Starting phenix.real_space_refine on Sun Aug 24 04:30:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p3y_17399/08_2025/8p3y_17399_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p3y_17399/08_2025/8p3y_17399.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8p3y_17399/08_2025/8p3y_17399_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p3y_17399/08_2025/8p3y_17399_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8p3y_17399/08_2025/8p3y_17399.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p3y_17399/08_2025/8p3y_17399.map" } resolution = 3.55 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.048 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: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 11128 2.51 5 N 2746 2.21 5 O 3018 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17012 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2865 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 391, 2854 Classifications: {'peptide': 391} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 379} Chain breaks: 4 Unresolved non-hydrogen bonds: 214 Unresolved non-hydrogen angles: 253 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 12, 'ASN:plan1': 2, 'PHE:plan': 1, 'ASP:plan': 5, 'GLN:plan1': 2, 'ARG:plan': 4, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 110 Conformer: "B" Number of residues, atoms: 391, 2854 Classifications: {'peptide': 391} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 379} Chain breaks: 4 Unresolved non-hydrogen bonds: 214 Unresolved non-hydrogen angles: 253 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 12, 'ASN:plan1': 2, 'PHE:plan': 1, 'ASP:plan': 5, 'GLN:plan1': 2, 'ARG:plan': 4, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 110 bond proxies already assigned to first conformer: 2905 Chain: "B" Number of atoms: 2878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 2878 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 383} Chain breaks: 3 Unresolved non-hydrogen bonds: 230 Unresolved non-hydrogen angles: 271 Unresolved non-hydrogen dihedrals: 194 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 14, 'ASN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 5, 'GLN:plan1': 3, 'ARG:plan': 5, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 124 Chain: "C" Number of atoms: 2859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 2859 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 381} Chain breaks: 4 Unresolved non-hydrogen bonds: 225 Unresolved non-hydrogen angles: 265 Unresolved non-hydrogen dihedrals: 190 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 13, 'ASN:plan1': 2, 'PHE:plan': 1, 'ASP:plan': 5, 'ARG:plan': 5, 'GLN:plan1': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 119 Chain: "D" Number of atoms: 2935 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 403, 2924 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 389} Chain breaks: 2 Unresolved non-hydrogen bonds: 239 Unresolved non-hydrogen angles: 280 Unresolved non-hydrogen dihedrals: 203 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 13, 'ASN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 5, 'GLN:plan1': 3, 'ARG:plan': 6, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 125 Conformer: "B" Number of residues, atoms: 403, 2924 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 389} Chain breaks: 2 Unresolved non-hydrogen bonds: 239 Unresolved non-hydrogen angles: 280 Unresolved non-hydrogen dihedrals: 203 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 13, 'ASN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 5, 'GLN:plan1': 3, 'ARG:plan': 6, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 125 bond proxies already assigned to first conformer: 2979 Chain: "E" Number of atoms: 1372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1372 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 174} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 1358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1358 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 174} Chain breaks: 3 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "G" Number of atoms: 1372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1372 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 174} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 1373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1373 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 174} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N APHE A 574 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 574 " occ=0.50 residue: pdb=" N APHE D 574 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE D 574 " occ=0.50 Time building chain proxies: 5.71, per 1000 atoms: 0.34 Number of scatterers: 17012 At special positions: 0 Unit cell: (118.531, 137.323, 145.996, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 3018 8.00 N 2746 7.00 C 11128 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.00 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.02 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 68 " distance=2.04 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " distance=2.04 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 68 " distance=2.04 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 77 " distance=2.03 Simple disulfide: pdb=" SG CYS G 40 " - pdb=" SG CYS G 68 " distance=2.04 Simple disulfide: pdb=" SG CYS G 67 " - pdb=" SG CYS G 77 " distance=2.05 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 68 " distance=2.03 Simple disulfide: pdb=" SG CYS H 67 " - pdb=" SG CYS H 77 " distance=2.05 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: 1.84 Conformation dependent library (CDL) restraints added in 833.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4462 Ramachandran restraints generated. 2231 Oldfield, 0 Emsley, 2231 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4186 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 29 sheets defined 60.5% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 416 through 419 removed outlier: 3.882A pdb=" N GLU A 419 " --> pdb=" O GLU A 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 416 through 419' Processing helix chain 'A' and resid 423 through 437 removed outlier: 3.657A pdb=" N ASP A 427 " --> pdb=" O GLY A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 469 Processing helix chain 'A' and resid 482 through 488 removed outlier: 3.815A pdb=" N VAL A 488 " --> pdb=" O VAL A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 519 removed outlier: 3.781A pdb=" N LEU A 518 " --> pdb=" O PHE A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 546 Processing helix chain 'A' and resid 547 through 551 Processing helix chain 'A' and resid 572 through 585 Processing helix chain 'A' and resid 595 through 624 Processing helix chain 'A' and resid 635 through 642 Processing helix chain 'A' and resid 653 through 662 Processing helix chain 'A' and resid 664 through 677 Processing helix chain 'A' and resid 685 through 695 Processing helix chain 'A' and resid 706 through 714 Processing helix chain 'A' and resid 742 through 757 removed outlier: 3.646A pdb=" N LEU A 748 " --> pdb=" O THR A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 768 Processing helix chain 'A' and resid 788 through 820 removed outlier: 3.574A pdb=" N VAL A 792 " --> pdb=" O SER A 788 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N GLY A 794 " --> pdb=" O SER A 790 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL A 795 " --> pdb=" O ASN A 791 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 415 Processing helix chain 'B' and resid 423 through 437 removed outlier: 3.722A pdb=" N ASP B 427 " --> pdb=" O GLY B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 469 Processing helix chain 'B' and resid 482 through 488 removed outlier: 3.811A pdb=" N VAL B 488 " --> pdb=" O VAL B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.620A pdb=" N LEU B 518 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 546 Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 595 through 624 Processing helix chain 'B' and resid 635 through 642 Processing helix chain 'B' and resid 653 through 661 Processing helix chain 'B' and resid 664 through 677 Processing helix chain 'B' and resid 685 through 695 Processing helix chain 'B' and resid 706 through 714 Processing helix chain 'B' and resid 742 through 757 removed outlier: 3.523A pdb=" N ASN B 747 " --> pdb=" O GLY B 743 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU B 748 " --> pdb=" O THR B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 768 Processing helix chain 'B' and resid 769 through 771 No H-bonds generated for 'chain 'B' and resid 769 through 771' Processing helix chain 'B' and resid 792 through 823 removed outlier: 3.547A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA B 822 " --> pdb=" O SER B 818 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LYS B 823 " --> pdb=" O ARG B 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 415 removed outlier: 3.626A pdb=" N MET C 414 " --> pdb=" O ASN C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 437 removed outlier: 3.529A pdb=" N ASP C 427 " --> pdb=" O GLY C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 469 Processing helix chain 'C' and resid 482 through 489 removed outlier: 3.836A pdb=" N VAL C 488 " --> pdb=" O VAL C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 519 Processing helix chain 'C' and resid 522 through 546 Processing helix chain 'C' and resid 547 through 551 removed outlier: 3.626A pdb=" N GLU C 550 " --> pdb=" O SER C 547 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TRP C 551 " --> pdb=" O PRO C 548 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 547 through 551' Processing helix chain 'C' and resid 572 through 585 Processing helix chain 'C' and resid 595 through 620 Processing helix chain 'C' and resid 635 through 642 Processing helix chain 'C' and resid 653 through 661 Processing helix chain 'C' and resid 664 through 677 Processing helix chain 'C' and resid 685 through 695 Processing helix chain 'C' and resid 706 through 714 Processing helix chain 'C' and resid 742 through 757 removed outlier: 3.684A pdb=" N ASN C 747 " --> pdb=" O GLY C 743 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU C 748 " --> pdb=" O THR C 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 768 removed outlier: 3.632A pdb=" N LYS C 761 " --> pdb=" O GLY C 757 " (cutoff:3.500A) Processing helix chain 'C' and resid 792 through 821 removed outlier: 3.662A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 415 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 437 removed outlier: 3.627A pdb=" N ASP D 427 " --> pdb=" O GLY D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 469 Processing helix chain 'D' and resid 482 through 488 removed outlier: 3.761A pdb=" N VAL D 488 " --> pdb=" O VAL D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.820A pdb=" N LEU D 518 " --> pdb=" O PHE D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 545 Processing helix chain 'D' and resid 572 through 585 removed outlier: 3.669A pdb=" N TRP D 578 " --> pdb=" O BPHE D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 624 removed outlier: 3.598A pdb=" N LEU D 624 " --> pdb=" O LEU D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 629 Processing helix chain 'D' and resid 635 through 642 Processing helix chain 'D' and resid 653 through 662 Processing helix chain 'D' and resid 664 through 677 Processing helix chain 'D' and resid 685 through 695 Processing helix chain 'D' and resid 706 through 714 Processing helix chain 'D' and resid 742 through 757 removed outlier: 3.685A pdb=" N LEU D 748 " --> pdb=" O THR D 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 768 Processing helix chain 'D' and resid 788 through 823 removed outlier: 3.791A pdb=" N VAL D 792 " --> pdb=" O SER D 788 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N GLY D 794 " --> pdb=" O SER D 790 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL D 795 " --> pdb=" O ASN D 791 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS D 823 " --> pdb=" O ARG D 819 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 30 Processing helix chain 'E' and resid 93 through 104 Processing helix chain 'E' and resid 105 through 124 Processing helix chain 'E' and resid 133 through 160 removed outlier: 3.824A pdb=" N SER E 137 " --> pdb=" O ASN E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 210 Processing helix chain 'F' and resid 6 through 28 Processing helix chain 'F' and resid 93 through 104 removed outlier: 3.513A pdb=" N LEU F 98 " --> pdb=" O ALA F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 127 removed outlier: 4.037A pdb=" N GLU F 126 " --> pdb=" O ILE F 122 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE F 127 " --> pdb=" O ALA F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 160 Processing helix chain 'F' and resid 177 through 209 Processing helix chain 'G' and resid 7 through 30 removed outlier: 3.581A pdb=" N LEU G 11 " --> pdb=" O GLY G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 104 Processing helix chain 'G' and resid 105 through 127 removed outlier: 4.166A pdb=" N GLU G 126 " --> pdb=" O ILE G 122 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N PHE G 127 " --> pdb=" O ALA G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 161 removed outlier: 3.868A pdb=" N SER G 137 " --> pdb=" O ASN G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 210 Processing helix chain 'H' and resid 6 through 30 removed outlier: 3.963A pdb=" N MET H 10 " --> pdb=" O ARG H 6 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU H 11 " --> pdb=" O GLY H 7 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 104 Processing helix chain 'H' and resid 105 through 124 Processing helix chain 'H' and resid 133 through 161 removed outlier: 3.562A pdb=" N ALA H 161 " --> pdb=" O ILE H 157 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 209 removed outlier: 3.938A pdb=" N TYR H 181 " --> pdb=" O GLY H 177 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 394 through 399 Processing sheet with id=AA2, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AA3, first strand: chain 'A' and resid 489 through 491 Processing sheet with id=AA4, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.464A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.208A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.464A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.208A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 394 through 399 Processing sheet with id=AA7, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AA8, first strand: chain 'B' and resid 451 through 453 removed outlier: 3.611A pdb=" N ALA B 452 " --> pdb=" O ASN B 461 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 489 through 491 Processing sheet with id=AB1, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.509A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.232A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.509A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.232A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 394 through 399 removed outlier: 6.432A pdb=" N VAL C 395 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N THR C 443 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N VAL C 397 " --> pdb=" O THR C 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AB5, first strand: chain 'C' and resid 453 through 454 removed outlier: 3.613A pdb=" N ILE C 459 " --> pdb=" O ASP C 454 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 480 through 481 removed outlier: 4.490A pdb=" N GLY C 731 " --> pdb=" O ILE C 481 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 480 through 481 removed outlier: 4.490A pdb=" N GLY C 731 " --> pdb=" O ILE C 481 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 490 through 491 Processing sheet with id=AB9, first strand: chain 'D' and resid 394 through 399 Processing sheet with id=AC1, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AC2, first strand: chain 'D' and resid 489 through 491 Processing sheet with id=AC3, first strand: chain 'D' and resid 646 through 649 removed outlier: 6.666A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.263A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.721A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 646 through 649 removed outlier: 6.666A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.263A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.721A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 34 through 38 Processing sheet with id=AC6, first strand: chain 'F' and resid 34 through 35 Processing sheet with id=AC7, first strand: chain 'F' and resid 37 through 38 Processing sheet with id=AC8, first strand: chain 'F' and resid 65 through 67 removed outlier: 3.753A pdb=" N LYS F 78 " --> pdb=" O THR F 66 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 77 through 79 Processing sheet with id=AD1, first strand: chain 'H' and resid 36 through 38 Processing sheet with id=AD2, first strand: chain 'H' and resid 65 through 67 1115 hydrogen bonds defined for protein. 3258 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: 2.71 Time building geometry restraints manager: 2.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2625 1.30 - 1.43: 4982 1.43 - 1.56: 9603 1.56 - 1.69: 0 1.69 - 1.82: 192 Bond restraints: 17402 Sorted by residual: bond pdb=" C LEU D 624 " pdb=" O LEU D 624 " ideal model delta sigma weight residual 1.235 1.306 -0.070 1.26e-02 6.30e+03 3.11e+01 bond pdb=" C PHE D 584 " pdb=" O PHE D 584 " ideal model delta sigma weight residual 1.237 1.172 0.065 1.19e-02 7.06e+03 2.99e+01 bond pdb=" CA SER A 592 " pdb=" CB SER A 592 " ideal model delta sigma weight residual 1.535 1.470 0.065 1.21e-02 6.83e+03 2.88e+01 bond pdb=" CA SER C 592 " pdb=" CB SER C 592 " ideal model delta sigma weight residual 1.536 1.460 0.076 1.48e-02 4.57e+03 2.64e+01 bond pdb=" C PHE A 584 " pdb=" O PHE A 584 " ideal model delta sigma weight residual 1.237 1.179 0.058 1.19e-02 7.06e+03 2.38e+01 ... (remaining 17397 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 19629 2.28 - 4.55: 3672 4.55 - 6.83: 320 6.83 - 9.10: 10 9.10 - 11.38: 5 Bond angle restraints: 23636 Sorted by residual: angle pdb=" N LEU C 620 " pdb=" CA LEU C 620 " pdb=" C LEU C 620 " ideal model delta sigma weight residual 113.37 102.49 10.88 1.38e+00 5.25e-01 6.22e+01 angle pdb=" N GLU A 772 " pdb=" CA GLU A 772 " pdb=" C GLU A 772 " ideal model delta sigma weight residual 113.61 102.23 11.38 1.50e+00 4.44e-01 5.75e+01 angle pdb=" O PHE D 623 " pdb=" C PHE D 623 " pdb=" N LEU D 624 " ideal model delta sigma weight residual 122.59 113.24 9.35 1.33e+00 5.65e-01 4.94e+01 angle pdb=" N ASP C 590 " pdb=" CA ASP C 590 " pdb=" C ASP C 590 " ideal model delta sigma weight residual 113.88 105.67 8.21 1.23e+00 6.61e-01 4.45e+01 angle pdb=" N LEU B 803 " pdb=" CA LEU B 803 " pdb=" C LEU B 803 " ideal model delta sigma weight residual 111.28 104.46 6.82 1.09e+00 8.42e-01 3.91e+01 ... (remaining 23631 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 8935 17.90 - 35.80: 866 35.80 - 53.70: 145 53.70 - 71.60: 24 71.60 - 89.49: 11 Dihedral angle restraints: 9981 sinusoidal: 3429 harmonic: 6552 Sorted by residual: dihedral pdb=" CB CYS F 40 " pdb=" SG CYS F 40 " pdb=" SG CYS F 68 " pdb=" CB CYS F 68 " ideal model delta sinusoidal sigma weight residual 93.00 22.51 70.49 1 1.00e+01 1.00e-02 6.39e+01 dihedral pdb=" CB CYS G 40 " pdb=" SG CYS G 40 " pdb=" SG CYS G 68 " pdb=" CB CYS G 68 " ideal model delta sinusoidal sigma weight residual 93.00 39.50 53.50 1 1.00e+01 1.00e-02 3.89e+01 dihedral pdb=" CB CYS E 40 " pdb=" SG CYS E 40 " pdb=" SG CYS E 68 " pdb=" CB CYS E 68 " ideal model delta sinusoidal sigma weight residual 93.00 41.10 51.90 1 1.00e+01 1.00e-02 3.68e+01 ... (remaining 9978 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 916 0.066 - 0.132: 1035 0.132 - 0.198: 614 0.198 - 0.264: 163 0.264 - 0.329: 11 Chirality restraints: 2739 Sorted by residual: chirality pdb=" CA CYS C 589 " pdb=" N CYS C 589 " pdb=" C CYS C 589 " pdb=" CB CYS C 589 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CB VAL D 795 " pdb=" CA VAL D 795 " pdb=" CG1 VAL D 795 " pdb=" CG2 VAL D 795 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA ILE C 734 " pdb=" N ILE C 734 " pdb=" C ILE C 734 " pdb=" CB ILE C 734 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.30 2.00e-01 2.50e+01 2.25e+00 ... (remaining 2736 not shown) Planarity restraints: 2905 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE D 623 " 0.072 2.00e-02 2.50e+03 1.37e-01 1.88e+02 pdb=" C PHE D 623 " -0.237 2.00e-02 2.50e+03 pdb=" O PHE D 623 " 0.092 2.00e-02 2.50e+03 pdb=" N LEU D 624 " 0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA BPHE D 574 " -0.032 2.00e-02 2.50e+03 6.58e-02 4.33e+01 pdb=" C BPHE D 574 " 0.114 2.00e-02 2.50e+03 pdb=" O BPHE D 574 " -0.042 2.00e-02 2.50e+03 pdb=" N ASN D 575 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 420 " 0.521 9.50e-02 1.11e+02 2.33e-01 3.34e+01 pdb=" NE ARG B 420 " -0.030 2.00e-02 2.50e+03 pdb=" CZ ARG B 420 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG B 420 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 420 " 0.019 2.00e-02 2.50e+03 ... (remaining 2902 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1656 2.71 - 3.26: 18508 3.26 - 3.81: 26906 3.81 - 4.35: 35539 4.35 - 4.90: 56841 Nonbonded interactions: 139450 Sorted by model distance: nonbonded pdb=" O PHE D 623 " pdb=" N THR D 625 " model vdw 2.163 3.120 nonbonded pdb=" O LYS E 129 " pdb=" OG1 THR E 130 " model vdw 2.232 3.040 nonbonded pdb=" O SER E 104 " pdb=" N ILE E 106 " model vdw 2.248 3.120 nonbonded pdb=" O ASP A 427 " pdb=" OE1 GLU A 431 " model vdw 2.293 3.040 nonbonded pdb=" O ASP B 427 " pdb=" OE1 GLU B 431 " model vdw 2.293 3.040 ... (remaining 139445 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 549 or (resid 550 and (name N or name CA or na \ me C or name O or name CB )) or resid 551 through 573 or resid 575 through 593 o \ r (resid 594 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 95 through 624 or resid 633 through 773 or resid 785 through 812 or (resid 813 a \ nd (name N or name CA or name C or name O or name CB )) or resid 814 through 818 \ or (resid 819 through 823 and (name N or name CA or name C or name O or name CB \ )))) selection = (chain 'B' and (resid 393 through 506 or resid 513 through 549 or (resid 550 and \ (name N or name CA or name C or name O or name CB )) or resid 551 or (resid 569 \ and (name N or name CA or name C or name O or name CB )) or resid 570 through 5 \ 73 or resid 575 or (resid 576 and (name N or name CA or name C or name O or name \ CB )) or resid 577 through 593 or (resid 594 and (name N or name CA or name C o \ r name O or name CB )) or resid 595 through 773 or resid 785 through 823)) selection = (chain 'C' and (resid 393 through 506 or resid 513 through 573 or resid 575 or ( \ resid 576 and (name N or name CA or name C or name O or name CB )) or resid 577 \ through 624 or resid 633 through 812 or (resid 813 and (name N or name CA or nam \ e C or name O or name CB )) or resid 814 through 818 or (resid 819 through 823 a \ nd (name N or name CA or name C or name O or name CB )))) selection = (chain 'D' and (resid 393 through 506 or resid 513 through 549 or (resid 550 and \ (name N or name CA or name C or name O or name CB )) or resid 551 or (resid 569 \ and (name N or name CA or name C or name O or name CB )) or resid 570 through 5 \ 73 or resid 575 or (resid 576 and (name N or name CA or name C or name O or name \ CB )) or resid 577 through 593 or (resid 594 and (name N or name CA or name C o \ r name O or name CB )) or resid 595 through 624 or resid 633 or (resid 634 and ( \ name N or name CA or name C or name O or name CB )) or resid 635 through 823)) } ncs_group { reference = (chain 'E' and (resid 5 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 42 or (resid 56 and (name N or name \ CA or name C or name O or name CB )) or resid 57 through 69 or (resid 70 and (n \ ame N or name CA or name C or name O or name CB )) or resid 71 through 84 or res \ id 93 through 210)) selection = (chain 'F' and (resid 5 through 42 or resid 56 through 84 or resid 93 through 21 \ 0)) selection = (chain 'G' and (resid 5 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 42 or (resid 56 and (name N or name \ CA or name C or name O or name CB )) or resid 57 through 69 or (resid 70 and (n \ ame N or name CA or name C or name O or name CB )) or resid 71 through 84 or res \ id 93 through 210)) selection = (chain 'H' and (resid 5 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 42 or (resid 56 and (name N or name \ CA or name C or name O or name CB )) or resid 57 through 69 or (resid 70 and (n \ ame N or name CA or name C or name O or name CB )) or resid 71 through 210)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.760 Find NCS groups from input model: 0.380 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6554 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 : 0.013 0.081 17414 Z= 0.924 Angle : 1.693 11.379 23660 Z= 1.280 Chirality : 0.115 0.329 2739 Planarity : 0.014 0.233 2905 Dihedral : 14.446 89.494 5759 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.54 % Allowed : 4.45 % Favored : 95.01 % Rotamer: Outliers : 2.22 % Allowed : 7.02 % Favored : 90.76 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 22.22 % 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 aren not related in a simple way. whole: -1.70 (0.15), residues: 2231 helix: -0.32 (0.12), residues: 1292 sheet: -2.10 (0.38), residues: 146 loop : -2.18 (0.20), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 694 TYR 0.046 0.004 TYR C 700 PHE 0.055 0.004 PHE C 667 TRP 0.037 0.006 TRP C 767 HIS 0.010 0.002 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.01289 (17402) covalent geometry : angle 1.69177 (23636) SS BOND : bond 0.01304 ( 12) SS BOND : angle 2.32464 ( 24) hydrogen bonds : bond 0.14693 ( 1099) hydrogen bonds : angle 5.99848 ( 3258) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4462 Ramachandran restraints generated. 2231 Oldfield, 0 Emsley, 2231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4462 Ramachandran restraints generated. 2231 Oldfield, 0 Emsley, 2231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 426 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 590 ASP cc_start: 0.8831 (p0) cc_final: 0.8330 (p0) REVERT: A 591 ILE cc_start: 0.9193 (tp) cc_final: 0.8993 (pt) REVERT: A 594 ARG cc_start: 0.9623 (mtm-85) cc_final: 0.9402 (ttm110) REVERT: C 422 GLU cc_start: 0.6089 (OUTLIER) cc_final: 0.5860 (pm20) REVERT: C 730 LYS cc_start: -0.2508 (OUTLIER) cc_final: -0.3620 (ttmt) REVERT: D 493 LYS cc_start: 0.5694 (OUTLIER) cc_final: 0.5036 (mmmt) REVERT: D 506 LYS cc_start: 0.7010 (OUTLIER) cc_final: 0.6444 (tptp) REVERT: D 533 TYR cc_start: 0.9090 (t80) cc_final: 0.8755 (t80) REVERT: D 545 ARG cc_start: 0.9144 (mtm180) cc_final: 0.8702 (mmm-85) REVERT: D 576 SER cc_start: 0.9592 (m) cc_final: 0.9357 (p) REVERT: E 24 MET cc_start: 0.8910 (tpt) cc_final: 0.8663 (tpt) REVERT: E 200 MET cc_start: 0.9331 (mtm) cc_final: 0.9061 (mtt) REVERT: F 76 LEU cc_start: 0.8270 (mm) cc_final: 0.7952 (tt) REVERT: F 174 TYR cc_start: 0.8575 (OUTLIER) cc_final: 0.8187 (p90) REVERT: F 206 LYS cc_start: 0.9246 (mtpt) cc_final: 0.8959 (mmmt) REVERT: G 126 GLU cc_start: 0.9304 (mm-30) cc_final: 0.8909 (pt0) REVERT: H 13 THR cc_start: 0.9466 (m) cc_final: 0.9015 (t) REVERT: H 24 MET cc_start: 0.9574 (tpt) cc_final: 0.9356 (tpp) REVERT: H 83 PHE cc_start: 0.8196 (m-80) cc_final: 0.7900 (m-80) REVERT: H 192 MET cc_start: 0.8704 (mtt) cc_final: 0.8459 (mtp) outliers start: 37 outliers final: 10 residues processed: 451 average time/residue: 0.1458 time to fit residues: 94.5061 Evaluate side-chains 256 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 241 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain B residue 506 LYS Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 422 GLU Chi-restraints excluded: chain C residue 620 LEU Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 730 LYS Chi-restraints excluded: chain C residue 747 ASN Chi-restraints excluded: chain D residue 493 LYS Chi-restraints excluded: chain D residue 506 LYS Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 631 SER Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 787 LEU Chi-restraints excluded: chain F residue 174 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 0.0980 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 0.0470 chunk 200 optimal weight: 0.9990 chunk 212 optimal weight: 2.9990 overall best weight: 0.5880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 412 HIS B 619 ASN C 412 HIS C 726 ASN E 160 ASN F 72 ASN F 205 HIS ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 GLN H 133 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.137190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.085122 restraints weight = 88457.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.086296 restraints weight = 27447.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.085764 restraints weight = 16147.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.085976 restraints weight = 15476.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.086351 restraints weight = 12998.352| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3281 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3281 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 17414 Z= 0.137 Angle : 0.628 11.736 23660 Z= 0.332 Chirality : 0.042 0.281 2739 Planarity : 0.004 0.055 2905 Dihedral : 5.205 59.510 2470 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.62 % Favored : 98.20 % Rotamer: Outliers : 2.22 % Allowed : 16.32 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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 aren not related in a simple way. whole: 0.64 (0.18), residues: 2231 helix: 1.86 (0.14), residues: 1324 sheet: -2.02 (0.33), residues: 178 loop : -1.68 (0.22), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 586 TYR 0.019 0.001 TYR A 673 PHE 0.020 0.001 PHE F 97 TRP 0.015 0.001 TRP D 766 HIS 0.006 0.001 HIS H 60 Details of bonding type rmsd covalent geometry : bond 0.00292 (17402) covalent geometry : angle 0.62502 (23636) SS BOND : bond 0.00670 ( 12) SS BOND : angle 2.05608 ( 24) hydrogen bonds : bond 0.04214 ( 1099) hydrogen bonds : angle 4.28076 ( 3258) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4462 Ramachandran restraints generated. 2231 Oldfield, 0 Emsley, 2231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4462 Ramachandran restraints generated. 2231 Oldfield, 0 Emsley, 2231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 293 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 519 ASP cc_start: 0.8135 (m-30) cc_final: 0.7863 (m-30) REVERT: A 708 MET cc_start: 0.8652 (mmm) cc_final: 0.8335 (mmm) REVERT: A 817 LYS cc_start: 0.9205 (mtpt) cc_final: 0.8881 (mtpp) REVERT: B 787 LEU cc_start: 0.9180 (tp) cc_final: 0.8915 (tp) REVERT: C 463 MET cc_start: 0.1024 (mtp) cc_final: 0.0697 (mtm) REVERT: C 496 MET cc_start: 0.1776 (ptm) cc_final: 0.1034 (mtm) REVERT: C 519 ASP cc_start: 0.8959 (m-30) cc_final: 0.8743 (m-30) REVERT: C 586 ARG cc_start: 0.8874 (tpp80) cc_final: 0.8664 (mmm-85) REVERT: C 730 LYS cc_start: -0.2946 (OUTLIER) cc_final: -0.3627 (ttmt) REVERT: C 791 ASN cc_start: 0.8624 (m110) cc_final: 0.8319 (m110) REVERT: D 407 MET cc_start: 0.8107 (ptp) cc_final: 0.7759 (pmm) REVERT: D 493 LYS cc_start: 0.6847 (OUTLIER) cc_final: 0.5976 (mmmt) REVERT: D 670 MET cc_start: 0.8417 (mmm) cc_final: 0.7941 (mmm) REVERT: D 708 MET cc_start: 0.9048 (mpp) cc_final: 0.8831 (mpp) REVERT: E 95 GLU cc_start: 0.8892 (tp30) cc_final: 0.8481 (tm-30) REVERT: E 203 ASP cc_start: 0.8936 (t0) cc_final: 0.8293 (t0) REVERT: E 206 LYS cc_start: 0.8843 (mmmt) cc_final: 0.8572 (mttp) REVERT: F 76 LEU cc_start: 0.8012 (mm) cc_final: 0.7736 (tp) REVERT: F 140 ILE cc_start: 0.9407 (mm) cc_final: 0.9118 (tp) REVERT: F 144 SER cc_start: 0.9601 (m) cc_final: 0.9308 (p) REVERT: F 174 TYR cc_start: 0.8239 (OUTLIER) cc_final: 0.7519 (p90) REVERT: F 206 LYS cc_start: 0.9182 (mtpt) cc_final: 0.8834 (mmmt) REVERT: G 56 GLU cc_start: 0.8802 (mm-30) cc_final: 0.8499 (mm-30) REVERT: G 58 MET cc_start: 0.8720 (mmm) cc_final: 0.8485 (mmm) REVERT: G 78 LYS cc_start: 0.9118 (OUTLIER) cc_final: 0.8736 (pttt) REVERT: G 95 GLU cc_start: 0.9238 (tp30) cc_final: 0.8739 (tm-30) REVERT: G 99 ARG cc_start: 0.8706 (mtt-85) cc_final: 0.8403 (mtm-85) REVERT: G 156 TYR cc_start: 0.9190 (t80) cc_final: 0.8949 (t80) REVERT: H 13 THR cc_start: 0.9372 (m) cc_final: 0.8932 (t) REVERT: H 24 MET cc_start: 0.9552 (tpt) cc_final: 0.8821 (tpp) REVERT: H 70 GLU cc_start: 0.8974 (mm-30) cc_final: 0.8502 (pp20) REVERT: H 81 ASP cc_start: 0.8640 (t0) cc_final: 0.8422 (t0) REVERT: H 83 PHE cc_start: 0.8106 (m-80) cc_final: 0.7894 (m-80) REVERT: H 99 ARG cc_start: 0.8960 (tpp-160) cc_final: 0.8669 (tpp80) REVERT: H 192 MET cc_start: 0.8199 (mtt) cc_final: 0.7999 (mtp) REVERT: H 203 ASP cc_start: 0.8971 (t70) cc_final: 0.8720 (t0) outliers start: 37 outliers final: 8 residues processed: 318 average time/residue: 0.1615 time to fit residues: 74.2497 Evaluate side-chains 244 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 232 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain C residue 730 LYS Chi-restraints excluded: chain D residue 493 LYS Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 132 HIS Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain F residue 174 TYR Chi-restraints excluded: chain G residue 78 LYS Chi-restraints excluded: chain G residue 82 HIS Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain H residue 120 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 145 optimal weight: 10.0000 chunk 138 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 213 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 189 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 170 optimal weight: 0.2980 chunk 100 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 461 ASN ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 619 ASN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 HIS F 149 ASN ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 205 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.134974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.082529 restraints weight = 90934.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.083431 restraints weight = 33282.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.082777 restraints weight = 21637.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.083178 restraints weight = 19722.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.085065 restraints weight = 15698.607| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3264 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3264 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 17414 Z= 0.128 Angle : 0.593 12.349 23660 Z= 0.310 Chirality : 0.041 0.257 2739 Planarity : 0.004 0.044 2905 Dihedral : 4.138 52.267 2444 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.98 % Favored : 97.89 % Rotamer: Outliers : 3.06 % Allowed : 16.32 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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 aren not related in a simple way. whole: 1.29 (0.18), residues: 2231 helix: 2.38 (0.14), residues: 1323 sheet: -1.91 (0.35), residues: 167 loop : -1.35 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 586 TYR 0.015 0.001 TYR A 673 PHE 0.018 0.001 PHE H 73 TRP 0.008 0.001 TRP H 178 HIS 0.011 0.001 HIS A 435 Details of bonding type rmsd covalent geometry : bond 0.00285 (17402) covalent geometry : angle 0.59029 (23636) SS BOND : bond 0.00420 ( 12) SS BOND : angle 1.89139 ( 24) hydrogen bonds : bond 0.03821 ( 1099) hydrogen bonds : angle 4.10961 ( 3258) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4462 Ramachandran restraints generated. 2231 Oldfield, 0 Emsley, 2231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4462 Ramachandran restraints generated. 2231 Oldfield, 0 Emsley, 2231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 249 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 MET cc_start: 0.6733 (mpp) cc_final: 0.6417 (mmt) REVERT: A 519 ASP cc_start: 0.8168 (m-30) cc_final: 0.7894 (m-30) REVERT: A 817 LYS cc_start: 0.9225 (mtpt) cc_final: 0.8924 (mtpp) REVERT: B 506 LYS cc_start: 0.5145 (OUTLIER) cc_final: 0.4763 (mmtp) REVERT: B 688 GLU cc_start: 0.6682 (tm-30) cc_final: 0.6454 (tm-30) REVERT: B 787 LEU cc_start: 0.9307 (tp) cc_final: 0.8922 (tp) REVERT: C 496 MET cc_start: 0.1668 (ptm) cc_final: 0.1379 (mtp) REVERT: C 519 ASP cc_start: 0.8967 (m-30) cc_final: 0.8718 (m-30) REVERT: C 730 LYS cc_start: -0.2942 (OUTLIER) cc_final: -0.3357 (ttmt) REVERT: D 463 MET cc_start: 0.6900 (mtt) cc_final: 0.6469 (mpp) REVERT: D 503 MET cc_start: 0.7861 (mmm) cc_final: 0.7046 (mmm) REVERT: D 519 ASP cc_start: 0.8727 (m-30) cc_final: 0.8490 (t70) REVERT: D 550 GLU cc_start: 0.6759 (tm-30) cc_final: 0.6550 (pp20) REVERT: D 748 LEU cc_start: 0.9307 (tp) cc_final: 0.8936 (pp) REVERT: E 95 GLU cc_start: 0.8982 (tp30) cc_final: 0.8651 (tm-30) REVERT: E 206 LYS cc_start: 0.8827 (mmmt) cc_final: 0.8435 (mttp) REVERT: F 76 LEU cc_start: 0.7838 (mm) cc_final: 0.7579 (tp) REVERT: F 140 ILE cc_start: 0.9397 (mm) cc_final: 0.9087 (tp) REVERT: F 144 SER cc_start: 0.9596 (m) cc_final: 0.9391 (p) REVERT: F 174 TYR cc_start: 0.8357 (OUTLIER) cc_final: 0.8088 (p90) REVERT: F 206 LYS cc_start: 0.9081 (mtpt) cc_final: 0.8810 (mmmt) REVERT: G 56 GLU cc_start: 0.8779 (mm-30) cc_final: 0.8565 (mm-30) REVERT: G 95 GLU cc_start: 0.9197 (tp30) cc_final: 0.8726 (tm-30) REVERT: G 156 TYR cc_start: 0.9216 (t80) cc_final: 0.8928 (t80) REVERT: H 13 THR cc_start: 0.9376 (m) cc_final: 0.8947 (t) REVERT: H 24 MET cc_start: 0.9575 (tpt) cc_final: 0.8750 (tpp) REVERT: H 69 LEU cc_start: 0.7423 (OUTLIER) cc_final: 0.6832 (pp) REVERT: H 70 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8536 (pp20) REVERT: H 81 ASP cc_start: 0.8434 (t0) cc_final: 0.8161 (t0) REVERT: H 83 PHE cc_start: 0.7750 (m-80) cc_final: 0.7479 (m-80) outliers start: 51 outliers final: 29 residues processed: 287 average time/residue: 0.1496 time to fit residues: 63.5693 Evaluate side-chains 259 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 226 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain B residue 506 LYS Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 730 LYS Chi-restraints excluded: chain D residue 493 LYS Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 712 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 132 HIS Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 174 TYR Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 82 HIS Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 160 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 38 optimal weight: 5.9990 chunk 42 optimal weight: 20.0000 chunk 98 optimal weight: 1.9990 chunk 3 optimal weight: 9.9990 chunk 139 optimal weight: 8.9990 chunk 116 optimal weight: 3.9990 chunk 67 optimal weight: 40.0000 chunk 224 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 132 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 GLN A 619 ASN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.131994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.075465 restraints weight = 67737.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.078793 restraints weight = 25242.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.078564 restraints weight = 11665.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.078666 restraints weight = 11883.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.078819 restraints weight = 10796.785| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3145 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3145 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 17414 Z= 0.265 Angle : 0.683 11.714 23660 Z= 0.358 Chirality : 0.044 0.222 2739 Planarity : 0.004 0.041 2905 Dihedral : 4.387 55.494 2444 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.52 % Favored : 97.35 % Rotamer: Outliers : 3.78 % Allowed : 17.28 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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 aren not related in a simple way. whole: 1.33 (0.18), residues: 2231 helix: 2.35 (0.14), residues: 1322 sheet: -1.83 (0.34), residues: 184 loop : -1.20 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 586 TYR 0.020 0.002 TYR D 700 PHE 0.032 0.002 PHE H 73 TRP 0.014 0.002 TRP A 605 HIS 0.035 0.002 HIS E 205 Details of bonding type rmsd covalent geometry : bond 0.00609 (17402) covalent geometry : angle 0.67998 (23636) SS BOND : bond 0.00533 ( 12) SS BOND : angle 2.01301 ( 24) hydrogen bonds : bond 0.04429 ( 1099) hydrogen bonds : angle 4.35431 ( 3258) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4462 Ramachandran restraints generated. 2231 Oldfield, 0 Emsley, 2231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4462 Ramachandran restraints generated. 2231 Oldfield, 0 Emsley, 2231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 225 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 407 MET cc_start: 0.6478 (ptm) cc_final: 0.6177 (mtm) REVERT: A 408 MET cc_start: 0.6131 (mmm) cc_final: 0.5522 (mmm) REVERT: A 409 LYS cc_start: 0.8234 (mttm) cc_final: 0.7942 (ptmm) REVERT: A 463 MET cc_start: 0.6658 (mpp) cc_final: 0.6349 (mmt) REVERT: A 519 ASP cc_start: 0.8284 (m-30) cc_final: 0.8028 (m-30) REVERT: A 670 MET cc_start: 0.7538 (mmm) cc_final: 0.7271 (mmm) REVERT: A 817 LYS cc_start: 0.9340 (mtpt) cc_final: 0.9050 (mtpp) REVERT: B 619 ASN cc_start: 0.9349 (t0) cc_final: 0.8974 (m-40) REVERT: B 688 GLU cc_start: 0.6617 (tm-30) cc_final: 0.6323 (tm-30) REVERT: B 708 MET cc_start: 0.7092 (mtm) cc_final: 0.6651 (ptm) REVERT: C 426 VAL cc_start: -0.1575 (OUTLIER) cc_final: -0.1779 (p) REVERT: C 496 MET cc_start: 0.2780 (ptm) cc_final: 0.2430 (mtp) REVERT: C 519 ASP cc_start: 0.8961 (m-30) cc_final: 0.8718 (m-30) REVERT: C 684 ARG cc_start: 0.8890 (mmt180) cc_final: 0.8377 (tmt170) REVERT: D 463 MET cc_start: 0.7333 (mtt) cc_final: 0.6677 (mpp) REVERT: D 503 MET cc_start: 0.8013 (mmm) cc_final: 0.7481 (mmm) REVERT: D 623 PHE cc_start: 0.7271 (OUTLIER) cc_final: 0.6836 (m-10) REVERT: D 674 MET cc_start: 0.8225 (mpp) cc_final: 0.7898 (mpp) REVERT: D 748 LEU cc_start: 0.9455 (tp) cc_final: 0.9060 (pp) REVERT: E 58 MET cc_start: 0.8628 (mmm) cc_final: 0.8255 (mmp) REVERT: E 95 GLU cc_start: 0.9042 (tp30) cc_final: 0.8818 (tp30) REVERT: E 206 LYS cc_start: 0.8734 (mmmt) cc_final: 0.8503 (mttp) REVERT: F 58 MET cc_start: 0.8036 (tpp) cc_final: 0.7822 (tpp) REVERT: F 61 SER cc_start: 0.9221 (t) cc_final: 0.8984 (t) REVERT: F 206 LYS cc_start: 0.9164 (mtpt) cc_final: 0.8836 (mmmt) REVERT: G 56 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8624 (mm-30) REVERT: G 58 MET cc_start: 0.9082 (mmm) cc_final: 0.8851 (mmp) REVERT: G 95 GLU cc_start: 0.9171 (tp30) cc_final: 0.8760 (tm-30) REVERT: H 13 THR cc_start: 0.9418 (m) cc_final: 0.8985 (t) REVERT: H 41 LYS cc_start: 0.8707 (tmmt) cc_final: 0.8473 (mmtt) REVERT: H 57 VAL cc_start: 0.8693 (OUTLIER) cc_final: 0.8345 (m) REVERT: H 69 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7010 (pp) REVERT: H 70 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8327 (pp20) REVERT: H 81 ASP cc_start: 0.8406 (t0) cc_final: 0.8127 (t0) outliers start: 63 outliers final: 45 residues processed: 272 average time/residue: 0.1522 time to fit residues: 61.2969 Evaluate side-chains 257 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 208 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 609 THR Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 422 GLU Chi-restraints excluded: chain D residue 493 LYS Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 623 PHE Chi-restraints excluded: chain D residue 712 ILE Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 174 TYR Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 82 HIS Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 134 ILE Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 160 ASN Chi-restraints excluded: chain H residue 205 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 2 optimal weight: 8.9990 chunk 221 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 chunk 139 optimal weight: 20.0000 chunk 15 optimal weight: 0.8980 chunk 50 optimal weight: 9.9990 chunk 17 optimal weight: 0.5980 chunk 89 optimal weight: 3.9990 chunk 151 optimal weight: 9.9990 chunk 85 optimal weight: 9.9990 chunk 40 optimal weight: 30.0000 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 756 GLN E 160 ASN ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 205 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.134595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.083772 restraints weight = 93378.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.083172 restraints weight = 40440.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.082626 restraints weight = 25452.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.083106 restraints weight = 23301.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.083233 restraints weight = 18789.190| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3251 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3251 r_free = 0.3251 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3251 r_free = 0.3251 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3251 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.4398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17414 Z= 0.149 Angle : 0.594 8.238 23660 Z= 0.309 Chirality : 0.040 0.151 2739 Planarity : 0.004 0.049 2905 Dihedral : 4.158 50.629 2440 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.16 % Favored : 97.75 % Rotamer: Outliers : 2.88 % Allowed : 18.78 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.58 (0.19), residues: 2231 helix: 2.55 (0.14), residues: 1324 sheet: -1.86 (0.37), residues: 163 loop : -1.13 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 586 TYR 0.014 0.001 TYR D 732 PHE 0.017 0.001 PHE H 73 TRP 0.010 0.001 TRP D 766 HIS 0.009 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00341 (17402) covalent geometry : angle 0.59293 (23636) SS BOND : bond 0.00580 ( 12) SS BOND : angle 1.20446 ( 24) hydrogen bonds : bond 0.03756 ( 1099) hydrogen bonds : angle 4.09691 ( 3258) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4462 Ramachandran restraints generated. 2231 Oldfield, 0 Emsley, 2231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4462 Ramachandran restraints generated. 2231 Oldfield, 0 Emsley, 2231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 234 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 LYS cc_start: 0.8223 (mttm) cc_final: 0.7775 (ptmm) REVERT: A 463 MET cc_start: 0.6842 (mpp) cc_final: 0.6286 (mmt) REVERT: A 519 ASP cc_start: 0.8272 (m-30) cc_final: 0.8024 (m-30) REVERT: A 817 LYS cc_start: 0.9338 (mtpt) cc_final: 0.9007 (mtpp) REVERT: B 688 GLU cc_start: 0.6599 (OUTLIER) cc_final: 0.6280 (tm-30) REVERT: B 708 MET cc_start: 0.7200 (mtm) cc_final: 0.6742 (ptm) REVERT: C 496 MET cc_start: 0.2861 (ptm) cc_final: 0.2582 (mtp) REVERT: C 684 ARG cc_start: 0.8878 (mmt180) cc_final: 0.8385 (tmt170) REVERT: D 463 MET cc_start: 0.7056 (mtt) cc_final: 0.6553 (mpp) REVERT: D 503 MET cc_start: 0.8191 (mmm) cc_final: 0.7460 (mmm) REVERT: D 623 PHE cc_start: 0.7113 (OUTLIER) cc_final: 0.6514 (m-10) REVERT: D 674 MET cc_start: 0.8214 (mpp) cc_final: 0.7932 (mpp) REVERT: D 748 LEU cc_start: 0.9437 (tp) cc_final: 0.9038 (pp) REVERT: E 58 MET cc_start: 0.8713 (mmm) cc_final: 0.8304 (mmp) REVERT: E 205 HIS cc_start: 0.8563 (OUTLIER) cc_final: 0.7667 (t-90) REVERT: E 206 LYS cc_start: 0.8661 (mmmt) cc_final: 0.8379 (mttp) REVERT: E 207 GLN cc_start: 0.8326 (pp30) cc_final: 0.8101 (pp30) REVERT: F 61 SER cc_start: 0.9258 (t) cc_final: 0.9031 (t) REVERT: F 144 SER cc_start: 0.9502 (m) cc_final: 0.9206 (p) REVERT: F 206 LYS cc_start: 0.9151 (mtpt) cc_final: 0.8830 (mmmt) REVERT: G 95 GLU cc_start: 0.9166 (tp30) cc_final: 0.8733 (tm-30) REVERT: G 203 ASP cc_start: 0.8655 (OUTLIER) cc_final: 0.8265 (t0) REVERT: H 13 THR cc_start: 0.9400 (m) cc_final: 0.8943 (t) REVERT: H 57 VAL cc_start: 0.8707 (OUTLIER) cc_final: 0.8497 (m) REVERT: H 69 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7026 (pp) REVERT: H 70 GLU cc_start: 0.8731 (mm-30) cc_final: 0.8461 (pp20) REVERT: H 81 ASP cc_start: 0.8730 (t0) cc_final: 0.8463 (t0) outliers start: 48 outliers final: 28 residues processed: 270 average time/residue: 0.1518 time to fit residues: 60.3567 Evaluate side-chains 248 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 214 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 688 GLU Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 623 PHE Chi-restraints excluded: chain D residue 712 ILE Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 132 HIS Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 82 HIS Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 67 CYS Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 160 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 155 optimal weight: 2.9990 chunk 190 optimal weight: 0.9990 chunk 219 optimal weight: 0.9980 chunk 172 optimal weight: 3.9990 chunk 83 optimal weight: 20.0000 chunk 71 optimal weight: 30.0000 chunk 57 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 205 optimal weight: 0.8980 chunk 182 optimal weight: 3.9990 chunk 94 optimal weight: 0.5980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 619 ASN B 461 ASN D 569 ASN E 160 ASN E 205 HIS ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 205 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.134151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.077134 restraints weight = 57616.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.080102 restraints weight = 20388.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.082003 restraints weight = 11452.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.083072 restraints weight = 8310.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.083252 restraints weight = 6977.188| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3273 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3273 r_free = 0.3273 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3273 r_free = 0.3273 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3273 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17414 Z= 0.132 Angle : 0.595 11.340 23660 Z= 0.307 Chirality : 0.040 0.160 2739 Planarity : 0.004 0.045 2905 Dihedral : 3.886 28.126 2434 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.34 % Favored : 97.57 % Rotamer: Outliers : 2.76 % Allowed : 19.62 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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 aren not related in a simple way. whole: 1.73 (0.19), residues: 2231 helix: 2.64 (0.14), residues: 1318 sheet: -1.69 (0.39), residues: 152 loop : -1.01 (0.23), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 684 TYR 0.023 0.001 TYR F 174 PHE 0.019 0.001 PHE H 73 TRP 0.010 0.001 TRP D 766 HIS 0.006 0.001 HIS A 435 Details of bonding type rmsd covalent geometry : bond 0.00299 (17402) covalent geometry : angle 0.59454 (23636) SS BOND : bond 0.00519 ( 12) SS BOND : angle 0.95562 ( 24) hydrogen bonds : bond 0.03650 ( 1099) hydrogen bonds : angle 3.99848 ( 3258) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4462 Ramachandran restraints generated. 2231 Oldfield, 0 Emsley, 2231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4462 Ramachandran restraints generated. 2231 Oldfield, 0 Emsley, 2231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 230 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 LYS cc_start: 0.8514 (mttm) cc_final: 0.7787 (ptmm) REVERT: A 463 MET cc_start: 0.6432 (mpp) cc_final: 0.5782 (mmt) REVERT: A 519 ASP cc_start: 0.8141 (m-30) cc_final: 0.7868 (m-30) REVERT: A 590 ASP cc_start: 0.8933 (p0) cc_final: 0.8624 (p0) REVERT: A 817 LYS cc_start: 0.9321 (mtpt) cc_final: 0.9080 (mtpp) REVERT: B 688 GLU cc_start: 0.6568 (OUTLIER) cc_final: 0.6275 (tm-30) REVERT: B 708 MET cc_start: 0.6959 (mtm) cc_final: 0.6661 (ptm) REVERT: C 519 ASP cc_start: 0.8772 (m-30) cc_final: 0.8564 (m-30) REVERT: C 586 ARG cc_start: 0.8667 (tpp80) cc_final: 0.8444 (mmm-85) REVERT: C 684 ARG cc_start: 0.8951 (mmt180) cc_final: 0.8469 (tmt170) REVERT: D 463 MET cc_start: 0.6891 (mtt) cc_final: 0.6450 (mpp) REVERT: D 503 MET cc_start: 0.8144 (mmm) cc_final: 0.7455 (mmm) REVERT: D 623 PHE cc_start: 0.7089 (OUTLIER) cc_final: 0.6367 (m-10) REVERT: D 670 MET cc_start: 0.8481 (mmm) cc_final: 0.8247 (mmm) REVERT: D 748 LEU cc_start: 0.9388 (tp) cc_final: 0.8931 (pp) REVERT: E 58 MET cc_start: 0.8371 (mmm) cc_final: 0.8149 (mmm) REVERT: E 205 HIS cc_start: 0.8264 (OUTLIER) cc_final: 0.7766 (t70) REVERT: E 206 LYS cc_start: 0.8622 (mmmt) cc_final: 0.8341 (mttm) REVERT: F 61 SER cc_start: 0.9140 (t) cc_final: 0.8912 (t) REVERT: F 144 SER cc_start: 0.9560 (m) cc_final: 0.9158 (p) REVERT: F 175 SER cc_start: 0.8896 (t) cc_final: 0.8672 (m) REVERT: F 206 LYS cc_start: 0.9124 (mtpt) cc_final: 0.8811 (mmmt) REVERT: G 60 HIS cc_start: 0.8735 (OUTLIER) cc_final: 0.8533 (p90) REVERT: G 95 GLU cc_start: 0.8974 (tp30) cc_final: 0.8647 (tm-30) REVERT: G 203 ASP cc_start: 0.8704 (OUTLIER) cc_final: 0.8318 (t0) REVERT: H 13 THR cc_start: 0.9411 (m) cc_final: 0.8945 (t) REVERT: H 57 VAL cc_start: 0.8474 (OUTLIER) cc_final: 0.8158 (m) REVERT: H 81 ASP cc_start: 0.8172 (t0) cc_final: 0.7867 (t0) REVERT: H 203 ASP cc_start: 0.8965 (t0) cc_final: 0.8667 (t0) outliers start: 46 outliers final: 30 residues processed: 264 average time/residue: 0.1422 time to fit residues: 56.6637 Evaluate side-chains 246 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 210 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 688 GLU Chi-restraints excluded: chain C residue 791 ASN Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 623 PHE Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 132 HIS Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 60 HIS Chi-restraints excluded: chain G residue 82 HIS Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 67 CYS Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 160 ASN Chi-restraints excluded: chain H residue 205 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 94 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 188 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 103 optimal weight: 40.0000 chunk 195 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN E 160 ASN ** G 149 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 = 0.4202 r_free = 0.4202 target = 0.133018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.081470 restraints weight = 81462.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.081852 restraints weight = 33209.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.081626 restraints weight = 19474.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.081857 restraints weight = 18423.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.081977 restraints weight = 14261.677| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3224 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3224 r_free = 0.3224 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3224 r_free = 0.3224 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3224 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.4733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 17414 Z= 0.190 Angle : 0.634 8.750 23660 Z= 0.329 Chirality : 0.041 0.158 2739 Planarity : 0.004 0.045 2905 Dihedral : 3.939 27.817 2434 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.56 % Favored : 97.35 % Rotamer: Outliers : 2.88 % Allowed : 19.86 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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 aren not related in a simple way. whole: 1.68 (0.19), residues: 2231 helix: 2.61 (0.14), residues: 1318 sheet: -1.81 (0.36), residues: 180 loop : -0.95 (0.23), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 594 TYR 0.014 0.001 TYR F 156 PHE 0.022 0.001 PHE H 73 TRP 0.009 0.001 TRP D 766 HIS 0.022 0.001 HIS E 205 Details of bonding type rmsd covalent geometry : bond 0.00439 (17402) covalent geometry : angle 0.63337 (23636) SS BOND : bond 0.00495 ( 12) SS BOND : angle 1.03175 ( 24) hydrogen bonds : bond 0.03894 ( 1099) hydrogen bonds : angle 4.10144 ( 3258) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4462 Ramachandran restraints generated. 2231 Oldfield, 0 Emsley, 2231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4462 Ramachandran restraints generated. 2231 Oldfield, 0 Emsley, 2231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 211 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 MET cc_start: 0.6579 (mpp) cc_final: 0.5986 (mmt) REVERT: A 519 ASP cc_start: 0.8208 (m-30) cc_final: 0.7929 (m-30) REVERT: A 590 ASP cc_start: 0.9038 (p0) cc_final: 0.8725 (p0) REVERT: B 670 MET cc_start: 0.6034 (mmp) cc_final: 0.5381 (mmp) REVERT: B 674 MET cc_start: 0.0708 (ptp) cc_final: -0.0799 (ttm) REVERT: B 688 GLU cc_start: 0.6664 (OUTLIER) cc_final: 0.6294 (tm-30) REVERT: B 708 MET cc_start: 0.6988 (mtm) cc_final: 0.6694 (ptm) REVERT: C 519 ASP cc_start: 0.8884 (m-30) cc_final: 0.8665 (m-30) REVERT: C 620 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8804 (tp) REVERT: C 684 ARG cc_start: 0.8765 (mmt180) cc_final: 0.8356 (tmt170) REVERT: D 463 MET cc_start: 0.7047 (mtt) cc_final: 0.6526 (mpp) REVERT: D 503 MET cc_start: 0.8191 (mmm) cc_final: 0.7496 (mmm) REVERT: D 623 PHE cc_start: 0.7178 (OUTLIER) cc_final: 0.6444 (m-10) REVERT: D 674 MET cc_start: 0.8218 (mpp) cc_final: 0.7806 (mpp) REVERT: E 58 MET cc_start: 0.8703 (mmm) cc_final: 0.8284 (mmp) REVERT: E 206 LYS cc_start: 0.8711 (mmmt) cc_final: 0.8395 (mttm) REVERT: F 61 SER cc_start: 0.9263 (t) cc_final: 0.9005 (t) REVERT: F 140 ILE cc_start: 0.9469 (tp) cc_final: 0.9267 (tp) REVERT: F 144 SER cc_start: 0.9601 (m) cc_final: 0.9304 (p) REVERT: F 206 LYS cc_start: 0.9179 (mtpt) cc_final: 0.8835 (mmmt) REVERT: G 95 GLU cc_start: 0.9127 (tp30) cc_final: 0.8706 (tm-30) REVERT: H 69 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7405 (pp) REVERT: H 81 ASP cc_start: 0.8513 (t0) cc_final: 0.8193 (t0) REVERT: H 203 ASP cc_start: 0.8983 (t0) cc_final: 0.8702 (t0) outliers start: 48 outliers final: 35 residues processed: 244 average time/residue: 0.1465 time to fit residues: 53.7329 Evaluate side-chains 237 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 198 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 688 GLU Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 620 LEU Chi-restraints excluded: chain C residue 791 ASN Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 493 LYS Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 623 PHE Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 132 HIS Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 82 HIS Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain H residue 67 CYS Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 160 ASN Chi-restraints excluded: chain H residue 205 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 23 optimal weight: 9.9990 chunk 128 optimal weight: 8.9990 chunk 14 optimal weight: 0.9980 chunk 1 optimal weight: 20.0000 chunk 81 optimal weight: 20.0000 chunk 43 optimal weight: 8.9990 chunk 106 optimal weight: 0.0270 chunk 53 optimal weight: 0.7980 chunk 178 optimal weight: 9.9990 chunk 221 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 overall best weight: 2.3642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 619 ASN ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN ** G 149 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 = 0.4192 r_free = 0.4192 target = 0.132263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.074969 restraints weight = 61057.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.077787 restraints weight = 21813.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.079637 restraints weight = 12382.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.080487 restraints weight = 9026.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 73)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.081211 restraints weight = 7707.096| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3233 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3233 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.4934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 17414 Z= 0.207 Angle : 0.652 9.590 23660 Z= 0.338 Chirality : 0.041 0.158 2739 Planarity : 0.004 0.045 2905 Dihedral : 4.028 27.302 2434 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.65 % Favored : 97.26 % Rotamer: Outliers : 3.18 % Allowed : 19.92 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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 aren not related in a simple way. whole: 1.72 (0.19), residues: 2231 helix: 2.62 (0.14), residues: 1316 sheet: -1.73 (0.39), residues: 160 loop : -0.94 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 594 TYR 0.016 0.001 TYR D 673 PHE 0.022 0.001 PHE H 73 TRP 0.010 0.001 TRP D 766 HIS 0.006 0.001 HIS A 435 Details of bonding type rmsd covalent geometry : bond 0.00480 (17402) covalent geometry : angle 0.65097 (23636) SS BOND : bond 0.00516 ( 12) SS BOND : angle 1.05226 ( 24) hydrogen bonds : bond 0.04035 ( 1099) hydrogen bonds : angle 4.16567 ( 3258) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4462 Ramachandran restraints generated. 2231 Oldfield, 0 Emsley, 2231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4462 Ramachandran restraints generated. 2231 Oldfield, 0 Emsley, 2231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 197 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 MET cc_start: 0.6604 (mpp) cc_final: 0.5984 (mmt) REVERT: A 519 ASP cc_start: 0.8280 (m-30) cc_final: 0.7969 (m-30) REVERT: A 590 ASP cc_start: 0.8963 (p0) cc_final: 0.8640 (p0) REVERT: B 688 GLU cc_start: 0.6234 (tm-30) cc_final: 0.5876 (tm-30) REVERT: C 519 ASP cc_start: 0.8851 (m-30) cc_final: 0.8620 (m-30) REVERT: C 620 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8863 (tp) REVERT: C 684 ARG cc_start: 0.8931 (mmt180) cc_final: 0.8560 (tmt170) REVERT: D 463 MET cc_start: 0.7081 (mtt) cc_final: 0.6560 (mpp) REVERT: D 503 MET cc_start: 0.8062 (mmm) cc_final: 0.7386 (mmm) REVERT: D 623 PHE cc_start: 0.7315 (OUTLIER) cc_final: 0.6546 (m-10) REVERT: D 674 MET cc_start: 0.7937 (mpp) cc_final: 0.7352 (mpp) REVERT: E 58 MET cc_start: 0.8399 (mmm) cc_final: 0.8043 (mmp) REVERT: E 205 HIS cc_start: 0.8383 (OUTLIER) cc_final: 0.7383 (t-90) REVERT: E 206 LYS cc_start: 0.8736 (mmmt) cc_final: 0.8422 (mttm) REVERT: F 61 SER cc_start: 0.9158 (t) cc_final: 0.8921 (t) REVERT: F 144 SER cc_start: 0.9621 (m) cc_final: 0.9315 (p) REVERT: F 206 LYS cc_start: 0.9154 (mtpt) cc_final: 0.8833 (mmmt) REVERT: G 70 GLU cc_start: 0.7434 (pp20) cc_final: 0.6575 (pp20) REVERT: G 95 GLU cc_start: 0.8955 (tp30) cc_final: 0.8630 (tm-30) REVERT: H 69 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7564 (pp) REVERT: H 81 ASP cc_start: 0.8167 (t0) cc_final: 0.7876 (t0) REVERT: H 203 ASP cc_start: 0.9002 (t0) cc_final: 0.8710 (t0) outliers start: 53 outliers final: 42 residues processed: 233 average time/residue: 0.1313 time to fit residues: 46.5854 Evaluate side-chains 237 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 191 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 620 LEU Chi-restraints excluded: chain C residue 791 ASN Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 493 LYS Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 623 PHE Chi-restraints excluded: chain D residue 712 ILE Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 132 HIS Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 82 HIS Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain H residue 67 CYS Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 160 ASN Chi-restraints excluded: chain H residue 205 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 67 optimal weight: 20.0000 chunk 209 optimal weight: 6.9990 chunk 220 optimal weight: 6.9990 chunk 202 optimal weight: 0.8980 chunk 79 optimal weight: 30.0000 chunk 194 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 64 optimal weight: 9.9990 chunk 203 optimal weight: 0.9990 chunk 93 optimal weight: 0.0570 chunk 178 optimal weight: 7.9990 overall best weight: 2.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 619 ASN ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 461 ASN E 160 ASN F 72 ASN ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.131185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.072821 restraints weight = 58605.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.075594 restraints weight = 21621.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 70)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.077351 restraints weight = 12487.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.078282 restraints weight = 9231.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.078619 restraints weight = 7840.768| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3191 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3191 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.5103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 17414 Z= 0.252 Angle : 0.685 10.832 23660 Z= 0.356 Chirality : 0.042 0.159 2739 Planarity : 0.004 0.047 2905 Dihedral : 4.176 28.216 2434 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.92 % Favored : 96.99 % Rotamer: Outliers : 3.06 % Allowed : 20.64 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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 aren not related in a simple way. whole: 1.56 (0.19), residues: 2231 helix: 2.47 (0.14), residues: 1318 sheet: -1.74 (0.38), residues: 167 loop : -0.96 (0.23), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 594 TYR 0.019 0.002 TYR D 700 PHE 0.023 0.002 PHE H 73 TRP 0.021 0.002 TRP B 460 HIS 0.006 0.001 HIS A 435 Details of bonding type rmsd covalent geometry : bond 0.00581 (17402) covalent geometry : angle 0.68398 (23636) SS BOND : bond 0.00519 ( 12) SS BOND : angle 1.09978 ( 24) hydrogen bonds : bond 0.04290 ( 1099) hydrogen bonds : angle 4.31322 ( 3258) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4462 Ramachandran restraints generated. 2231 Oldfield, 0 Emsley, 2231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4462 Ramachandran restraints generated. 2231 Oldfield, 0 Emsley, 2231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 197 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 MET cc_start: 0.6742 (mpp) cc_final: 0.6081 (mmt) REVERT: A 519 ASP cc_start: 0.8315 (m-30) cc_final: 0.8011 (m-30) REVERT: B 407 MET cc_start: 0.5454 (mmm) cc_final: 0.5184 (mmm) REVERT: B 674 MET cc_start: 0.1398 (ptp) cc_final: -0.0208 (ttt) REVERT: B 688 GLU cc_start: 0.6233 (tm-30) cc_final: 0.5919 (tm-30) REVERT: C 620 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8895 (tp) REVERT: C 684 ARG cc_start: 0.8866 (mmt180) cc_final: 0.8471 (tmt170) REVERT: D 463 MET cc_start: 0.7235 (mtt) cc_final: 0.6693 (mpp) REVERT: D 503 MET cc_start: 0.8146 (mmm) cc_final: 0.7370 (mmm) REVERT: D 623 PHE cc_start: 0.7336 (OUTLIER) cc_final: 0.6616 (m-10) REVERT: D 674 MET cc_start: 0.7905 (mpp) cc_final: 0.7448 (mpp) REVERT: E 58 MET cc_start: 0.8318 (mmm) cc_final: 0.7918 (mmp) REVERT: E 206 LYS cc_start: 0.8693 (mmmt) cc_final: 0.8319 (mttm) REVERT: F 61 SER cc_start: 0.9205 (t) cc_final: 0.8970 (t) REVERT: F 144 SER cc_start: 0.9663 (m) cc_final: 0.9360 (p) REVERT: F 206 LYS cc_start: 0.9175 (mtpt) cc_final: 0.8841 (mmmt) REVERT: G 95 GLU cc_start: 0.8997 (tp30) cc_final: 0.8652 (tm-30) REVERT: H 13 THR cc_start: 0.9438 (m) cc_final: 0.9012 (t) REVERT: H 81 ASP cc_start: 0.8194 (t0) cc_final: 0.7910 (t0) outliers start: 51 outliers final: 44 residues processed: 232 average time/residue: 0.1395 time to fit residues: 48.7886 Evaluate side-chains 235 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 189 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 620 LEU Chi-restraints excluded: chain C residue 791 ASN Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 493 LYS Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 623 PHE Chi-restraints excluded: chain D residue 712 ILE Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 132 HIS Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 117 MET Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 82 HIS Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain H residue 67 CYS Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 160 ASN Chi-restraints excluded: chain H residue 205 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 188 optimal weight: 0.9990 chunk 162 optimal weight: 1.9990 chunk 88 optimal weight: 7.9990 chunk 169 optimal weight: 1.9990 chunk 124 optimal weight: 10.0000 chunk 207 optimal weight: 0.8980 chunk 104 optimal weight: 10.0000 chunk 36 optimal weight: 0.8980 chunk 112 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 62 optimal weight: 30.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 619 ASN E 160 ASN ** G 149 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 = 0.4202 r_free = 0.4202 target = 0.133126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.077810 restraints weight = 56846.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.080541 restraints weight = 23449.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.080924 restraints weight = 11692.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.080853 restraints weight = 12438.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.081110 restraints weight = 10412.527| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3212 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3212 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.5205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17414 Z= 0.151 Angle : 0.657 11.800 23660 Z= 0.335 Chirality : 0.041 0.173 2739 Planarity : 0.004 0.052 2905 Dihedral : 4.109 25.679 2434 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.34 % Favored : 97.57 % Rotamer: Outliers : 2.46 % Allowed : 21.42 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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 aren not related in a simple way. whole: 1.73 (0.19), residues: 2231 helix: 2.61 (0.14), residues: 1315 sheet: -1.68 (0.40), residues: 159 loop : -0.92 (0.23), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 594 TYR 0.017 0.001 TYR B 424 PHE 0.021 0.001 PHE H 73 TRP 0.011 0.001 TRP D 766 HIS 0.006 0.001 HIS A 435 Details of bonding type rmsd covalent geometry : bond 0.00346 (17402) covalent geometry : angle 0.65628 (23636) SS BOND : bond 0.00468 ( 12) SS BOND : angle 1.06328 ( 24) hydrogen bonds : bond 0.03888 ( 1099) hydrogen bonds : angle 4.11326 ( 3258) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4462 Ramachandran restraints generated. 2231 Oldfield, 0 Emsley, 2231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4462 Ramachandran restraints generated. 2231 Oldfield, 0 Emsley, 2231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 202 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 MET cc_start: 0.6757 (mpp) cc_final: 0.6112 (mmt) REVERT: A 519 ASP cc_start: 0.8280 (m-30) cc_final: 0.7959 (m-30) REVERT: B 407 MET cc_start: 0.5241 (mmm) cc_final: 0.4941 (mmm) REVERT: B 674 MET cc_start: 0.0665 (ptp) cc_final: -0.0727 (ttt) REVERT: B 688 GLU cc_start: 0.6210 (tm-30) cc_final: 0.5842 (tm-30) REVERT: C 620 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8665 (tp) REVERT: C 684 ARG cc_start: 0.8770 (mmt180) cc_final: 0.8456 (tmt170) REVERT: D 463 MET cc_start: 0.7076 (mtt) cc_final: 0.6632 (mpp) REVERT: D 503 MET cc_start: 0.8128 (mmm) cc_final: 0.7415 (mmm) REVERT: D 623 PHE cc_start: 0.7130 (OUTLIER) cc_final: 0.6324 (m-10) REVERT: D 674 MET cc_start: 0.7993 (mpp) cc_final: 0.7603 (mpp) REVERT: E 58 MET cc_start: 0.8602 (mmm) cc_final: 0.8079 (mmp) REVERT: E 206 LYS cc_start: 0.8658 (mmmt) cc_final: 0.8270 (mttm) REVERT: F 61 SER cc_start: 0.9269 (t) cc_final: 0.9009 (t) REVERT: F 144 SER cc_start: 0.9632 (m) cc_final: 0.9333 (p) REVERT: F 206 LYS cc_start: 0.9153 (mtpt) cc_final: 0.8817 (mmmt) REVERT: G 70 GLU cc_start: 0.7921 (pp20) cc_final: 0.7218 (pp20) REVERT: G 95 GLU cc_start: 0.9103 (tp30) cc_final: 0.8700 (tm-30) REVERT: G 203 ASP cc_start: 0.8848 (OUTLIER) cc_final: 0.8509 (t0) REVERT: H 81 ASP cc_start: 0.8379 (t0) cc_final: 0.8088 (t0) outliers start: 41 outliers final: 31 residues processed: 230 average time/residue: 0.1155 time to fit residues: 40.6402 Evaluate side-chains 231 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 197 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 620 LEU Chi-restraints excluded: chain C residue 791 ASN Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 493 LYS Chi-restraints excluded: chain D residue 623 PHE Chi-restraints excluded: chain D residue 712 ILE Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 132 HIS Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 82 HIS Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain H residue 67 CYS Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 160 ASN Chi-restraints excluded: chain H residue 205 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 81 optimal weight: 20.0000 chunk 136 optimal weight: 0.8980 chunk 217 optimal weight: 0.8980 chunk 140 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 164 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 200 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 619 ASN E 160 ASN ** G 149 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 = 0.4217 r_free = 0.4217 target = 0.134048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.078019 restraints weight = 84194.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.081176 restraints weight = 27380.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.083037 restraints weight = 12711.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.082377 restraints weight = 11904.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.082711 restraints weight = 10393.800| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3240 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3240 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.5299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17414 Z= 0.132 Angle : 0.643 12.319 23660 Z= 0.331 Chirality : 0.040 0.167 2739 Planarity : 0.004 0.049 2905 Dihedral : 4.026 25.194 2434 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.34 % Favored : 97.57 % Rotamer: Outliers : 2.04 % Allowed : 21.72 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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 aren not related in a simple way. whole: 1.79 (0.19), residues: 2231 helix: 2.63 (0.15), residues: 1315 sheet: -1.62 (0.39), residues: 161 loop : -0.83 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 594 TYR 0.024 0.001 TYR E 128 PHE 0.020 0.001 PHE H 73 TRP 0.010 0.001 TRP D 766 HIS 0.006 0.001 HIS A 435 Details of bonding type rmsd covalent geometry : bond 0.00297 (17402) covalent geometry : angle 0.64297 (23636) SS BOND : bond 0.00460 ( 12) SS BOND : angle 0.99187 ( 24) hydrogen bonds : bond 0.03700 ( 1099) hydrogen bonds : angle 4.03463 ( 3258) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4301.43 seconds wall clock time: 74 minutes 31.57 seconds (4471.57 seconds total)