Starting phenix.real_space_refine on Sun Jun 15 05:43:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p3y_17399/06_2025/8p3y_17399_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p3y_17399/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8p3y_17399/06_2025/8p3y_17399.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p3y_17399/06_2025/8p3y_17399.map" model { file = "/net/cci-nas-00/data/ceres_data/8p3y_17399/06_2025/8p3y_17399_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p3y_17399/06_2025/8p3y_17399_neut.cif" } resolution = 3.55 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.048 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 4} 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: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 4} 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: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 14, 'ARG:plan': 5} 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: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 5} 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: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 6} 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: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 6} 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: {'GLU:plan': 2, 'ARG: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: 13.80, per 1000 atoms: 0.81 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: 5.40 Conformation dependent library (CDL) restraints added in 3.9 seconds 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: 2.20 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: 6.78 Time building geometry restraints manager: 6.04 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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 48.250 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.040 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (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 TRP 0.037 0.006 TRP C 767 HIS 0.010 0.002 HIS H 205 PHE 0.055 0.004 PHE C 667 TYR 0.046 0.004 TYR C 700 ARG 0.018 0.001 ARG C 694 Details of bonding type rmsd hydrogen bonds : bond 0.14693 ( 1099) hydrogen bonds : angle 5.99848 ( 3258) SS BOND : bond 0.01304 ( 12) SS BOND : angle 2.32464 ( 24) covalent geometry : bond 0.01289 (17402) covalent geometry : angle 1.69177 (23636) *********************** 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 : 2.013 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: 0.5857 (pm20) REVERT: C 730 LYS cc_start: -0.2508 (OUTLIER) cc_final: -0.3624 (ttmt) REVERT: D 493 LYS cc_start: 0.5694 (OUTLIER) cc_final: 0.5035 (mmmt) REVERT: D 506 LYS cc_start: 0.7010 (OUTLIER) cc_final: 0.6454 (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: 0.8701 (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: 0.9060 (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: 0.9355 (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: 0.8460 (mtp) outliers start: 37 outliers final: 10 residues processed: 451 average time/residue: 0.3880 time to fit residues: 249.9523 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 : 3.489 ------------------------------------------------------------------------------- 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 189 optimal weight: 0.6980 chunk 170 optimal weight: 0.5980 chunk 94 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 176 optimal weight: 0.8980 chunk 68 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 131 optimal weight: 0.5980 chunk 204 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 E 160 ASN F 205 HIS ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 GLN H 133 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.136853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.084690 restraints weight = 80165.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.085928 restraints weight = 27756.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.085523 restraints weight = 15914.314| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3259 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3258 r_free = 0.3258 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3258 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 17414 Z= 0.143 Angle : 0.631 11.826 23660 Z= 0.335 Chirality : 0.042 0.279 2739 Planarity : 0.004 0.054 2905 Dihedral : 5.211 59.290 2470 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.80 % Favored : 98.02 % Rotamer: Outliers : 2.16 % Allowed : 16.50 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.18), residues: 2231 helix: 1.88 (0.14), residues: 1322 sheet: -2.08 (0.33), residues: 173 loop : -1.68 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 766 HIS 0.007 0.001 HIS D 412 PHE 0.019 0.001 PHE F 97 TYR 0.019 0.001 TYR A 673 ARG 0.007 0.001 ARG D 586 Details of bonding type rmsd hydrogen bonds : bond 0.04354 ( 1099) hydrogen bonds : angle 4.30204 ( 3258) SS BOND : bond 0.00388 ( 12) SS BOND : angle 2.45863 ( 24) covalent geometry : bond 0.00303 (17402) covalent geometry : angle 0.62639 (23636) *********************** 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 324 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 288 time to evaluate : 1.959 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: 0.8169 (m-30) cc_final: 0.7904 (m-30) REVERT: A 817 LYS cc_start: 0.9201 (mtpt) cc_final: 0.8887 (mtpp) REVERT: B 787 LEU cc_start: 0.9165 (tp) cc_final: 0.8917 (tp) REVERT: C 463 MET cc_start: 0.1001 (mtp) cc_final: 0.0746 (mtm) REVERT: C 496 MET cc_start: 0.1799 (ptm) cc_final: 0.1052 (mtm) REVERT: C 519 ASP cc_start: 0.8889 (m-30) cc_final: 0.8655 (m-30) REVERT: C 586 ARG cc_start: 0.8927 (tpp80) cc_final: 0.8718 (mmm-85) REVERT: C 730 LYS cc_start: -0.2892 (OUTLIER) cc_final: -0.3571 (ttmt) REVERT: C 791 ASN cc_start: 0.8718 (m110) cc_final: 0.8447 (m110) REVERT: D 407 MET cc_start: 0.8142 (ptp) cc_final: 0.7812 (pmm) REVERT: D 493 LYS cc_start: 0.6851 (OUTLIER) cc_final: 0.6042 (mmmt) REVERT: D 670 MET cc_start: 0.8496 (mmm) cc_final: 0.8032 (mmm) REVERT: E 30 THR cc_start: 0.8934 (m) cc_final: 0.8703 (p) REVERT: E 32 TYR cc_start: 0.8594 (m-10) cc_final: 0.8320 (m-10) REVERT: E 95 GLU cc_start: 0.8910 (tp30) cc_final: 0.8503 (tm-30) REVERT: E 203 ASP cc_start: 0.8921 (t0) cc_final: 0.8259 (t0) REVERT: E 206 LYS cc_start: 0.8848 (mmmt) cc_final: 0.8506 (mttp) REVERT: F 6 ARG cc_start: 0.7321 (ttp80) cc_final: 0.7037 (ttp80) REVERT: F 76 LEU cc_start: 0.8006 (mm) cc_final: 0.7723 (tp) REVERT: F 140 ILE cc_start: 0.9394 (mm) cc_final: 0.9112 (tp) REVERT: F 144 SER cc_start: 0.9601 (m) cc_final: 0.9313 (p) REVERT: F 174 TYR cc_start: 0.8268 (OUTLIER) cc_final: 0.7583 (p90) REVERT: F 206 LYS cc_start: 0.9177 (mtpt) cc_final: 0.8848 (mmmt) REVERT: G 10 MET cc_start: 0.7643 (ptt) cc_final: 0.7407 (ptt) REVERT: G 37 ARG cc_start: 0.8393 (mtp85) cc_final: 0.8193 (tpt-90) REVERT: G 78 LYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8779 (pttt) REVERT: G 95 GLU cc_start: 0.9080 (tp30) cc_final: 0.8541 (tm-30) REVERT: G 156 TYR cc_start: 0.9208 (t80) cc_final: 0.8961 (t80) REVERT: H 13 THR cc_start: 0.9381 (m) cc_final: 0.8946 (t) REVERT: H 24 MET cc_start: 0.9495 (tpt) cc_final: 0.8828 (tpp) REVERT: H 61 SER cc_start: 0.9104 (t) cc_final: 0.8895 (t) REVERT: H 70 GLU cc_start: 0.8971 (mm-30) cc_final: 0.8511 (pp20) REVERT: H 83 PHE cc_start: 0.8108 (m-80) cc_final: 0.7884 (m-80) REVERT: H 99 ARG cc_start: 0.8942 (tpp-160) cc_final: 0.8660 (tpp80) REVERT: H 192 MET cc_start: 0.8276 (mtt) cc_final: 0.8048 (mtp) REVERT: H 203 ASP cc_start: 0.8937 (t70) cc_final: 0.8682 (t0) outliers start: 36 outliers final: 10 residues processed: 312 average time/residue: 0.3260 time to fit residues: 147.1736 Evaluate side-chains 247 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 233 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain C residue 730 LYS Chi-restraints excluded: chain D residue 493 LYS Chi-restraints excluded: chain D residue 787 LEU 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 75 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 137 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 chunk 138 optimal weight: 0.8980 chunk 175 optimal weight: 7.9990 chunk 169 optimal weight: 3.9990 chunk 161 optimal weight: 9.9990 chunk 215 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 C 791 ASN E 205 HIS F 149 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 = 0.4177 r_free = 0.4177 target = 0.131835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.073232 restraints weight = 65882.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.076116 restraints weight = 23293.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.077845 restraints weight = 13141.411| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- 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 = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3145 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 17414 Z= 0.197 Angle : 0.636 12.416 23660 Z= 0.334 Chirality : 0.042 0.236 2739 Planarity : 0.004 0.045 2905 Dihedral : 4.462 59.008 2446 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.25 % Favored : 97.62 % Rotamer: Outliers : 3.66 % Allowed : 16.68 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.18), residues: 2231 helix: 2.33 (0.14), residues: 1327 sheet: -1.90 (0.33), residues: 181 loop : -1.39 (0.22), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 605 HIS 0.010 0.001 HIS A 435 PHE 0.029 0.002 PHE H 73 TYR 0.018 0.001 TYR D 700 ARG 0.009 0.001 ARG D 684 Details of bonding type rmsd hydrogen bonds : bond 0.04276 ( 1099) hydrogen bonds : angle 4.26105 ( 3258) SS BOND : bond 0.00634 ( 12) SS BOND : angle 1.71286 ( 24) covalent geometry : bond 0.00452 (17402) covalent geometry : angle 0.63435 (23636) *********************** 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 301 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 240 time to evaluate : 1.821 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 487 GLU cc_start: 0.8710 (pt0) cc_final: 0.8287 (pp20) REVERT: A 519 ASP cc_start: 0.8252 (m-30) cc_final: 0.7998 (m-30) REVERT: A 817 LYS cc_start: 0.9268 (mtpt) cc_final: 0.8939 (mtpp) REVERT: B 506 LYS cc_start: 0.5465 (OUTLIER) cc_final: 0.5228 (mmtp) REVERT: B 619 ASN cc_start: 0.9292 (t0) cc_final: 0.8940 (m-40) REVERT: B 688 GLU cc_start: 0.6739 (tm-30) cc_final: 0.6531 (tm-30) REVERT: C 496 MET cc_start: 0.2106 (ptm) cc_final: 0.1622 (mtp) REVERT: C 519 ASP cc_start: 0.8963 (m-30) cc_final: 0.8687 (m-30) REVERT: C 730 LYS cc_start: -0.1285 (OUTLIER) cc_final: -0.1928 (ttmt) REVERT: C 791 ASN cc_start: 0.8805 (m-40) cc_final: 0.8567 (m110) REVERT: D 463 MET cc_start: 0.7180 (mtt) cc_final: 0.6560 (mpp) REVERT: D 674 MET cc_start: 0.7843 (mpp) cc_final: 0.7558 (mpp) REVERT: D 748 LEU cc_start: 0.9378 (tp) cc_final: 0.8937 (pp) REVERT: E 30 THR cc_start: 0.8871 (m) cc_final: 0.8591 (p) REVERT: E 95 GLU cc_start: 0.8976 (tp30) cc_final: 0.8675 (tm-30) REVERT: E 191 GLU cc_start: 0.8959 (mm-30) cc_final: 0.8725 (mm-30) REVERT: E 206 LYS cc_start: 0.8889 (mmmt) cc_final: 0.8487 (mttp) REVERT: F 76 LEU cc_start: 0.7797 (mm) cc_final: 0.7564 (tp) REVERT: F 95 GLU cc_start: 0.8361 (tt0) cc_final: 0.8026 (pt0) REVERT: F 140 ILE cc_start: 0.9398 (mm) cc_final: 0.9193 (tp) REVERT: F 174 TYR cc_start: 0.8484 (OUTLIER) cc_final: 0.8246 (p90) REVERT: F 206 LYS cc_start: 0.9166 (mtpt) cc_final: 0.8837 (mmmt) REVERT: G 60 HIS cc_start: 0.8939 (OUTLIER) cc_final: 0.8589 (p90) REVERT: G 78 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8737 (pttt) REVERT: G 95 GLU cc_start: 0.9065 (tp30) cc_final: 0.8672 (tm-30) REVERT: H 13 THR cc_start: 0.9400 (m) cc_final: 0.8991 (t) REVERT: H 69 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7422 (pp) REVERT: H 192 MET cc_start: 0.8246 (mtt) cc_final: 0.7982 (mtp) outliers start: 61 outliers final: 36 residues processed: 287 average time/residue: 0.2926 time to fit residues: 125.3738 Evaluate side-chains 262 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 220 time to evaluate : 1.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 ASP 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 506 LYS 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 427 ASP Chi-restraints excluded: chain C residue 536 VAL 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 40 CYS 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 195 VAL 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 112 VAL Chi-restraints excluded: chain F residue 174 TYR 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 60 HIS Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 78 LYS 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 69 LEU Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 150 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 201 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 192 optimal weight: 6.9990 chunk 223 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 155 optimal weight: 4.9990 chunk 111 optimal weight: 30.0000 chunk 119 optimal weight: 6.9990 chunk 208 optimal weight: 1.9990 chunk 180 optimal weight: 9.9990 chunk 135 optimal weight: 0.0570 overall best weight: 1.7704 ------------------------------------------------------------------------------- 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 E 160 ASN ** E 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4210 r_free = 0.4210 target = 0.133506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.081724 restraints weight = 81598.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.081045 restraints weight = 35903.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.081439 restraints weight = 19167.665| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3183 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 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 = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3183 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17414 Z= 0.168 Angle : 0.608 11.612 23660 Z= 0.316 Chirality : 0.041 0.188 2739 Planarity : 0.004 0.040 2905 Dihedral : 4.303 53.025 2444 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.20 % Favored : 97.66 % Rotamer: Outliers : 3.66 % Allowed : 17.04 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.18), residues: 2231 helix: 2.55 (0.14), residues: 1318 sheet: -1.82 (0.37), residues: 162 loop : -1.23 (0.22), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 766 HIS 0.008 0.001 HIS A 435 PHE 0.023 0.001 PHE H 73 TYR 0.016 0.001 TYR C 405 ARG 0.006 0.001 ARG D 684 Details of bonding type rmsd hydrogen bonds : bond 0.03883 ( 1099) hydrogen bonds : angle 4.09393 ( 3258) SS BOND : bond 0.00850 ( 12) SS BOND : angle 1.72756 ( 24) covalent geometry : bond 0.00385 (17402) covalent geometry : angle 0.60570 (23636) *********************** 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 295 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 234 time to evaluate : 1.799 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 409 LYS cc_start: 0.8207 (mttm) cc_final: 0.7727 (ptmm) REVERT: A 519 ASP cc_start: 0.8332 (m-30) cc_final: 0.8074 (m-30) REVERT: A 817 LYS cc_start: 0.9306 (mtpt) cc_final: 0.8909 (mtpp) REVERT: B 619 ASN cc_start: 0.9260 (t0) cc_final: 0.8919 (m-40) REVERT: B 688 GLU cc_start: 0.6571 (tm-30) cc_final: 0.6227 (tm-30) REVERT: B 708 MET cc_start: 0.7082 (mtm) cc_final: 0.6642 (ptm) REVERT: C 496 MET cc_start: 0.2767 (ptm) cc_final: 0.2394 (mtp) REVERT: C 519 ASP cc_start: 0.9002 (m-30) cc_final: 0.8781 (m-30) REVERT: C 684 ARG cc_start: 0.8824 (mmt180) cc_final: 0.8325 (tmt170) REVERT: D 463 MET cc_start: 0.7038 (mtt) cc_final: 0.6505 (mpp) REVERT: D 503 MET cc_start: 0.8267 (tpp) cc_final: 0.7364 (mmm) REVERT: D 623 PHE cc_start: 0.7060 (OUTLIER) cc_final: 0.6587 (m-10) REVERT: D 748 LEU cc_start: 0.9358 (tp) cc_final: 0.8944 (pp) REVERT: E 30 THR cc_start: 0.8882 (m) cc_final: 0.8618 (p) REVERT: E 205 HIS cc_start: 0.8349 (OUTLIER) cc_final: 0.7333 (t-90) REVERT: E 206 LYS cc_start: 0.8747 (mmmt) cc_final: 0.8499 (mttp) REVERT: F 95 GLU cc_start: 0.8675 (tt0) cc_final: 0.8244 (pt0) REVERT: F 140 ILE cc_start: 0.9440 (mm) cc_final: 0.9115 (tp) REVERT: F 144 SER cc_start: 0.9588 (m) cc_final: 0.9289 (p) REVERT: F 206 LYS cc_start: 0.9190 (mtpt) cc_final: 0.8834 (mmmt) REVERT: G 95 GLU cc_start: 0.9141 (tp30) cc_final: 0.8694 (tm-30) REVERT: G 156 TYR cc_start: 0.9219 (t80) cc_final: 0.8957 (t80) REVERT: H 13 THR cc_start: 0.9393 (m) cc_final: 0.8950 (t) REVERT: H 41 LYS cc_start: 0.8770 (tmmt) cc_final: 0.8541 (mmtt) REVERT: H 69 LEU cc_start: 0.7424 (OUTLIER) cc_final: 0.7056 (pp) REVERT: H 192 MET cc_start: 0.8235 (mtt) cc_final: 0.7954 (mtp) outliers start: 61 outliers final: 39 residues processed: 277 average time/residue: 0.3230 time to fit residues: 133.1820 Evaluate side-chains 256 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 214 time to evaluate : 1.803 ------------------------------------------------------------------------------- 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 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 427 ASP 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 D residue 787 LEU Chi-restraints excluded: chain E residue 40 CYS 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 151 ILE 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 66 THR Chi-restraints excluded: chain F residue 112 VAL 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 83 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 162 optimal weight: 2.9990 chunk 154 optimal weight: 0.5980 chunk 101 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 106 optimal weight: 20.0000 chunk 145 optimal weight: 1.9990 chunk 123 optimal weight: 7.9990 chunk 191 optimal weight: 4.9990 chunk 30 optimal weight: 30.0000 overall best weight: 1.9188 ------------------------------------------------------------------------------- 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 = 0.4230 r_free = 0.4230 target = 0.133393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.081341 restraints weight = 83642.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.081158 restraints weight = 36818.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.080622 restraints weight = 23335.100| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3202 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3202 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.4375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17414 Z= 0.176 Angle : 0.604 7.999 23660 Z= 0.314 Chirality : 0.041 0.145 2739 Planarity : 0.004 0.046 2905 Dihedral : 4.111 51.953 2438 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.47 % Favored : 97.44 % Rotamer: Outliers : 3.78 % Allowed : 17.82 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.19), residues: 2231 helix: 2.57 (0.14), residues: 1322 sheet: -1.89 (0.36), residues: 175 loop : -1.03 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 766 HIS 0.006 0.001 HIS A 435 PHE 0.020 0.001 PHE H 73 TYR 0.023 0.001 TYR F 174 ARG 0.006 0.001 ARG H 204 Details of bonding type rmsd hydrogen bonds : bond 0.03927 ( 1099) hydrogen bonds : angle 4.09476 ( 3258) SS BOND : bond 0.00598 ( 12) SS BOND : angle 1.15172 ( 24) covalent geometry : bond 0.00404 (17402) covalent geometry : angle 0.60330 (23636) *********************** 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 288 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 225 time to evaluate : 1.905 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 519 ASP cc_start: 0.8326 (m-30) cc_final: 0.8089 (m-30) REVERT: A 590 ASP cc_start: 0.8954 (p0) cc_final: 0.8700 (p0) REVERT: B 688 GLU cc_start: 0.6618 (OUTLIER) cc_final: 0.6293 (tm-30) REVERT: B 708 MET cc_start: 0.6931 (mtm) cc_final: 0.6569 (ptm) REVERT: C 496 MET cc_start: 0.2808 (ptm) cc_final: 0.2512 (mtp) REVERT: C 684 ARG cc_start: 0.8853 (mmt180) cc_final: 0.8378 (tmt170) REVERT: D 463 MET cc_start: 0.7122 (mtt) cc_final: 0.6593 (mpp) REVERT: D 503 MET cc_start: 0.8159 (tpp) cc_final: 0.7233 (mmm) REVERT: D 623 PHE cc_start: 0.7246 (OUTLIER) cc_final: 0.6607 (m-10) REVERT: D 674 MET cc_start: 0.8216 (mpp) cc_final: 0.7864 (mpp) REVERT: D 748 LEU cc_start: 0.9355 (tp) cc_final: 0.8938 (pp) REVERT: E 30 THR cc_start: 0.9079 (m) cc_final: 0.8829 (p) REVERT: E 58 MET cc_start: 0.8541 (mmm) cc_final: 0.8306 (mmm) REVERT: E 205 HIS cc_start: 0.8436 (OUTLIER) cc_final: 0.7352 (t-90) REVERT: E 206 LYS cc_start: 0.8730 (mmmt) cc_final: 0.8419 (mttm) REVERT: F 140 ILE cc_start: 0.9490 (mm) cc_final: 0.9196 (tp) REVERT: F 144 SER cc_start: 0.9571 (m) cc_final: 0.9262 (p) REVERT: F 206 LYS cc_start: 0.9206 (mtpt) cc_final: 0.8851 (mmmt) REVERT: G 76 LEU cc_start: 0.9142 (tp) cc_final: 0.8941 (tp) REVERT: G 95 GLU cc_start: 0.9138 (tp30) cc_final: 0.8660 (tm-30) REVERT: H 13 THR cc_start: 0.9418 (m) cc_final: 0.8955 (t) REVERT: H 69 LEU cc_start: 0.7407 (OUTLIER) cc_final: 0.6786 (pp) REVERT: H 192 MET cc_start: 0.8134 (mtt) cc_final: 0.7930 (mtp) REVERT: H 203 ASP cc_start: 0.8941 (t0) cc_final: 0.8688 (t0) outliers start: 63 outliers final: 43 residues processed: 269 average time/residue: 0.3427 time to fit residues: 138.3569 Evaluate side-chains 253 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 206 time to evaluate : 1.531 ------------------------------------------------------------------------------- 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 543 VAL 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 688 GLU Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 536 VAL 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 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 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 60 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 196 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 54 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 161 optimal weight: 9.9990 chunk 207 optimal weight: 0.6980 chunk 104 optimal weight: 5.9990 chunk 193 optimal weight: 5.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 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 = 0.4205 r_free = 0.4205 target = 0.133250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.076166 restraints weight = 56297.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.078980 restraints weight = 20300.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.080747 restraints weight = 11478.212| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3213 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3213 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.4583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17414 Z= 0.163 Angle : 0.604 8.863 23660 Z= 0.312 Chirality : 0.041 0.165 2739 Planarity : 0.004 0.044 2905 Dihedral : 4.078 51.357 2438 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.47 % Favored : 97.44 % Rotamer: Outliers : 2.94 % Allowed : 19.14 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.19), residues: 2231 helix: 2.61 (0.14), residues: 1321 sheet: -1.66 (0.41), residues: 149 loop : -1.03 (0.22), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 766 HIS 0.007 0.001 HIS A 435 PHE 0.022 0.001 PHE H 73 TYR 0.014 0.001 TYR F 174 ARG 0.006 0.001 ARG D 586 Details of bonding type rmsd hydrogen bonds : bond 0.03827 ( 1099) hydrogen bonds : angle 4.04250 ( 3258) SS BOND : bond 0.00570 ( 12) SS BOND : angle 1.06683 ( 24) covalent geometry : bond 0.00374 (17402) covalent geometry : angle 0.60371 (23636) *********************** 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 267 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 218 time to evaluate : 2.015 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 519 ASP cc_start: 0.8330 (m-30) cc_final: 0.8049 (m-30) REVERT: A 590 ASP cc_start: 0.8944 (p0) cc_final: 0.8669 (p0) REVERT: B 688 GLU cc_start: 0.6599 (OUTLIER) cc_final: 0.6293 (tm-30) REVERT: B 708 MET cc_start: 0.6968 (mtm) cc_final: 0.6678 (ptm) REVERT: C 496 MET cc_start: 0.2856 (ptm) cc_final: 0.2590 (mtp) REVERT: C 519 ASP cc_start: 0.8845 (m-30) cc_final: 0.8610 (m-30) REVERT: C 684 ARG cc_start: 0.8962 (mmt180) cc_final: 0.8458 (tmt170) REVERT: D 463 MET cc_start: 0.7017 (mtt) cc_final: 0.6502 (mpp) REVERT: D 503 MET cc_start: 0.7970 (tpp) cc_final: 0.7290 (mmm) REVERT: D 623 PHE cc_start: 0.7274 (OUTLIER) cc_final: 0.6525 (m-10) REVERT: D 674 MET cc_start: 0.8097 (mpp) cc_final: 0.7754 (mpp) REVERT: D 748 LEU cc_start: 0.9282 (tp) cc_final: 0.8818 (pp) REVERT: E 30 THR cc_start: 0.9061 (m) cc_final: 0.8824 (p) REVERT: E 41 LYS cc_start: 0.7642 (tmtt) cc_final: 0.7187 (tmtt) REVERT: E 205 HIS cc_start: 0.8424 (OUTLIER) cc_final: 0.7340 (t-90) REVERT: E 206 LYS cc_start: 0.8734 (mmmt) cc_final: 0.8399 (mttm) REVERT: F 61 SER cc_start: 0.9178 (t) cc_final: 0.8943 (t) REVERT: F 140 ILE cc_start: 0.9441 (mm) cc_final: 0.9138 (tp) REVERT: F 144 SER cc_start: 0.9595 (m) cc_final: 0.9242 (p) REVERT: F 206 LYS cc_start: 0.9172 (mtpt) cc_final: 0.8823 (mmmt) REVERT: G 95 GLU cc_start: 0.9029 (tp30) cc_final: 0.8632 (tm-30) REVERT: H 13 THR cc_start: 0.9412 (m) cc_final: 0.8959 (t) REVERT: H 192 MET cc_start: 0.8216 (mtt) cc_final: 0.7966 (mtp) REVERT: H 203 ASP cc_start: 0.8982 (t0) cc_final: 0.8731 (t0) outliers start: 49 outliers final: 39 residues processed: 252 average time/residue: 0.3017 time to fit residues: 113.3561 Evaluate side-chains 246 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 204 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 543 VAL 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 688 GLU Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain C 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 D residue 787 LEU 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 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 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 G residue 205 HIS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 224 optimal weight: 2.9990 chunk 142 optimal weight: 8.9990 chunk 219 optimal weight: 0.9980 chunk 44 optimal weight: 20.0000 chunk 88 optimal weight: 40.0000 chunk 128 optimal weight: 6.9990 chunk 111 optimal weight: 40.0000 chunk 103 optimal weight: 40.0000 chunk 73 optimal weight: 30.0000 chunk 99 optimal weight: 0.4980 chunk 102 optimal weight: 5.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- 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 461 ASN A 619 ASN C 412 HIS D 461 ASN E 160 ASN ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.130258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.078783 restraints weight = 102961.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.077269 restraints weight = 41070.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.077641 restraints weight = 23939.032| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3111 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3111 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.4842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 17414 Z= 0.290 Angle : 0.699 10.143 23660 Z= 0.364 Chirality : 0.043 0.159 2739 Planarity : 0.004 0.046 2905 Dihedral : 4.394 54.577 2438 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.15 % Favored : 96.76 % Rotamer: Outliers : 3.60 % Allowed : 19.08 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.19), residues: 2231 helix: 2.33 (0.14), residues: 1321 sheet: -1.84 (0.38), residues: 165 loop : -0.95 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 766 HIS 0.007 0.001 HIS A 435 PHE 0.024 0.002 PHE H 73 TYR 0.020 0.002 TYR D 700 ARG 0.007 0.001 ARG C 586 Details of bonding type rmsd hydrogen bonds : bond 0.04588 ( 1099) hydrogen bonds : angle 4.36642 ( 3258) SS BOND : bond 0.00568 ( 12) SS BOND : angle 1.28592 ( 24) covalent geometry : bond 0.00666 (17402) covalent geometry : angle 0.69767 (23636) *********************** 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 255 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 195 time to evaluate : 3.026 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: A 519 ASP cc_start: 0.8350 (m-30) cc_final: 0.8079 (m-30) REVERT: A 674 MET cc_start: 0.6920 (mpp) cc_final: 0.5680 (mpp) REVERT: B 619 ASN cc_start: 0.9323 (t0) cc_final: 0.8940 (m-40) REVERT: B 688 GLU cc_start: 0.6307 (OUTLIER) cc_final: 0.5917 (tm-30) REVERT: B 708 MET cc_start: 0.6844 (mtm) cc_final: 0.6615 (ptm) REVERT: C 496 MET cc_start: 0.2942 (ptm) cc_final: 0.2615 (mtp) REVERT: C 519 ASP cc_start: 0.8987 (m-30) cc_final: 0.8755 (m-30) REVERT: C 620 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8868 (tp) REVERT: C 684 ARG cc_start: 0.8758 (mmt180) cc_final: 0.8368 (tmt170) REVERT: D 463 MET cc_start: 0.7395 (mtt) cc_final: 0.6737 (mpp) REVERT: D 503 MET cc_start: 0.8281 (tpp) cc_final: 0.7043 (mmm) REVERT: D 623 PHE cc_start: 0.7468 (OUTLIER) cc_final: 0.6731 (m-80) REVERT: D 674 MET cc_start: 0.8034 (mpp) cc_final: 0.7699 (mpp) REVERT: E 30 THR cc_start: 0.9117 (m) cc_final: 0.8908 (p) REVERT: E 41 LYS cc_start: 0.8021 (tmtt) cc_final: 0.7641 (tmtt) REVERT: F 13 THR cc_start: 0.9013 (OUTLIER) cc_final: 0.8703 (t) REVERT: F 61 SER cc_start: 0.9357 (t) cc_final: 0.9110 (t) REVERT: F 95 GLU cc_start: 0.8776 (tt0) cc_final: 0.8301 (pt0) REVERT: F 206 LYS cc_start: 0.9249 (mtpt) cc_final: 0.8866 (mmmt) REVERT: G 95 GLU cc_start: 0.9118 (tp30) cc_final: 0.8693 (tp30) REVERT: H 13 THR cc_start: 0.9415 (m) cc_final: 0.8948 (t) REVERT: H 192 MET cc_start: 0.8198 (mtt) cc_final: 0.7920 (mtp) outliers start: 60 outliers final: 45 residues processed: 240 average time/residue: 0.3908 time to fit residues: 142.5507 Evaluate side-chains 235 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 186 time to evaluate : 2.189 ------------------------------------------------------------------------------- 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 543 VAL 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 688 GLU Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 427 ASP 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 811 LEU 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 703 LEU 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 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 63 optimal weight: 20.0000 chunk 201 optimal weight: 7.9990 chunk 43 optimal weight: 0.0370 chunk 174 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 218 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 88 optimal weight: 10.0000 chunk 154 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 overall best weight: 1.7662 ------------------------------------------------------------------------------- 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** G 205 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.132542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.080672 restraints weight = 79333.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.081485 restraints weight = 32679.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.080819 restraints weight = 18339.423| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3170 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3170 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.4968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17414 Z= 0.170 Angle : 0.645 11.543 23660 Z= 0.328 Chirality : 0.041 0.161 2739 Planarity : 0.004 0.046 2905 Dihedral : 4.197 51.836 2438 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.47 % Favored : 97.44 % Rotamer: Outliers : 2.70 % Allowed : 20.34 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.19), residues: 2231 helix: 2.56 (0.14), residues: 1323 sheet: -1.74 (0.40), residues: 159 loop : -0.93 (0.23), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 766 HIS 0.006 0.001 HIS A 435 PHE 0.025 0.001 PHE H 73 TYR 0.014 0.001 TYR B 424 ARG 0.007 0.001 ARG C 586 Details of bonding type rmsd hydrogen bonds : bond 0.03986 ( 1099) hydrogen bonds : angle 4.08101 ( 3258) SS BOND : bond 0.00514 ( 12) SS BOND : angle 1.04680 ( 24) covalent geometry : bond 0.00391 (17402) covalent geometry : angle 0.64418 (23636) *********************** 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 249 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 204 time to evaluate : 1.991 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: B 619 ASN cc_start: 0.9325 (t0) cc_final: 0.8981 (m-40) REVERT: B 688 GLU cc_start: 0.6263 (tm-30) cc_final: 0.5860 (tm-30) REVERT: C 519 ASP cc_start: 0.8881 (m-30) cc_final: 0.8624 (m-30) REVERT: C 684 ARG cc_start: 0.8694 (mmt180) cc_final: 0.8393 (tmt170) REVERT: D 463 MET cc_start: 0.7149 (mtt) cc_final: 0.6668 (mpp) REVERT: D 503 MET cc_start: 0.8148 (tpp) cc_final: 0.7031 (mmm) REVERT: D 623 PHE cc_start: 0.7212 (OUTLIER) cc_final: 0.6418 (m-10) REVERT: E 30 THR cc_start: 0.9112 (m) cc_final: 0.8876 (p) REVERT: E 41 LYS cc_start: 0.7868 (tmtt) cc_final: 0.7502 (tmtt) REVERT: F 13 THR cc_start: 0.9030 (m) cc_final: 0.8824 (t) REVERT: F 61 SER cc_start: 0.9318 (t) cc_final: 0.9057 (t) REVERT: F 95 GLU cc_start: 0.8691 (tt0) cc_final: 0.8248 (pt0) REVERT: F 144 SER cc_start: 0.9615 (m) cc_final: 0.9290 (p) REVERT: F 206 LYS cc_start: 0.9217 (mtpt) cc_final: 0.8829 (mmmt) REVERT: G 95 GLU cc_start: 0.9109 (tp30) cc_final: 0.8689 (tp30) REVERT: G 203 ASP cc_start: 0.8864 (OUTLIER) cc_final: 0.8520 (t0) REVERT: H 13 THR cc_start: 0.9370 (m) cc_final: 0.8886 (t) REVERT: H 192 MET cc_start: 0.8176 (mtt) cc_final: 0.7966 (mtp) REVERT: H 203 ASP cc_start: 0.8980 (t0) cc_final: 0.8778 (t0) outliers start: 45 outliers final: 37 residues processed: 237 average time/residue: 0.3668 time to fit residues: 130.5407 Evaluate side-chains 238 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 199 time to evaluate : 3.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 543 VAL 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 536 VAL 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 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 117 MET 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 G residue 205 HIS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 18 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 167 optimal weight: 10.0000 chunk 104 optimal weight: 0.3980 chunk 180 optimal weight: 7.9990 chunk 75 optimal weight: 0.8980 chunk 189 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 219 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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** ** G 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.133358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.075002 restraints weight = 81914.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.078104 restraints weight = 24882.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.080136 restraints weight = 13091.128| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3206 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 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 = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3206 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.5085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17414 Z= 0.151 Angle : 0.638 12.610 23660 Z= 0.324 Chirality : 0.040 0.156 2739 Planarity : 0.004 0.048 2905 Dihedral : 4.111 51.408 2438 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.61 % Favored : 97.30 % Rotamer: Outliers : 2.58 % Allowed : 21.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.19), residues: 2231 helix: 2.62 (0.14), residues: 1323 sheet: -1.40 (0.43), residues: 141 loop : -0.93 (0.23), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 671 HIS 0.014 0.001 HIS G 205 PHE 0.024 0.001 PHE H 73 TYR 0.014 0.001 TYR B 424 ARG 0.007 0.001 ARG D 586 Details of bonding type rmsd hydrogen bonds : bond 0.03866 ( 1099) hydrogen bonds : angle 3.97161 ( 3258) SS BOND : bond 0.00503 ( 12) SS BOND : angle 1.00127 ( 24) covalent geometry : bond 0.00347 (17402) covalent geometry : angle 0.63795 (23636) *********************** 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 255 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 212 time to evaluate : 2.631 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 670 MET cc_start: 0.7091 (OUTLIER) cc_final: 0.6768 (mmm) REVERT: B 688 GLU cc_start: 0.6188 (tm-30) cc_final: 0.5855 (tm-30) REVERT: C 496 MET cc_start: 0.2736 (ptm) cc_final: 0.2457 (mtp) REVERT: C 519 ASP cc_start: 0.8962 (m-30) cc_final: 0.8707 (m-30) REVERT: C 620 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8649 (tp) REVERT: C 684 ARG cc_start: 0.8840 (mmt180) cc_final: 0.8464 (tmt170) REVERT: D 463 MET cc_start: 0.7022 (mtt) cc_final: 0.6572 (mpp) REVERT: D 503 MET cc_start: 0.8043 (tpp) cc_final: 0.6971 (mmm) REVERT: D 623 PHE cc_start: 0.7306 (OUTLIER) cc_final: 0.6425 (m-10) REVERT: D 674 MET cc_start: 0.7922 (mpp) cc_final: 0.7301 (mpp) REVERT: E 30 THR cc_start: 0.9086 (m) cc_final: 0.8843 (p) REVERT: E 41 LYS cc_start: 0.7636 (tmtt) cc_final: 0.7310 (tmtt) REVERT: F 61 SER cc_start: 0.9257 (t) cc_final: 0.8999 (t) REVERT: F 95 GLU cc_start: 0.8487 (tt0) cc_final: 0.8117 (pt0) REVERT: F 144 SER cc_start: 0.9618 (m) cc_final: 0.9242 (p) REVERT: F 206 LYS cc_start: 0.9229 (mtpt) cc_final: 0.8822 (mmmt) REVERT: G 70 GLU cc_start: 0.7693 (pp20) cc_final: 0.7028 (pp20) REVERT: G 95 GLU cc_start: 0.9029 (tp30) cc_final: 0.8664 (tp30) REVERT: H 192 MET cc_start: 0.8207 (mtt) cc_final: 0.7987 (mtp) outliers start: 43 outliers final: 36 residues processed: 242 average time/residue: 0.4055 time to fit residues: 146.9439 Evaluate side-chains 241 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 202 time to evaluate : 3.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 670 MET Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 620 LEU 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 117 MET 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 G residue 205 HIS 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 158 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 162 optimal weight: 0.6980 chunk 146 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 202 optimal weight: 0.7980 chunk 136 optimal weight: 0.6980 chunk 93 optimal weight: 4.9990 chunk 167 optimal weight: 10.0000 chunk 74 optimal weight: 20.0000 chunk 179 optimal weight: 4.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- 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 B 461 ASN C 587 GLN E 160 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 = 0.4200 r_free = 0.4200 target = 0.132696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.078918 restraints weight = 91190.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.080626 restraints weight = 33842.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.080297 restraints weight = 16689.202| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3156 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 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 = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3157 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.5176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17414 Z= 0.175 Angle : 0.656 12.953 23660 Z= 0.336 Chirality : 0.041 0.163 2739 Planarity : 0.004 0.048 2905 Dihedral : 4.139 52.156 2438 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.61 % Favored : 97.30 % Rotamer: Outliers : 2.52 % Allowed : 21.30 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.19), residues: 2231 helix: 2.58 (0.14), residues: 1324 sheet: -1.45 (0.41), residues: 156 loop : -0.85 (0.23), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 671 HIS 0.006 0.001 HIS A 435 PHE 0.025 0.001 PHE H 73 TYR 0.019 0.001 TYR A 673 ARG 0.009 0.001 ARG B 594 Details of bonding type rmsd hydrogen bonds : bond 0.03954 ( 1099) hydrogen bonds : angle 4.03111 ( 3258) SS BOND : bond 0.00494 ( 12) SS BOND : angle 0.98313 ( 24) covalent geometry : bond 0.00402 (17402) covalent geometry : angle 0.65512 (23636) ********************** 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 244 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 202 time to evaluate : 2.578 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 670 MET cc_start: 0.7198 (OUTLIER) cc_final: 0.6983 (mmm) REVERT: B 407 MET cc_start: 0.4823 (mmm) cc_final: 0.4537 (mmm) REVERT: B 688 GLU cc_start: 0.6259 (tm-30) cc_final: 0.5849 (tm-30) REVERT: C 496 MET cc_start: 0.2708 (ptm) cc_final: 0.2400 (mtp) REVERT: C 620 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8816 (tp) REVERT: C 684 ARG cc_start: 0.8674 (mmt180) cc_final: 0.8416 (tmt170) REVERT: D 463 MET cc_start: 0.7092 (mtt) cc_final: 0.6653 (mpp) REVERT: D 503 MET cc_start: 0.8143 (tpp) cc_final: 0.7073 (mmm) REVERT: D 623 PHE cc_start: 0.7258 (OUTLIER) cc_final: 0.6413 (m-10) REVERT: D 674 MET cc_start: 0.7979 (mpp) cc_final: 0.7773 (mpp) REVERT: E 30 THR cc_start: 0.9098 (m) cc_final: 0.8865 (p) REVERT: E 41 LYS cc_start: 0.7907 (tmtt) cc_final: 0.7553 (tmtt) REVERT: E 95 GLU cc_start: 0.8766 (tp30) cc_final: 0.8536 (tp30) REVERT: E 128 TYR cc_start: 0.7276 (t80) cc_final: 0.6775 (t80) REVERT: F 61 SER cc_start: 0.9326 (t) cc_final: 0.9069 (t) REVERT: F 95 GLU cc_start: 0.8761 (tt0) cc_final: 0.8361 (pt0) REVERT: F 144 SER cc_start: 0.9619 (m) cc_final: 0.9325 (p) REVERT: F 206 LYS cc_start: 0.9231 (mtpt) cc_final: 0.8831 (mmmt) REVERT: G 70 GLU cc_start: 0.8233 (pp20) cc_final: 0.7686 (pp20) REVERT: G 95 GLU cc_start: 0.9103 (tp30) cc_final: 0.8637 (tp30) REVERT: G 99 ARG cc_start: 0.8828 (mtt-85) cc_final: 0.8315 (ttm170) REVERT: G 203 ASP cc_start: 0.8851 (OUTLIER) cc_final: 0.8509 (t0) REVERT: H 192 MET cc_start: 0.8234 (mtt) cc_final: 0.8027 (mtp) outliers start: 42 outliers final: 34 residues processed: 232 average time/residue: 0.4212 time to fit residues: 146.7130 Evaluate side-chains 234 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 196 time to evaluate : 1.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 670 MET Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 620 LEU 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 117 MET Chi-restraints excluded: chain F residue 200 MET 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 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 128 optimal weight: 4.9990 chunk 111 optimal weight: 40.0000 chunk 50 optimal weight: 6.9990 chunk 186 optimal weight: 0.9980 chunk 51 optimal weight: 0.0970 chunk 116 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 68 optimal weight: 10.0000 chunk 154 optimal weight: 0.6980 chunk 144 optimal weight: 8.9990 overall best weight: 1.5580 ------------------------------------------------------------------------------- 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 = 0.4204 r_free = 0.4204 target = 0.133063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.077414 restraints weight = 66639.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.080944 restraints weight = 24274.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.080345 restraints weight = 11783.857| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3183 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3183 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.5222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17414 Z= 0.159 Angle : 0.657 12.284 23660 Z= 0.335 Chirality : 0.040 0.173 2739 Planarity : 0.004 0.048 2905 Dihedral : 4.123 51.684 2438 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.61 % Favored : 97.30 % Rotamer: Outliers : 2.46 % Allowed : 21.18 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.19), residues: 2231 helix: 2.60 (0.14), residues: 1324 sheet: -1.41 (0.41), residues: 151 loop : -0.84 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 671 HIS 0.006 0.001 HIS A 435 PHE 0.024 0.001 PHE H 73 TYR 0.016 0.001 TYR A 673 ARG 0.009 0.001 ARG B 594 Details of bonding type rmsd hydrogen bonds : bond 0.03888 ( 1099) hydrogen bonds : angle 3.98632 ( 3258) SS BOND : bond 0.00487 ( 12) SS BOND : angle 0.95072 ( 24) covalent geometry : bond 0.00366 (17402) covalent geometry : angle 0.65646 (23636) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8491.54 seconds wall clock time: 153 minutes 16.07 seconds (9196.07 seconds total)