolved non-hydrogen bonds: 192 Unresolved non-hydrogen angles: 226 Unresolved non-hydrogen dihedrals: 160 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 11, 'ASN:plan1': 2, 'GLN:plan1': 2, 'PHE:plan': 1, 'ASP:plan': 8, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 118 Chain: "B" Number of atoms: 2954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 2954 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 391} Chain breaks: 1 Unresolved non-hydrogen bonds: 195 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 167 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 12, 'ARG:plan': 3, 'ASP:plan': 6, 'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 103 Chain: "C" Number of atoms: 2972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 2972 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 13, 'TRANS': 389} Chain breaks: 1 Unresolved non-hydrogen bonds: 186 Unresolved non-hydrogen angles: 219 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 11, 'ASN:plan1': 2, 'GLN:plan1': 2, 'PHE:plan': 1, 'ASP:plan': 8, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 118 Chain: "D" Number of atoms: 2962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 2962 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 391} Chain breaks: 1 Unresolved non-hydrogen bonds: 187 Unresolved non-hydrogen angles: 220 Unresolved non-hydrogen dihedrals: 159 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 12, 'ARG:plan': 3, 'ASP:plan': 6, 'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 103 Chain: "E" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain breaks: 2 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2, 'ASN:plan1': 2, 'ARG:plan': 3, 'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 51 Chain: "F" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 984 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "G" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1353 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1353 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 190 Unusual residues: {'OLC': 3, 'PLM': 3, 'POV': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1, 'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 58 Unusual residues: {'OLC': 1, 'PLM': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 166 Unusual residues: {'OLC': 2, 'PLM': 3, 'POV': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1, 'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 118 Unusual residues: {'OLC': 2, 'PLM': 3, 'POV': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "G" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "H" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Time building chain proxies: 4.09, per 1000 atoms: 0.24 Number of scatterers: 17195 At special positions: 0 Unit cell: (119.625, 122.1, 132, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 112 16.00 P 8 15.00 O 3006 8.00 N 2669 7.00 C 11400 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 714 " - pdb=" SG CYS A 769 " distance=2.02 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 714 " - pdb=" SG CYS C 769 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS G 52 " - pdb=" SG CYS G 91 " distance=2.03 Simple disulfide: pdb=" SG CYS G 90 " - pdb=" SG CYS G 100 " distance=2.03 Simple disulfide: pdb=" SG CYS H 52 " - pdb=" SG CYS H 91 " distance=2.03 Simple disulfide: pdb=" SG CYS H 90 " - pdb=" SG CYS H 100 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.39 Conformation dependent library (CDL) restraints added in 785.0 milliseconds 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4062 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 20 sheets defined 60.9% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 413 through 415 No H-bonds generated for 'chain 'A' and resid 413 through 415' Processing helix chain 'A' and resid 419 through 433 Processing helix chain 'A' and resid 458 through 465 Processing helix chain 'A' and resid 478 through 483 Processing helix chain 'A' and resid 511 through 515 removed outlier: 3.775A pdb=" N LEU A 514 " --> pdb=" O PHE A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 541 Processing helix chain 'A' and resid 568 through 581 Processing helix chain 'A' and resid 591 through 626 Processing helix chain 'A' and resid 631 through 636 removed outlier: 3.755A pdb=" N LEU A 635 " --> pdb=" O SER A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 656 Processing helix chain 'A' and resid 660 through 672 Processing helix chain 'A' and resid 681 through 693 removed outlier: 3.912A pdb=" N LYS A 693 " --> pdb=" O VAL A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 711 Processing helix chain 'A' and resid 739 through 751 removed outlier: 3.580A pdb=" N GLU A 751 " --> pdb=" O LEU A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 765 removed outlier: 3.775A pdb=" N LYS A 759 " --> pdb=" O LEU A 755 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP A 765 " --> pdb=" O LYS A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 775 Processing helix chain 'A' and resid 788 through 813 removed outlier: 3.642A pdb=" N PHE A 792 " --> pdb=" O VAL A 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 419 No H-bonds generated for 'chain 'B' and resid 417 through 419' Processing helix chain 'B' and resid 423 through 437 Processing helix chain 'B' and resid 461 through 469 Processing helix chain 'B' and resid 482 through 487 removed outlier: 3.623A pdb=" N GLU B 487 " --> pdb=" O LEU B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.648A pdb=" N LEU B 518 " --> pdb=" O PHE B 515 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASP B 519 " --> pdb=" O SER B 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 515 through 519' Processing helix chain 'B' and resid 522 through 547 Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 595 through 626 Processing helix chain 'B' and resid 635 through 643 removed outlier: 3.615A pdb=" N LEU B 639 " --> pdb=" O SER B 635 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR B 643 " --> pdb=" O LEU B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 661 removed outlier: 3.888A pdb=" N PHE B 659 " --> pdb=" O THR B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 676 Processing helix chain 'B' and resid 685 through 694 Processing helix chain 'B' and resid 706 through 714 removed outlier: 3.747A pdb=" N GLN B 714 " --> pdb=" O GLU B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 743 through 757 Processing helix chain 'B' and resid 757 through 767 removed outlier: 3.561A pdb=" N TRP B 767 " --> pdb=" O LYS B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 792 through 819 Processing helix chain 'C' and resid 412 through 415 removed outlier: 4.340A pdb=" N ASP C 415 " --> pdb=" O GLU C 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 412 through 415' Processing helix chain 'C' and resid 419 through 433 removed outlier: 3.552A pdb=" N HIS C 431 " --> pdb=" O GLU C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 466 Processing helix chain 'C' and resid 478 through 483 Processing helix chain 'C' and resid 511 through 515 removed outlier: 3.685A pdb=" N LEU C 514 " --> pdb=" O PHE C 511 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP C 515 " --> pdb=" O SER C 512 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 511 through 515' Processing helix chain 'C' and resid 518 through 541 Processing helix chain 'C' and resid 568 through 581 Processing helix chain 'C' and resid 591 through 626 Processing helix chain 'C' and resid 631 through 636 removed outlier: 3.686A pdb=" N LEU C 635 " --> pdb=" O SER C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 657 Processing helix chain 'C' and resid 660 through 672 Processing helix chain 'C' and resid 681 through 693 removed outlier: 3.925A pdb=" N LYS C 693 " --> pdb=" O VAL C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 702 through 711 Processing helix chain 'C' and resid 739 through 751 Processing helix chain 'C' and resid 753 through 764 removed outlier: 3.746A pdb=" N LYS C 759 " --> pdb=" O LEU C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 788 through 813 removed outlier: 3.609A pdb=" N PHE C 792 " --> pdb=" O VAL C 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 419 No H-bonds generated for 'chain 'D' and resid 417 through 419' Processing helix chain 'D' and resid 423 through 436 removed outlier: 3.621A pdb=" N ASP D 427 " --> pdb=" O GLY D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 469 Processing helix chain 'D' and resid 482 through 487 removed outlier: 3.569A pdb=" N GLU D 487 " --> pdb=" O LEU D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.836A pdb=" N LEU D 518 " --> pdb=" O PHE D 515 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP D 519 " --> pdb=" O SER D 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 515 through 519' Processing helix chain 'D' and resid 522 through 547 Processing helix chain 'D' and resid 572 through 585 Processing helix chain 'D' and resid 595 through 626 Processing helix chain 'D' and resid 635 through 643 removed outlier: 3.595A pdb=" N THR D 643 " --> pdb=" O LEU D 639 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 661 removed outlier: 3.964A pdb=" N PHE D 659 " --> pdb=" O THR D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 676 Processing helix chain 'D' and resid 685 through 696 Processing helix chain 'D' and resid 706 through 713 Processing helix chain 'D' and resid 744 through 756 Processing helix chain 'D' and resid 757 through 767 removed outlier: 3.524A pdb=" N TRP D 767 " --> pdb=" O LYS D 763 " (cutoff:3.500A) Processing helix chain 'D' and resid 775 through 779 Processing helix chain 'D' and resid 792 through 819 Processing helix chain 'E' and resid 4 through 37 removed outlier: 3.704A pdb=" N SER E 19 " --> pdb=" O VAL E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 85 Proline residue: E 70 - end of helix Processing helix chain 'E' and resid 87 through 108 Proline residue: E 96 - end of helix removed outlier: 3.572A pdb=" N ARG E 108 " --> pdb=" O ARG E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 159 removed outlier: 3.580A pdb=" N PHE E 147 " --> pdb=" O LEU E 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 37 Processing helix chain 'F' and resid 57 through 85 Proline residue: F 70 - end of helix Processing helix chain 'F' and resid 87 through 108 Proline residue: F 96 - end of helix Processing helix chain 'F' and resid 127 through 159 Processing helix chain 'G' and resid 16 through 41 removed outlier: 3.545A pdb=" N PHE G 29 " --> pdb=" O THR G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 128 Processing helix chain 'G' and resid 128 through 151 removed outlier: 3.875A pdb=" N ARG G 149 " --> pdb=" O VAL G 145 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL G 150 " --> pdb=" O ALA G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 156 through 183 Processing helix chain 'G' and resid 202 through 235 removed outlier: 3.925A pdb=" N TYR G 206 " --> pdb=" O GLY G 202 " (cutoff:3.500A) Processing helix chain 'H' and resid 16 through 41 removed outlier: 3.511A pdb=" N PHE H 29 " --> pdb=" O THR H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 116 through 128 Processing helix chain 'H' and resid 128 through 151 removed outlier: 3.850A pdb=" N ARG H 149 " --> pdb=" O VAL H 145 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL H 150 " --> pdb=" O ALA H 146 " (cutoff:3.500A) Processing helix chain 'H' and resid 156 through 183 removed outlier: 3.546A pdb=" N ILE H 174 " --> pdb=" O LEU H 170 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 235 removed outlier: 3.972A pdb=" N TYR H 206 " --> pdb=" O GLY H 202 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 436 through 440 removed outlier: 6.193A pdb=" N TYR A 391 " --> pdb=" O ARG A 437 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N GLU A 439 " --> pdb=" O TYR A 391 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N VAL A 393 " --> pdb=" O GLU A 439 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL A 472 " --> pdb=" O THR A 394 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ALA A 473 " --> pdb=" O GLY A 729 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N GLY A 729 " --> pdb=" O ALA A 473 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU A 475 " --> pdb=" O GLY A 727 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLY A 727 " --> pdb=" O LEU A 475 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR A 732 " --> pdb=" O ASP A 486 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 436 through 440 removed outlier: 6.193A pdb=" N TYR A 391 " --> pdb=" O ARG A 437 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N GLU A 439 " --> pdb=" O TYR A 391 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N VAL A 393 " --> pdb=" O GLU A 439 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL A 472 " --> pdb=" O THR A 394 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ALA A 473 " --> pdb=" O GLY A 729 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N GLY A 729 " --> pdb=" O ALA A 473 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU A 475 " --> pdb=" O GLY A 727 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLY A 727 " --> pdb=" O LEU A 475 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N MET A 492 " --> pdb=" O TYR A 728 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 403 through 404 Processing sheet with id=AA4, first strand: chain 'A' and resid 642 through 644 removed outlier: 6.737A pdb=" N ALA A 642 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N LEU A 699 " --> pdb=" O ALA A 642 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N GLY A 644 " --> pdb=" O LEU A 699 " (cutoff:3.500A) removed outlier: 9.532A pdb=" N GLU A 701 " --> pdb=" O GLY A 644 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N TYR A 696 " --> pdb=" O LYS A 501 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LYS A 501 " --> pdb=" O TYR A 696 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE A 498 " --> pdb=" O VAL A 719 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 397 through 399 Processing sheet with id=AA6, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AA7, first strand: chain 'B' and resid 490 through 491 Processing sheet with id=AA8, first strand: chain 'B' and resid 496 through 498 removed outlier: 3.815A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 646 through 649 removed outlier: 6.231A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.523A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 436 through 440 removed outlier: 3.593A pdb=" N VAL C 472 " --> pdb=" O THR C 394 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N ALA C 473 " --> pdb=" O GLY C 729 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N GLY C 729 " --> pdb=" O ALA C 473 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU C 475 " --> pdb=" O GLY C 727 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N GLY C 727 " --> pdb=" O LEU C 475 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 436 through 440 removed outlier: 3.593A pdb=" N VAL C 472 " --> pdb=" O THR C 394 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N ALA C 473 " --> pdb=" O GLY C 729 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N GLY C 729 " --> pdb=" O ALA C 473 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU C 475 " --> pdb=" O GLY C 727 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N GLY C 727 " --> pdb=" O LEU C 475 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N MET C 492 " --> pdb=" O TYR C 728 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 403 through 404 Processing sheet with id=AB4, first strand: chain 'C' and resid 642 through 644 removed outlier: 6.786A pdb=" N ALA C 642 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N LEU C 699 " --> pdb=" O ALA C 642 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N GLY C 644 " --> pdb=" O LEU C 699 " (cutoff:3.500A) removed outlier: 9.464A pdb=" N GLU C 701 " --> pdb=" O GLY C 644 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N TYR C 696 " --> pdb=" O LYS C 501 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LYS C 501 " --> pdb=" O TYR C 696 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ILE C 498 " --> pdb=" O VAL C 719 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 397 through 399 Processing sheet with id=AB6, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AB7, first strand: chain 'D' and resid 475 through 480 removed outlier: 10.336A pdb=" N ALA D 475 " --> pdb=" O PRO D 737 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N ALA D 477 " --> pdb=" O ALA D 735 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ALA D 735 " --> pdb=" O ALA D 477 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N LEU D 479 " --> pdb=" O GLY D 733 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY D 733 " --> pdb=" O LEU D 479 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 475 through 480 removed outlier: 10.336A pdb=" N ALA D 475 " --> pdb=" O PRO D 737 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N ALA D 477 " --> pdb=" O ALA D 735 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ALA D 735 " --> pdb=" O ALA D 477 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N LEU D 479 " --> pdb=" O GLY D 733 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY D 733 " --> pdb=" O LEU D 479 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 646 through 649 removed outlier: 6.428A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.456A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 100 through 102 Processing sheet with id=AC2, first strand: chain 'H' and resid 45 through 48 1070 hydrogen bonds defined for protein. 3147 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.03 Time building geometry restraints manager: 1.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2823 1.33 - 1.45: 4786 1.45 - 1.58: 9754 1.58 - 1.70: 16 1.70 - 1.83: 168 Bond restraints: 17547 Sorted by residual: bond pdb=" O12 POV G 501 " pdb=" P POV G 501 " ideal model delta sigma weight residual 1.657 1.606 0.051 2.00e-02 2.50e+03 6.56e+00 bond pdb=" O12 POV F 201 " pdb=" P POV F 201 " ideal model delta sigma weight residual 1.657 1.606 0.051 2.00e-02 2.50e+03 6.53e+00 bond pdb=" O12 POV D1003 " pdb=" P POV D1003 " ideal model delta sigma weight residual 1.657 1.606 0.051 2.00e-02 2.50e+03 6.52e+00 bond pdb=" O12 POV A1004 " pdb=" P POV A1004 " ideal model delta sigma weight residual 1.657 1.606 0.051 2.00e-02 2.50e+03 6.48e+00 bond pdb=" CA TYR B 440 " pdb=" CB TYR B 440 " ideal model delta sigma weight residual 1.528 1.563 -0.035 1.39e-02 5.18e+03 6.45e+00 ... (remaining 17542 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 23192 2.36 - 4.71: 401 4.71 - 7.07: 67 7.07 - 9.42: 11 9.42 - 11.78: 3 Bond angle restraints: 23674 Sorted by residual: angle pdb=" N VAL A 472 " pdb=" CA VAL A 472 " pdb=" C VAL A 472 " ideal model delta sigma weight residual 113.53 108.06 5.47 9.80e-01 1.04e+00 3.12e+01 angle pdb=" CB MET D 708 " pdb=" CG MET D 708 " pdb=" SD MET D 708 " ideal model delta sigma weight residual 112.70 124.48 -11.78 3.00e+00 1.11e-01 1.54e+01 angle pdb=" CA ARG G 149 " pdb=" CB ARG G 149 " pdb=" CG ARG G 149 " ideal model delta sigma weight residual 114.10 121.79 -7.69 2.00e+00 2.50e-01 1.48e+01 angle pdb=" N VAL D 488 " pdb=" CA VAL D 488 " pdb=" C VAL D 488 " ideal model delta sigma weight residual 112.96 109.41 3.55 1.00e+00 1.00e+00 1.26e+01 angle pdb=" CG1 VAL F 68 " pdb=" CB VAL F 68 " pdb=" CG2 VAL F 68 " ideal model delta sigma weight residual 110.80 103.66 7.14 2.20e+00 2.07e-01 1.05e+01 ... (remaining 23669 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.07: 10065 35.07 - 70.13: 164 70.13 - 105.20: 18 105.20 - 140.26: 20 140.26 - 175.33: 4 Dihedral angle restraints: 10271 sinusoidal: 3906 harmonic: 6365 Sorted by residual: dihedral pdb=" CB CYS H 52 " pdb=" SG CYS H 52 " pdb=" SG CYS H 91 " pdb=" CB CYS H 91 " ideal model delta sinusoidal sigma weight residual -86.00 -156.06 70.06 1 1.00e+01 1.00e-02 6.33e+01 dihedral pdb=" CB CYS A 714 " pdb=" SG CYS A 714 " pdb=" SG CYS A 769 " pdb=" CB CYS A 769 " ideal model delta sinusoidal sigma weight residual 93.00 135.70 -42.70 1 1.00e+01 1.00e-02 2.54e+01 dihedral pdb=" CA ARG C 541 " pdb=" C ARG C 541 " pdb=" N PHE C 542 " pdb=" CA PHE C 542 " ideal model delta harmonic sigma weight residual 180.00 156.12 23.88 0 5.00e+00 4.00e-02 2.28e+01 ... (remaining 10268 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2015 0.048 - 0.096: 538 0.096 - 0.144: 117 0.144 - 0.192: 16 0.192 - 0.240: 4 Chirality restraints: 2690 Sorted by residual: chirality pdb=" C2 POV D1003 " pdb=" C1 POV D1003 " pdb=" C3 POV D1003 " pdb=" O21 POV D1003 " both_signs ideal model delta sigma weight residual False 2.43 2.19 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CB VAL A 719 " pdb=" CA VAL A 719 " pdb=" CG1 VAL A 719 " pdb=" CG2 VAL A 719 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA SER D 403 " pdb=" N SER D 403 " pdb=" C SER D 403 " pdb=" CB SER D 403 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 2687 not shown) Planarity restraints: 2859 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL D 626 " -0.015 2.00e-02 2.50e+03 3.01e-02 9.09e+00 pdb=" C VAL D 626 " 0.052 2.00e-02 2.50e+03 pdb=" O VAL D 626 " -0.020 2.00e-02 2.50e+03 pdb=" N GLU D 627 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 626 " -0.015 2.00e-02 2.50e+03 2.92e-02 8.50e+00 pdb=" C VAL B 626 " 0.050 2.00e-02 2.50e+03 pdb=" O VAL B 626 " -0.019 2.00e-02 2.50e+03 pdb=" N GLU B 627 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 72 " -0.020 2.00e-02 2.50e+03 1.82e-02 6.65e+00 pdb=" CG TYR F 72 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR F 72 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR F 72 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR F 72 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR F 72 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR F 72 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR F 72 " -0.000 2.00e-02 2.50e+03 ... (remaining 2856 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 4252 2.79 - 3.32: 16340 3.32 - 3.85: 28403 3.85 - 4.37: 32432 4.37 - 4.90: 56127 Nonbonded interactions: 137554 Sorted by model distance: nonbonded pdb=" OG SER D 706 " pdb=" OD1 ASN D 726 " model vdw 2.267 3.040 nonbonded pdb=" O LEU E 16 " pdb=" OG SER E 19 " model vdw 2.277 3.040 nonbonded pdb=" O THR A 668 " pdb=" OG SER A 672 " model vdw 2.300 3.040 nonbonded pdb=" O LYS G 152 " pdb=" NH2 ARG G 229 " model vdw 2.307 3.120 nonbonded pdb=" O THR C 668 " pdb=" OG SER C 672 " model vdw 2.319 3.040 ... (remaining 137549 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 393 through 398 or resid 400 through 403 or resid 405 thro \ ugh 407 or resid 412 through 414 or resid 416 through 422 or resid 424 through 4 \ 29 or (resid 430 and (name N or name CA or name C or name O or name CB )) or res \ id 431 or resid 433 or resid 436 or resid 438 or resid 440 through 441 or resid \ 443 through 450 or resid 452 through 454 or resid 456 through 461 or (resid 462 \ and (name N or name CA or name C or name O or name CB )) or resid 463 through 46 \ 6 or (resid 468 through 469 and (name N or name CA or name C or name O or name C \ B )) or resid 471 or resid 473 through 481 or (resid 482 through 483 and (name N \ or name CA or name C or name O or name CB )) or resid 484 through 543 or (resid \ 565 and (name N or name CA or name C or name O or name CB )) or resid 566 throu \ gh 581 or resid 583 through 629 or (resid 630 and (name N or name CA or name C o \ r name O or name CB )) or resid 631 through 635 or (resid 637 through 640 and (n \ ame N or name CA or name C or name O or name CB )) or resid 641 through 646 or r \ esid 649 or (resid 650 and (name N or name CA or name C or name O or name CB )) \ or resid 651 or (resid 652 through 653 and (name N or name CA or name C or name \ O or name CB )) or resid 654 through 663 or resid 665 through 669 or (resid 670 \ and (name N or name CA or name C or name O or name CB )) or resid 672 through 67 \ 5 or (resid 676 and (name N or name CA or name C or name O or name CB )) or resi \ d 677 through 682 or resid 684 through 685 or resid 688 through 733 or (resid 73 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 735 through \ 736 or resid 738 through 739 or resid 742 through 749 or resid 751 through 753 o \ r resid 755 through 759 or resid 761 through 771 or resid 776 through 777 or res \ id 779 through 795 or resid 797 through 811 or (resid 812 through 813 and (name \ N or name CA or name C or name O or name CB )))) selection = (chain 'B' and (resid 397 through 401 or (resid 402 and (name N or name CA or na \ me C or name O or name CB )) or resid 404 through 407 or resid 409 through 411 o \ r resid 416 through 418 or resid 420 through 426 or resid 428 through 435 or res \ id 437 or resid 440 or resid 442 or resid 444 through 445 or resid 447 through 4 \ 54 or (resid 456 through 458 and (name N or name CA or name C or name O or name \ CB )) or resid 460 through 470 or resid 472 through 473 or resid 475 or resid 47 \ 7 through 486 or (resid 487 and (name N or name CA or name C or name O or name C \ B )) or resid 488 through 507 or (resid 508 through 509 and (name N or name CA o \ r name C or name O or name CB )) or resid 510 through 585 or resid 587 through 6 \ 39 or resid 641 through 650 or resid 653 through 659 or (resid 660 through 661 a \ nd (name N or name CA or name C or name O or name CB )) or resid 662 or (resid 6 \ 63 and (name N or name CA or name C or name O or name CB )) or resid 664 through \ 667 or resid 669 through 674 or resid 676 through 684 or (resid 685 and (name N \ or name CA or name C or name O or name CB )) or resid 686 or (resid 688 and (na \ me N or name CA or name C or name O or name CB )) or resid 689 or (resid 692 and \ (name N or name CA or name C or name O or name CB )) or resid 693 through 695 o \ r (resid 696 through 697 and (name N or name CA or name C or name O or name CB ) \ ) or resid 698 through 714 or (resid 715 through 716 and (name N or name CA or n \ ame C or name O or name CB )) or resid 717 through 740 or resid 742 through 743 \ or resid 746 through 753 or resid 755 through 757 or resid 759 through 763 or re \ sid 765 through 768 or (resid 769 and (name N or name CA or name C or name O or \ name CB )) or resid 770 through 775 or resid 780 through 781 or (resid 783 throu \ gh 784 and (name N or name CA or name C or name O or name CB )) or resid 785 thr \ ough 799 or resid 801 through 817)) selection = (chain 'C' and (resid 393 through 398 or resid 400 through 403 or resid 405 thro \ ugh 407 or resid 412 through 414 or resid 416 through 422 or resid 424 through 4 \ 29 or (resid 430 and (name N or name CA or name C or name O or name CB )) or res \ id 431 or resid 433 or resid 436 or resid 438 or resid 440 through 441 or resid \ 443 through 450 or resid 452 through 454 or resid 456 through 461 or (resid 462 \ and (name N or name CA or name C or name O or name CB )) or resid 463 through 46 \ 6 or (resid 468 through 469 and (name N or name CA or name C or name O or name C \ B )) or resid 471 or resid 473 through 481 or (resid 482 through 483 and (name N \ or name CA or name C or name O or name CB )) or resid 484 through 504 or (resid \ 505 and (name N or name CA or name C or name O or name CB )) or resid 506 throu \ gh 543 or (resid 565 and (name N or name CA or name C or name O or name CB )) or \ resid 566 through 581 or resid 583 through 629 or (resid 630 and (name N or nam \ e CA or name C or name O or name CB )) or resid 631 through 635 or (resid 637 th \ rough 640 and (name N or name CA or name C or name O or name CB )) or resid 641 \ through 646 or resid 649 or (resid 650 and (name N or name CA or name C or name \ O or name CB )) or resid 651 or (resid 652 through 653 and (name N or name CA or \ name C or name O or name CB )) or resid 654 through 663 or resid 665 through 66 \ 9 or (resid 670 and (name N or name CA or name C or name O or name CB )) or resi \ d 672 through 675 or (resid 676 and (name N or name CA or name C or name O or na \ me CB )) or resid 677 through 682 or resid 684 through 685 or resid 688 through \ 733 or (resid 734 and (name N or name CA or name C or name O or name CB )) or re \ sid 735 through 736 or resid 738 through 739 or resid 742 through 749 or resid 7 \ 51 through 753 or resid 755 through 759 or resid 761 through 771 or resid 776 th \ rough 777 or (resid 779 through 780 and (name N or name CA or name C or name O o \ r name CB )) or resid 781 through 795 or resid 797 through 811 or (resid 812 thr \ ough 813 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'D' and (resid 397 through 401 or (resid 402 and (name N or name CA or na \ me C or name O or name CB )) or resid 404 through 407 or resid 409 through 411 o \ r resid 416 through 418 or resid 420 through 426 or resid 428 through 435 or res \ id 437 or resid 440 or resid 442 or resid 444 through 445 or resid 447 through 4 \ 54 or (resid 456 through 458 and (name N or name CA or name C or name O or name \ CB )) or resid 460 through 470 or resid 472 through 473 or resid 475 or resid 47 \ 7 through 486 or (resid 487 and (name N or name CA or name C or name O or name C \ B )) or resid 488 through 504 or (resid 505 and (name N or name CA or name C or \ name O or name CB )) or resid 506 through 507 or (resid 508 through 509 and (nam \ e N or name CA or name C or name O or name CB )) or resid 510 through 585 or res \ id 587 through 639 or resid 641 through 650 or resid 653 through 659 or (resid 6 \ 60 through 661 and (name N or name CA or name C or name O or name CB )) or resid \ 662 or (resid 663 and (name N or name CA or name C or name O or name CB )) or r \ esid 664 through 667 or resid 669 through 674 or resid 676 through 684 or (resid \ 685 and (name N or name CA or name C or name O or name CB )) or resid 686 or (r \ esid 688 and (name N or name CA or name C or name O or name CB )) or resid 689 o \ r (resid 692 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 93 through 695 or (resid 696 through 697 and (name N or name CA or name C or nam \ e O or name CB )) or resid 698 through 714 or (resid 715 through 716 and (name N \ or name CA or name C or name O or name CB )) or resid 717 through 740 or resid \ 742 through 743 or resid 746 through 753 or resid 755 through 757 or resid 759 t \ hrough 763 or resid 765 through 768 or (resid 769 and (name N or name CA or name \ C or name O or name CB )) or resid 770 through 775 or resid 780 through 781 or \ (resid 783 through 784 and (name N or name CA or name C or name O or name CB )) \ or resid 785 through 799 or resid 801 through 817)) } ncs_group { reference = (chain 'E' and resid 2 through 159) selection = (chain 'F' and (resid 2 through 106 or (resid 107 through 126 and (name N or nam \ e CA or name C or name O or name CB )) or resid 127 through 159)) } ncs_group { reference = (chain 'G' and (resid 15 through 107 or (resid 108 and (name N or name CA or nam \ e C or name O or name CB )) or resid 115 through 501)) selection = (chain 'H' and (resid 15 through 185 or (resid 196 and (name N or name CA or nam \ e C or name O or name CB )) or resid 197 through 501)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 16.470 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6720 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 : 0.005 0.064 17555 Z= 0.239 Angle : 0.780 11.779 23690 Z= 0.400 Chirality : 0.046 0.240 2690 Planarity : 0.006 0.064 2859 Dihedral : 15.971 175.328 6185 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.17), residues: 2171 helix: 0.63 (0.14), residues: 1327 sheet: -1.93 (0.43), residues: 132 loop : -1.83 (0.21), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 122 TYR 0.043 0.002 TYR H 199 PHE 0.035 0.002 PHE B 574 TRP 0.037 0.002 TRP C 763 HIS 0.018 0.003 HIS E 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.24 (17547) covalent geometry : angle 0.77906 / 0.40 (23674) SS BOND : bond 0.00472 / 0.27 ( 8) SS BOND : angle 1.35723 / 0.84 ( 16) hydrogen bonds : bond 0.12395 / 8.37 ( 1058) hydrogen bonds : angle 5.63995 / 3.94 ( 3147) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 384 time to evaluate : 0.621 Fit side-chains revert: symmetry clash REVERT: A 515 ASP cc_start: 0.8201 (m-30) cc_final: 0.7752 (m-30) REVERT: A 638 GLN cc_start: 0.6987 (pp30) cc_final: 0.6731 (pp30) REVERT: A 665 LYS cc_start: 0.8605 (mtmt) cc_final: 0.8049 (tmtt) REVERT: A 704 MET cc_start: 0.7648 (tpp) cc_final: 0.7355 (tpt) REVERT: B 402 GLU cc_start: 0.7295 (tp30) cc_final: 0.6972 (mm-30) REVERT: B 405 TYR cc_start: 0.6736 (m-80) cc_final: 0.6458 (m-10) REVERT: B 666 VAL cc_start: 0.7744 (m) cc_final: 0.7385 (p) REVERT: B 768 TYR cc_start: 0.8056 (m-10) cc_final: 0.7576 (m-80) REVERT: B 813 GLU cc_start: 0.6316 (tm-30) cc_final: 0.6071 (tm-30) REVERT: C 417 TYR cc_start: 0.8315 (m-80) cc_final: 0.8019 (m-10) REVERT: C 439 GLU cc_start: 0.7031 (pp20) cc_final: 0.6695 (pp20) REVERT: C 527 PHE cc_start: 0.6705 (m-10) cc_final: 0.6320 (m-80) REVERT: C 566 GLU cc_start: 0.6789 (mt-10) cc_final: 0.6378 (mm-30) REVERT: C 643 TYR cc_start: 0.7139 (p90) cc_final: 0.6798 (p90) REVERT: C 704 MET cc_start: 0.7460 (tpp) cc_final: 0.7064 (tpt) REVERT: D 708 MET cc_start: 0.7437 (mmm) cc_final: 0.7138 (tpt) REVERT: E 23 PHE cc_start: 0.6950 (m-80) cc_final: 0.6678 (m-80) REVERT: E 143 LEU cc_start: 0.7052 (mt) cc_final: 0.6703 (mm) REVERT: F 23 PHE cc_start: 0.7187 (m-80) cc_final: 0.6834 (m-80) REVERT: F 67 LEU cc_start: 0.8015 (tp) cc_final: 0.7700 (tp) REVERT: F 99 PHE cc_start: 0.7950 (m-80) cc_final: 0.7669 (m-80) REVERT: F 104 ARG cc_start: 0.5952 (tpt-90) cc_final: 0.5576 (tpt-90) REVERT: G 102 LYS cc_start: 0.6592 (mtpp) cc_final: 0.6322 (mtpp) outliers start: 0 outliers final: 0 residues processed: 384 average time/residue: 0.1461 time to fit residues: 82.6921 Evaluate side-chains 302 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 0.7980 chunk 212 optimal weight: 0.6980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 752 GLN B 435 HIS B 709 ASN D 508 GLN ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 726 ASN E 27 HIS F 75 HIS H 105 HIS H 224 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.209074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 109)---------------| | r_work = 0.3747 r_free = 0.3747 target = 0.143316 restraints weight = 21093.335| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 2.77 r_work: 0.3452 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17555 Z= 0.180 Angle : 0.569 6.453 23690 Z= 0.300 Chirality : 0.040 0.161 2690 Planarity : 0.005 0.054 2859 Dihedral : 12.832 166.516 2899 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.72 % Allowed : 8.15 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.18), residues: 2171 helix: 1.33 (0.14), residues: 1317 sheet: -1.69 (0.45), residues: 130 loop : -1.71 (0.21), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 590 TYR 0.021 0.002 TYR F 149 PHE 0.022 0.002 PHE D 574 TRP 0.017 0.001 TRP E 103 HIS 0.008 0.002 HIS F 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.18 (17547) covalent geometry : angle 0.56852 / 0.30 (23674) SS BOND : bond 0.00292 / 0.14 ( 8) SS BOND : angle 1.14795 / 0.75 ( 16) hydrogen bonds : bond 0.04467 / 3.00 ( 1058) hydrogen bonds : angle 4.37193 / 3.06 ( 3147) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 325 time to evaluate : 0.396 Fit side-chains REVERT: A 515 ASP cc_start: 0.8396 (m-30) cc_final: 0.8055 (m-30) REVERT: A 665 LYS cc_start: 0.8526 (mtmt) cc_final: 0.8086 (tmtt) REVERT: A 704 MET cc_start: 0.8385 (tpp) cc_final: 0.8089 (tpt) REVERT: B 402 GLU cc_start: 0.7105 (tp30) cc_final: 0.6837 (mm-30) REVERT: B 435 HIS cc_start: 0.6502 (m-70) cc_final: 0.6255 (m90) REVERT: B 490 ASP cc_start: 0.7094 (m-30) cc_final: 0.6629 (m-30) REVERT: B 768 TYR cc_start: 0.8350 (m-10) cc_final: 0.8138 (m-80) REVERT: B 813 GLU cc_start: 0.7342 (tm-30) cc_final: 0.7091 (tm-30) REVERT: C 515 ASP cc_start: 0.8346 (m-30) cc_final: 0.8138 (m-30) REVERT: C 527 PHE cc_start: 0.7598 (m-10) cc_final: 0.7258 (m-80) REVERT: C 643 TYR cc_start: 0.7424 (p90) cc_final: 0.7141 (p90) REVERT: C 666 MET cc_start: 0.7401 (mtt) cc_final: 0.7037 (mtt) REVERT: C 704 MET cc_start: 0.8369 (tpp) cc_final: 0.8036 (tpt) REVERT: E 143 LEU cc_start: 0.7577 (mt) cc_final: 0.7335 (mm) REVERT: F 67 LEU cc_start: 0.8232 (tp) cc_final: 0.7876 (tp) REVERT: F 101 HIS cc_start: 0.8084 (m-70) cc_final: 0.7718 (m-70) REVERT: F 104 ARG cc_start: 0.6127 (tpt-90) cc_final: 0.5806 (tpt-90) REVERT: F 144 LEU cc_start: 0.8532 (mt) cc_final: 0.7941 (tp) REVERT: G 22 LEU cc_start: 0.7985 (mm) cc_final: 0.7605 (mt) outliers start: 28 outliers final: 20 residues processed: 343 average time/residue: 0.1331 time to fit residues: 67.6757 Evaluate side-chains 325 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 305 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain B residue 708 MET Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 770 LYS Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 784 SER Chi-restraints excluded: chain D residue 508 GLN Chi-restraints excluded: chain D residue 595 SER Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain G residue 42 ASP Chi-restraints excluded: chain G residue 173 ILE Chi-restraints excluded: chain H residue 173 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 99 optimal weight: 0.1980 chunk 87 optimal weight: 0.0670 chunk 20 optimal weight: 1.9990 chunk 206 optimal weight: 20.0000 chunk 2 optimal weight: 10.0000 chunk 178 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 216 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 192 optimal weight: 0.9990 chunk 97 optimal weight: 0.0970 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 508 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.211818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 120)---------------| | r_work = 0.3744 r_free = 0.3744 target = 0.147313 restraints weight = 21303.903| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.69 r_work: 0.3432 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17555 Z= 0.114 Angle : 0.495 7.187 23690 Z= 0.262 Chirality : 0.038 0.155 2690 Planarity : 0.004 0.068 2859 Dihedral : 11.627 147.421 2899 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.72 % Allowed : 10.30 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.18), residues: 2171 helix: 1.73 (0.14), residues: 1317 sheet: -1.59 (0.45), residues: 130 loop : -1.57 (0.21), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 88 TYR 0.019 0.001 TYR A 643 PHE 0.019 0.001 PHE A 604 TRP 0.016 0.001 TRP E 103 HIS 0.006 0.001 HIS F 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (17547) covalent geometry : angle 0.49453 / 0.26 (23674) SS BOND : bond 0.00155 / 0.09 ( 8) SS BOND : angle 0.75793 / 0.49 ( 16) hydrogen bonds : bond 0.03977 / 2.67 ( 1058) hydrogen bonds : angle 4.04805 / 2.82 ( 3147) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 326 time to evaluate : 0.765 Fit side-chains revert: symmetry clash REVERT: A 515 ASP cc_start: 0.8506 (m-30) cc_final: 0.8141 (m-30) REVERT: A 665 LYS cc_start: 0.8611 (mtmt) cc_final: 0.8125 (tmtt) REVERT: A 704 MET cc_start: 0.8386 (tpp) cc_final: 0.8126 (tpt) REVERT: B 768 TYR cc_start: 0.8412 (m-10) cc_final: 0.8200 (m-80) REVERT: B 813 GLU cc_start: 0.7159 (tm-30) cc_final: 0.6889 (tm-30) REVERT: C 515 ASP cc_start: 0.8504 (m-30) cc_final: 0.8208 (m-30) REVERT: C 527 PHE cc_start: 0.7540 (m-10) cc_final: 0.7143 (m-80) REVERT: C 643 TYR cc_start: 0.7463 (p90) cc_final: 0.7221 (p90) REVERT: C 704 MET cc_start: 0.8261 (tpp) cc_final: 0.7962 (tpp) REVERT: D 515 PHE cc_start: 0.8774 (m-80) cc_final: 0.8466 (m-10) REVERT: D 813 GLU cc_start: 0.7364 (tm-30) cc_final: 0.7092 (tm-30) REVERT: E 10 TYR cc_start: 0.7577 (m-80) cc_final: 0.7288 (m-80) REVERT: E 143 LEU cc_start: 0.7464 (mt) cc_final: 0.7164 (mm) REVERT: F 10 TYR cc_start: 0.7522 (m-80) cc_final: 0.7239 (m-80) REVERT: F 23 PHE cc_start: 0.7821 (m-80) cc_final: 0.7596 (m-80) REVERT: F 67 LEU cc_start: 0.8168 (tp) cc_final: 0.7707 (tp) REVERT: F 101 HIS cc_start: 0.8045 (m-70) cc_final: 0.7487 (m-70) REVERT: F 104 ARG cc_start: 0.6038 (tpt-90) cc_final: 0.5672 (tpt-90) REVERT: G 22 LEU cc_start: 0.7863 (mm) cc_final: 0.7473 (mt) REVERT: G 88 ARG cc_start: 0.7688 (mtm110) cc_final: 0.7368 (mtm-85) outliers start: 28 outliers final: 19 residues processed: 342 average time/residue: 0.1425 time to fit residues: 72.3480 Evaluate side-chains 324 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 305 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 708 MET Chi-restraints excluded: chain B residue 770 LYS Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 784 SER Chi-restraints excluded: chain D residue 595 SER Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 770 LYS Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 153 MET Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 42 ASP Chi-restraints excluded: chain H residue 90 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 132 optimal weight: 0.9980 chunk 146 optimal weight: 0.0040 chunk 124 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 chunk 70 optimal weight: 4.9990 chunk 194 optimal weight: 9.9990 chunk 114 optimal weight: 4.9990 chunk 174 optimal weight: 10.0000 chunk 136 optimal weight: 2.9990 overall best weight: 1.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.208105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.156151 restraints weight = 21196.840| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 2.34 r_work: 0.3387 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 17555 Z= 0.180 Angle : 0.545 6.952 23690 Z= 0.286 Chirality : 0.040 0.151 2690 Planarity : 0.004 0.050 2859 Dihedral : 11.553 124.086 2899 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.39 % Allowed : 11.96 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.18), residues: 2171 helix: 1.70 (0.14), residues: 1333 sheet: -1.72 (0.44), residues: 136 loop : -1.64 (0.21), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 122 TYR 0.021 0.002 TYR A 643 PHE 0.024 0.002 PHE E 31 TRP 0.015 0.001 TRP E 103 HIS 0.006 0.001 HIS G 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.18 (17547) covalent geometry : angle 0.54496 / 0.29 (23674) SS BOND : bond 0.00268 / 0.13 ( 8) SS BOND : angle 0.88081 / 0.56 ( 16) hydrogen bonds : bond 0.04233 / 2.84 ( 1058) hydrogen bonds : angle 4.07049 / 2.86 ( 3147) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 312 time to evaluate : 0.641 Fit side-chains REVERT: A 515 ASP cc_start: 0.8430 (m-30) cc_final: 0.8122 (m-30) REVERT: A 665 LYS cc_start: 0.8542 (mtmt) cc_final: 0.8098 (tmtt) REVERT: A 704 MET cc_start: 0.8492 (tpp) cc_final: 0.8277 (tpt) REVERT: B 402 GLU cc_start: 0.7078 (OUTLIER) cc_final: 0.6816 (mm-30) REVERT: B 813 GLU cc_start: 0.7375 (tm-30) cc_final: 0.7094 (tm-30) REVERT: C 515 ASP cc_start: 0.8457 (m-30) cc_final: 0.8215 (m-30) REVERT: C 527 PHE cc_start: 0.7692 (m-10) cc_final: 0.7407 (m-10) REVERT: C 638 GLN cc_start: 0.8325 (pp30) cc_final: 0.7481 (pp30) REVERT: C 643 TYR cc_start: 0.7526 (p90) cc_final: 0.7190 (p90) REVERT: C 704 MET cc_start: 0.8461 (tpp) cc_final: 0.8189 (tpt) REVERT: D 813 GLU cc_start: 0.7540 (tm-30) cc_final: 0.7291 (tm-30) REVERT: E 143 LEU cc_start: 0.7584 (mt) cc_final: 0.7317 (mm) REVERT: F 67 LEU cc_start: 0.8129 (tp) cc_final: 0.7733 (tp) REVERT: F 101 HIS cc_start: 0.8035 (m-70) cc_final: 0.7352 (m-70) REVERT: G 22 LEU cc_start: 0.7960 (mm) cc_final: 0.7532 (mt) outliers start: 39 outliers final: 25 residues processed: 335 average time/residue: 0.1464 time to fit residues: 72.8014 Evaluate side-chains 323 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 297 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 708 MET Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 770 LYS Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 608 ILE Chi-restraints excluded: chain C residue 650 SER Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 756 ASP Chi-restraints excluded: chain C residue 784 SER Chi-restraints excluded: chain D residue 708 MET Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 770 LYS Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 153 MET Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain G residue 42 ASP Chi-restraints excluded: chain G residue 173 ILE Chi-restraints excluded: chain H residue 90 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 109 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 170 optimal weight: 10.0000 chunk 99 optimal weight: 0.9980 chunk 212 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 146 optimal weight: 9.9990 chunk 153 optimal weight: 3.9990 chunk 213 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 103 optimal weight: 7.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 435 HIS ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.209334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 99)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.145641 restraints weight = 21141.140| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 2.68 r_work: 0.3411 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17555 Z= 0.137 Angle : 0.506 7.289 23690 Z= 0.266 Chirality : 0.039 0.144 2690 Planarity : 0.004 0.048 2859 Dihedral : 11.054 114.060 2899 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.27 % Allowed : 13.06 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.18), residues: 2171 helix: 1.87 (0.14), residues: 1335 sheet: -1.74 (0.43), residues: 136 loop : -1.59 (0.21), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 88 TYR 0.022 0.001 TYR A 643 PHE 0.022 0.001 PHE F 23 TRP 0.017 0.001 TRP E 103 HIS 0.006 0.001 HIS F 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (17547) covalent geometry : angle 0.50509 / 0.27 (23674) SS BOND : bond 0.00195 / 0.10 ( 8) SS BOND : angle 0.98014 / 0.63 ( 16) hydrogen bonds : bond 0.03928 / 2.63 ( 1058) hydrogen bonds : angle 3.93606 / 2.76 ( 3147) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 302 time to evaluate : 0.647 Fit side-chains REVERT: A 515 ASP cc_start: 0.8502 (m-30) cc_final: 0.8145 (m-30) REVERT: A 665 LYS cc_start: 0.8624 (mtmt) cc_final: 0.8130 (tmtt) REVERT: A 704 MET cc_start: 0.8392 (tpp) cc_final: 0.8165 (tpt) REVERT: B 402 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6858 (mm-30) REVERT: B 813 GLU cc_start: 0.7180 (tm-30) cc_final: 0.6883 (tm-30) REVERT: C 515 ASP cc_start: 0.8546 (m-30) cc_final: 0.8249 (m-30) REVERT: C 527 PHE cc_start: 0.7682 (m-10) cc_final: 0.7384 (m-10) REVERT: C 638 GLN cc_start: 0.8166 (pp30) cc_final: 0.7313 (pp30) REVERT: C 643 TYR cc_start: 0.7415 (p90) cc_final: 0.6822 (p90) REVERT: C 704 MET cc_start: 0.8304 (tpp) cc_final: 0.7895 (tpt) REVERT: D 515 PHE cc_start: 0.8791 (m-80) cc_final: 0.8501 (m-10) REVERT: D 813 GLU cc_start: 0.7317 (tm-30) cc_final: 0.7053 (tm-30) REVERT: E 10 TYR cc_start: 0.7566 (m-80) cc_final: 0.7287 (m-80) REVERT: E 143 LEU cc_start: 0.7447 (mt) cc_final: 0.7125 (mm) REVERT: F 10 TYR cc_start: 0.7549 (m-80) cc_final: 0.7286 (m-80) REVERT: F 23 PHE cc_start: 0.7742 (m-80) cc_final: 0.7492 (m-80) REVERT: F 101 HIS cc_start: 0.7972 (m-70) cc_final: 0.7431 (m-70) REVERT: G 22 LEU cc_start: 0.7863 (mm) cc_final: 0.7490 (mt) REVERT: G 88 ARG cc_start: 0.7929 (mtm110) cc_final: 0.6920 (ptt180) outliers start: 37 outliers final: 25 residues processed: 324 average time/residue: 0.1455 time to fit residues: 69.2622 Evaluate side-chains 321 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 295 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 708 MET Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 770 LYS Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain C residue 430 LYS Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 608 ILE Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 784 SER Chi-restraints excluded: chain D residue 708 MET Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 770 LYS Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 153 MET Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain G residue 42 ASP Chi-restraints excluded: chain G residue 173 ILE Chi-restraints excluded: chain H residue 90 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 139 optimal weight: 0.9980 chunk 154 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 96 optimal weight: 0.6980 chunk 211 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 212 optimal weight: 1.9990 chunk 193 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.207931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.139293 restraints weight = 21049.886| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.78 r_work: 0.3365 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 17555 Z= 0.171 Angle : 0.527 6.124 23690 Z= 0.276 Chirality : 0.039 0.146 2690 Planarity : 0.004 0.048 2859 Dihedral : 11.161 114.446 2899 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.51 % Allowed : 13.30 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.18), residues: 2171 helix: 1.82 (0.14), residues: 1335 sheet: -1.81 (0.43), residues: 138 loop : -1.62 (0.22), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 88 TYR 0.020 0.001 TYR A 643 PHE 0.022 0.002 PHE E 23 TRP 0.015 0.001 TRP E 103 HIS 0.006 0.001 HIS G 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.17 (17547) covalent geometry : angle 0.52637 / 0.28 (23674) SS BOND : bond 0.00276 / 0.14 ( 8) SS BOND : angle 0.92810 / 0.60 ( 16) hydrogen bonds : bond 0.04090 / 2.74 ( 1058) hydrogen bonds : angle 3.97076 / 2.79 ( 3147) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 297 time to evaluate : 0.576 Fit side-chains REVERT: A 515 ASP cc_start: 0.8550 (m-30) cc_final: 0.8216 (m-30) REVERT: A 638 GLN cc_start: 0.7757 (pp30) cc_final: 0.6701 (pp30) REVERT: A 665 LYS cc_start: 0.8648 (mtmt) cc_final: 0.8138 (tmtt) REVERT: A 704 MET cc_start: 0.8458 (tpp) cc_final: 0.8235 (tpt) REVERT: A 739 ARG cc_start: 0.7898 (ttp-170) cc_final: 0.7692 (ttp80) REVERT: B 402 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6845 (mm-30) REVERT: B 813 GLU cc_start: 0.7221 (tm-30) cc_final: 0.6904 (tm-30) REVERT: C 515 ASP cc_start: 0.8586 (m-30) cc_final: 0.8323 (m-30) REVERT: C 527 PHE cc_start: 0.7728 (m-10) cc_final: 0.7430 (m-10) REVERT: C 638 GLN cc_start: 0.8168 (pp30) cc_final: 0.7322 (pp30) REVERT: C 704 MET cc_start: 0.8379 (tpp) cc_final: 0.7989 (tpt) REVERT: D 813 GLU cc_start: 0.7350 (tm-30) cc_final: 0.7070 (tm-30) REVERT: E 104 ARG cc_start: 0.6883 (mmp-170) cc_final: 0.6658 (mmp-170) REVERT: E 134 GLU cc_start: 0.6641 (OUTLIER) cc_final: 0.6380 (pm20) REVERT: E 143 LEU cc_start: 0.7414 (mt) cc_final: 0.7127 (mm) REVERT: F 10 TYR cc_start: 0.7563 (m-80) cc_final: 0.7323 (m-80) REVERT: F 23 PHE cc_start: 0.7806 (m-80) cc_final: 0.7566 (m-80) REVERT: G 22 LEU cc_start: 0.7867 (mm) cc_final: 0.7482 (mt) REVERT: G 88 ARG cc_start: 0.7939 (mtm110) cc_final: 0.7706 (mtm-85) REVERT: H 92 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7478 (tt) outliers start: 41 outliers final: 28 residues processed: 322 average time/residue: 0.1425 time to fit residues: 68.4357 Evaluate side-chains 315 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 284 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 TYR Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 708 MET Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 770 LYS Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain C residue 430 LYS Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 608 ILE Chi-restraints excluded: chain C residue 650 SER Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 756 ASP Chi-restraints excluded: chain C residue 784 SER Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 595 SER Chi-restraints excluded: chain D residue 708 MET Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 770 LYS Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 153 MET Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain G residue 173 ILE Chi-restraints excluded: chain H residue 90 CYS Chi-restraints excluded: chain H residue 92 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 63 optimal weight: 5.9990 chunk 152 optimal weight: 6.9990 chunk 142 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 202 optimal weight: 6.9990 chunk 149 optimal weight: 0.4980 chunk 100 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 126 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 435 HIS ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.194707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.157337 restraints weight = 20991.603| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 1.82 r_work: 0.3422 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.110 17555 Z= 0.375 Angle : 0.728 8.718 23690 Z= 0.373 Chirality : 0.047 0.209 2690 Planarity : 0.005 0.064 2859 Dihedral : 13.137 126.191 2899 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.33 % Favored : 95.62 % Rotamer: Outliers : 2.58 % Allowed : 14.41 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.18), residues: 2171 helix: 1.24 (0.14), residues: 1317 sheet: -1.82 (0.43), residues: 136 loop : -1.89 (0.21), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 88 TYR 0.028 0.003 TYR B 647 PHE 0.029 0.003 PHE F 8 TRP 0.015 0.002 TRP A 601 HIS 0.008 0.002 HIS H 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00942 / 0.38 (17547) covalent geometry : angle 0.72704 / 0.37 (23674) SS BOND : bond 0.00612 / 0.29 ( 8) SS BOND : angle 1.36251 / 0.84 ( 16) hydrogen bonds : bond 0.05193 / 3.46 ( 1058) hydrogen bonds : angle 4.47200 / 3.17 ( 3147) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 297 time to evaluate : 0.633 Fit side-chains REVERT: A 515 ASP cc_start: 0.8123 (m-30) cc_final: 0.7861 (m-30) REVERT: A 704 MET cc_start: 0.8353 (tpp) cc_final: 0.8141 (tpt) REVERT: B 627 GLU cc_start: 0.7437 (pm20) cc_final: 0.7181 (mp0) REVERT: C 527 PHE cc_start: 0.7624 (m-10) cc_final: 0.7307 (m-80) REVERT: F 67 LEU cc_start: 0.7992 (tp) cc_final: 0.7678 (tp) REVERT: F 101 HIS cc_start: 0.7812 (m-70) cc_final: 0.7471 (m-70) REVERT: F 143 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7121 (mm) REVERT: G 22 LEU cc_start: 0.8014 (mm) cc_final: 0.7693 (mt) outliers start: 42 outliers final: 30 residues processed: 323 average time/residue: 0.1438 time to fit residues: 69.0073 Evaluate side-chains 314 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 283 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 TYR Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 708 MET Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 770 LYS Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 608 ILE Chi-restraints excluded: chain C residue 650 SER Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 756 ASP Chi-restraints excluded: chain C residue 784 SER Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 595 SER Chi-restraints excluded: chain D residue 708 MET Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 770 LYS Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain G residue 42 ASP Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 173 ILE Chi-restraints excluded: chain H residue 90 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 167 optimal weight: 1.9990 chunk 217 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 140 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 chunk 205 optimal weight: 0.9980 chunk 194 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 435 HIS ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.201026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.162764 restraints weight = 20921.148| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 1.75 r_work: 0.3459 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17555 Z= 0.154 Angle : 0.559 10.376 23690 Z= 0.291 Chirality : 0.040 0.164 2690 Planarity : 0.004 0.065 2859 Dihedral : 11.932 118.996 2899 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.22 % Favored : 96.73 % Rotamer: Outliers : 1.66 % Allowed : 15.57 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.18), residues: 2171 helix: 1.71 (0.14), residues: 1319 sheet: -1.68 (0.43), residues: 136 loop : -1.68 (0.21), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 97 TYR 0.026 0.001 TYR A 643 PHE 0.035 0.002 PHE E 23 TRP 0.013 0.001 TRP A 601 HIS 0.006 0.001 HIS F 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.15 (17547) covalent geometry : angle 0.55915 / 0.29 (23674) SS BOND : bond 0.00219 / 0.11 ( 8) SS BOND : angle 0.86695 / 0.57 ( 16) hydrogen bonds : bond 0.04178 / 2.79 ( 1058) hydrogen bonds : angle 4.08854 / 2.88 ( 3147) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 291 time to evaluate : 0.707 Fit side-chains REVERT: A 515 ASP cc_start: 0.8063 (m-30) cc_final: 0.7751 (m-30) REVERT: A 638 GLN cc_start: 0.8167 (pp30) cc_final: 0.7267 (pp30) REVERT: A 741 PRO cc_start: 0.8289 (Cg_exo) cc_final: 0.8084 (Cg_endo) REVERT: B 402 GLU cc_start: 0.6874 (OUTLIER) cc_final: 0.6597 (mm-30) REVERT: C 527 PHE cc_start: 0.7578 (m-10) cc_final: 0.7273 (m-10) REVERT: C 638 GLN cc_start: 0.8487 (pp30) cc_final: 0.7909 (pp30) REVERT: E 10 TYR cc_start: 0.7772 (m-80) cc_final: 0.7465 (m-80) REVERT: E 23 PHE cc_start: 0.7531 (m-80) cc_final: 0.7220 (m-80) REVERT: E 143 LEU cc_start: 0.7573 (mt) cc_final: 0.7348 (mm) REVERT: F 10 TYR cc_start: 0.7793 (m-80) cc_final: 0.7564 (m-80) REVERT: F 67 LEU cc_start: 0.8006 (tp) cc_final: 0.7618 (tp) REVERT: F 143 LEU cc_start: 0.7386 (OUTLIER) cc_final: 0.7022 (mm) REVERT: G 22 LEU cc_start: 0.7962 (mm) cc_final: 0.7616 (mt) REVERT: G 133 LEU cc_start: 0.8327 (tt) cc_final: 0.8068 (tt) outliers start: 27 outliers final: 22 residues processed: 309 average time/residue: 0.1414 time to fit residues: 64.7752 Evaluate side-chains 304 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 280 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 708 MET Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 770 LYS Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 608 ILE Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 756 ASP Chi-restraints excluded: chain C residue 784 SER Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 595 SER Chi-restraints excluded: chain D residue 708 MET Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 770 LYS Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain G residue 42 ASP Chi-restraints excluded: chain G residue 173 ILE Chi-restraints excluded: chain H residue 90 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 23 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 41 optimal weight: 8.9990 chunk 2 optimal weight: 10.0000 chunk 77 optimal weight: 0.9980 chunk 67 optimal weight: 7.9990 chunk 175 optimal weight: 30.0000 chunk 60 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 165 optimal weight: 4.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 435 HIS D 435 HIS ** D 709 ASN ** 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 = 0.4275 r_free = 0.4275 target = 0.197659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.158714 restraints weight = 20948.262| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 1.84 r_work: 0.3396 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.084 17555 Z= 0.300 Angle : 0.667 9.394 23690 Z= 0.343 Chirality : 0.044 0.169 2690 Planarity : 0.005 0.052 2859 Dihedral : 12.429 122.582 2899 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.24 % Favored : 95.72 % Rotamer: Outliers : 2.08 % Allowed : 15.57 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.18), residues: 2171 helix: 1.43 (0.14), residues: 1321 sheet: -1.80 (0.42), residues: 136 loop : -1.79 (0.21), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 97 TYR 0.026 0.002 TYR A 643 PHE 0.038 0.002 PHE E 23 TRP 0.014 0.002 TRP E 103 HIS 0.007 0.002 HIS G 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00751 / 0.30 (17547) covalent geometry : angle 0.66647 / 0.34 (23674) SS BOND : bond 0.00457 / 0.22 ( 8) SS BOND : angle 1.10245 / 0.69 ( 16) hydrogen bonds : bond 0.04810 / 3.21 ( 1058) hydrogen bonds : angle 4.31854 / 3.05 ( 3147) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 282 time to evaluate : 0.677 Fit side-chains REVERT: A 515 ASP cc_start: 0.8146 (m-30) cc_final: 0.7874 (m-30) REVERT: C 527 PHE cc_start: 0.7634 (m-10) cc_final: 0.7326 (m-10) REVERT: C 638 GLN cc_start: 0.8453 (pp30) cc_final: 0.8034 (pp30) REVERT: E 23 PHE cc_start: 0.7611 (m-80) cc_final: 0.7377 (m-80) REVERT: E 104 ARG cc_start: 0.7060 (mmp-170) cc_final: 0.6751 (mmp-170) REVERT: F 67 LEU cc_start: 0.8014 (tp) cc_final: 0.7649 (tp) REVERT: F 101 HIS cc_start: 0.7844 (m-70) cc_final: 0.7401 (m-70) REVERT: F 143 LEU cc_start: 0.7481 (OUTLIER) cc_final: 0.7060 (mm) REVERT: G 22 LEU cc_start: 0.8020 (mm) cc_final: 0.7675 (mt) outliers start: 34 outliers final: 28 residues processed: 304 average time/residue: 0.1388 time to fit residues: 62.7836 Evaluate side-chains 308 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 279 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 TYR Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 708 MET Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 770 LYS Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain C residue 430 LYS Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 608 ILE Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 756 ASP Chi-restraints excluded: chain C residue 784 SER Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 595 SER Chi-restraints excluded: chain D residue 708 MET Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 770 LYS Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain G residue 42 ASP Chi-restraints excluded: chain G residue 173 ILE Chi-restraints excluded: chain H residue 90 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 82 optimal weight: 0.6980 chunk 202 optimal weight: 8.9990 chunk 95 optimal weight: 0.1980 chunk 9 optimal weight: 0.7980 chunk 77 optimal weight: 0.5980 chunk 184 optimal weight: 0.0470 chunk 84 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 chunk 138 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 435 HIS ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 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 = 0.4328 r_free = 0.4328 target = 0.203382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.164259 restraints weight = 20914.772| |-----------------------------------------------------------------------------| r_work (start): 0.3898 rms_B_bonded: 1.80 r_work: 0.3467 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17555 Z= 0.118 Angle : 0.544 12.045 23690 Z= 0.281 Chirality : 0.039 0.159 2690 Planarity : 0.004 0.054 2859 Dihedral : 11.105 114.010 2899 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.35 % Allowed : 16.31 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.18), residues: 2171 helix: 1.92 (0.15), residues: 1323 sheet: -1.60 (0.43), residues: 134 loop : -1.55 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 97 TYR 0.030 0.001 TYR F 149 PHE 0.035 0.001 PHE F 23 TRP 0.015 0.001 TRP A 601 HIS 0.005 0.001 HIS F 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (17547) covalent geometry : angle 0.54401 / 0.28 (23674) SS BOND : bond 0.00134 / 0.09 ( 8) SS BOND : angle 0.73220 / 0.48 ( 16) hydrogen bonds : bond 0.03888 / 2.59 ( 1058) hydrogen bonds : angle 3.98291 / 2.79 ( 3147) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 294 time to evaluate : 0.662 Fit side-chains REVERT: A 515 ASP cc_start: 0.8115 (m-30) cc_final: 0.7801 (m-30) REVERT: A 638 GLN cc_start: 0.8182 (pp30) cc_final: 0.7378 (pp30) REVERT: C 527 PHE cc_start: 0.7576 (m-10) cc_final: 0.7273 (m-10) REVERT: C 638 GLN cc_start: 0.8424 (pp30) cc_final: 0.8039 (pp30) REVERT: D 509 LYS cc_start: 0.7954 (tppt) cc_final: 0.7393 (tmtt) REVERT: E 10 TYR cc_start: 0.7728 (m-80) cc_final: 0.7429 (m-80) REVERT: E 104 ARG cc_start: 0.7131 (mmp-170) cc_final: 0.6827 (mmp-170) REVERT: E 143 LEU cc_start: 0.7518 (mt) cc_final: 0.7277 (mm) REVERT: F 67 LEU cc_start: 0.7939 (tp) cc_final: 0.7738 (tp) REVERT: F 143 LEU cc_start: 0.7381 (OUTLIER) cc_final: 0.6993 (mm) REVERT: G 22 LEU cc_start: 0.7931 (mm) cc_final: 0.7584 (mt) REVERT: H 133 LEU cc_start: 0.8229 (tt) cc_final: 0.7979 (tt) outliers start: 22 outliers final: 18 residues processed: 310 average time/residue: 0.1476 time to fit residues: 67.2786 Evaluate side-chains 302 residues out of total 1867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 283 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain B residue 708 MET Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain C residue 430 LYS Chi-restraints excluded: chain C residue 608 ILE Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 784 SER Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 595 SER Chi-restraints excluded: chain D residue 708 MET Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain H residue 90 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 52 optimal weight: 0.8980 chunk 190 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 147 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 193 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 126 optimal weight: 0.4980 chunk 120 optimal weight: 0.0980 chunk 56 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 435 HIS ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 HIS ** D 709 ASN ** 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 = 0.4311 r_free = 0.4311 target = 0.201495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.162560 restraints weight = 20950.441| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 1.76 r_work: 0.3457 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 17555 Z= 0.157 Angle : 0.568 11.850 23690 Z= 0.293 Chirality : 0.040 0.156 2690 Planarity : 0.004 0.053 2859 Dihedral : 11.082 114.516 2899 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.47 % Allowed : 17.11 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.18), residues: 2171 helix: 1.93 (0.15), residues: 1323 sheet: -1.57 (0.43), residues: 134 loop : -1.58 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 97 TYR 0.023 0.001 TYR H 226 PHE 0.041 0.002 PHE F 23 TRP 0.012 0.001 TRP A 601 HIS 0.005 0.001 HIS F 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 (17547) covalent geometry : angle 0.56740 / 0.29 (23674) SS BOND : bond 0.00219 / 0.11 ( 8) SS BOND : angle 0.82872 / 0.54 ( 16) hydrogen bonds : bond 0.04068 / 2.71 ( 1058) hydrogen bonds : angle 4.00153 / 2.81 ( 3147) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4708.20 seconds wall clock time: 81 minutes 14.81 seconds (4874.81 seconds total)