Starting phenix.real_space_refine on Sun Aug 24 08:50:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8piv_17692/08_2025/8piv_17692.cif Found real_map, /net/cci-nas-00/data/ceres_data/8piv_17692/08_2025/8piv_17692.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8piv_17692/08_2025/8piv_17692.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8piv_17692/08_2025/8piv_17692.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8piv_17692/08_2025/8piv_17692.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8piv_17692/08_2025/8piv_17692.map" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 5 5.49 5 S 124 5.16 5 C 11892 2.51 5 N 2845 2.21 5 O 3223 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 98 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18089 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 3078 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 399, 3056 Classifications: {'peptide': 399} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 11} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 386} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 4, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 35 Conformer: "B" Number of residues, atoms: 399, 3056 Classifications: {'peptide': 399} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 11} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 386} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 4, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 35 bond proxies already assigned to first conformer: 3096 Chain: "B" Number of atoms: 3027 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 395, 3016 Classifications: {'peptide': 395} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 10} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 383} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 6, 'ASP:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 45 Conformer: "B" Number of residues, atoms: 395, 3016 Classifications: {'peptide': 395} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 10} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 383} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 6, 'ASP:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 45 bond proxies already assigned to first conformer: 3067 Chain: "C" Number of atoms: 3041 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 397, 3030 Classifications: {'peptide': 397} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 11} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 384} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 4, 'ASP:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 40 Conformer: "B" Number of residues, atoms: 397, 3030 Classifications: {'peptide': 397} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 11} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 384} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 4, 'ASP:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 40 bond proxies already assigned to first conformer: 3084 Chain: "D" Number of atoms: 3018 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 393, 2996 Classifications: {'peptide': 393} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 12} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 381} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 6, 'ASP:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 45 Conformer: "B" Number of residues, atoms: 393, 2996 Classifications: {'peptide': 393} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 12} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 381} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 6, 'ASP:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 45 bond proxies already assigned to first conformer: 3034 Chain: "E" Number of atoms: 1373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1373 Classifications: {'peptide': 177} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 174} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 1382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1382 Classifications: {'peptide': 178} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 1373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1373 Classifications: {'peptide': 177} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 174} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1370 Classifications: {'peptide': 177} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 174} Chain breaks: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {'OLC': 1, 'PLM': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "B" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 85 Unusual residues: {'OLC': 1, 'PLM': 1, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'OLC': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'OLC': 1, 'PLM': 1, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "F" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 94 Unusual residues: {'PLM': 1, 'POV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 6 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 A 623 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 623 " occ=0.50 residue: pdb=" N APHE B 623 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE B 623 " occ=0.50 residue: pdb=" N APHE C 623 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE C 623 " occ=0.50 residue: pdb=" N APHE D 574 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE D 574 " occ=0.50 residue: pdb=" N APHE D 623 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE D 623 " occ=0.50 Time building chain proxies: 6.28, per 1000 atoms: 0.35 Number of scatterers: 18089 At special positions: 0 Unit cell: (115.64, 124.313, 137.323, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 124 16.00 P 5 15.00 O 3223 8.00 N 2845 7.00 C 11892 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.02 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.04 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 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=2.06 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=2.06 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 68 " distance=2.02 Simple disulfide: pdb=" SG CYS H 67 " - pdb=" SG CYS H 77 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.63 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4150 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 27 sheets defined 60.5% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 416 through 419 Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 461 through 469 Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 515 through 519 removed outlier: 3.700A 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 629 Processing helix chain 'A' and resid 635 through 641 Processing helix chain 'A' and resid 653 through 662 Processing helix chain 'A' and resid 664 through 677 removed outlier: 3.719A pdb=" N SER A 676 " --> pdb=" O THR A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 696 Processing helix chain 'A' and resid 706 through 714 removed outlier: 3.548A pdb=" N GLN A 714 " --> pdb=" O GLU A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 756 Processing helix chain 'A' and resid 757 through 768 Processing helix chain 'A' and resid 788 through 791 Processing helix chain 'A' and resid 792 through 820 removed outlier: 3.584A 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 416 through 419 Processing helix chain 'B' and resid 423 through 437 Processing helix chain 'B' and resid 461 through 469 Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.626A 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 625 Processing helix chain 'B' and resid 636 through 637 No H-bonds generated for 'chain 'B' and resid 636 through 637' Processing helix chain 'B' and resid 639 through 642 Processing helix chain 'B' and resid 653 through 662 Processing helix chain 'B' and resid 664 through 677 removed outlier: 3.670A pdb=" N SER B 676 " --> pdb=" O THR B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 696 Processing helix chain 'B' and resid 706 through 714 removed outlier: 3.541A pdb=" N GLN B 714 " --> pdb=" O GLU B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 756 Processing helix chain 'B' and resid 757 through 768 Processing helix chain 'B' and resid 792 through 823 removed outlier: 3.594A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LYS B 823 " --> pdb=" O ARG B 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 415 Processing helix chain 'C' and resid 416 through 419 Processing helix chain 'C' and resid 423 through 437 Processing helix chain 'C' and resid 461 through 469 Processing helix chain 'C' and resid 482 through 487 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: 3.646A pdb=" N GLU C 550 " --> pdb=" O SER C 547 " (cutoff:3.500A) removed outlier: 3.896A 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 626 Processing helix chain 'C' and resid 635 through 641 Processing helix chain 'C' and resid 653 through 662 Processing helix chain 'C' and resid 664 through 677 removed outlier: 3.720A pdb=" N SER C 676 " --> pdb=" O THR C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 685 through 696 Processing helix chain 'C' and resid 706 through 714 removed outlier: 3.561A pdb=" N GLN C 714 " --> pdb=" O GLU C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 742 through 756 Processing helix chain 'C' and resid 757 through 768 Processing helix chain 'C' and resid 792 through 821 removed outlier: 3.684A 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 416 through 419 Processing helix chain 'D' and resid 423 through 437 Processing helix chain 'D' and resid 461 through 469 Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.745A 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: 3.614A pdb=" N TRP D 578 " --> pdb=" O BPHE D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 626 Processing helix chain 'D' and resid 653 through 662 Processing helix chain 'D' and resid 664 through 677 removed outlier: 3.617A pdb=" N SER D 676 " --> pdb=" O THR D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 696 Processing helix chain 'D' and resid 708 through 709 No H-bonds generated for 'chain 'D' and resid 708 through 709' Processing helix chain 'D' and resid 711 through 715 Processing helix chain 'D' and resid 742 through 756 Processing helix chain 'D' and resid 757 through 768 Processing helix chain 'D' and resid 788 through 791 Processing helix chain 'D' and resid 792 through 823 removed outlier: 3.535A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (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 125 Processing helix chain 'E' and resid 133 through 160 removed outlier: 3.735A 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: 3.565A pdb=" N LEU F 98 " --> pdb=" O ALA F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 127 removed outlier: 3.864A pdb=" N GLU F 126 " --> pdb=" O ILE F 122 " (cutoff:3.500A) removed outlier: 3.812A 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: 3.560A 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: 4.044A pdb=" N GLU G 126 " --> pdb=" O ILE G 122 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N PHE G 127 " --> pdb=" O ALA G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 162 removed outlier: 3.811A 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: 3.990A pdb=" N MET H 10 " --> pdb=" O ARG H 6 " (cutoff:3.500A) removed outlier: 4.132A 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: 3.525A pdb=" N ALA H 161 " --> pdb=" O ILE H 157 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 210 removed outlier: 4.014A pdb=" N TYR H 181 " --> pdb=" O GLY H 177 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 440 through 444 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 496 through 498 removed outlier: 3.844A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.354A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 440 through 444 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 489 through 491 Processing sheet with id=AA9, first strand: chain 'B' and resid 496 through 498 removed outlier: 3.824A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.332A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 440 through 444 Processing sheet with id=AB3, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AB4, first strand: chain 'C' and resid 489 through 491 Processing sheet with id=AB5, first strand: chain 'C' and resid 496 through 498 removed outlier: 3.854A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.358A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 8.823A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 440 through 444 Processing sheet with id=AB8, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AB9, first strand: chain 'D' and resid 489 through 491 Processing sheet with id=AC1, first strand: chain 'D' and resid 496 through 498 removed outlier: 3.818A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 500 through 501 Processing sheet with id=AC3, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.312A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'E' and resid 34 through 38 Processing sheet with id=AC5, first strand: chain 'F' and resid 37 through 38 Processing sheet with id=AC6, first strand: chain 'F' and resid 65 through 67 removed outlier: 3.829A pdb=" N LYS F 78 " --> pdb=" O THR F 66 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 77 through 79 Processing sheet with id=AC8, first strand: chain 'H' and resid 36 through 38 Processing sheet with id=AC9, first strand: chain 'H' and resid 65 through 67 1117 hydrogen bonds defined for protein. 3220 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.61 Time building geometry restraints manager: 2.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.52: 14694 1.52 - 1.88: 3769 1.88 - 2.24: 0 2.24 - 2.61: 0 2.61 - 2.97: 1 Bond restraints: 18464 Sorted by residual: bond pdb=" C PRO D 717 " pdb=" N ASP D 719 " ideal model delta sigma weight residual 1.332 2.966 -1.634 1.40e-02 5.10e+03 1.36e+04 bond pdb=" C SER C 785 " pdb=" O SER C 785 " ideal model delta sigma weight residual 1.235 1.162 0.073 1.26e-02 6.30e+03 3.36e+01 bond pdb=" N LEU B 624 " pdb=" CA LEU B 624 " ideal model delta sigma weight residual 1.458 1.397 0.060 1.29e-02 6.01e+03 2.18e+01 bond pdb=" N VAL B 488 " pdb=" CA VAL B 488 " ideal model delta sigma weight residual 1.456 1.498 -0.042 9.50e-03 1.11e+04 1.91e+01 bond pdb=" N VAL D 488 " pdb=" CA VAL D 488 " ideal model delta sigma weight residual 1.456 1.498 -0.041 9.50e-03 1.11e+04 1.88e+01 ... (remaining 18459 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.82: 24813 6.82 - 13.63: 30 13.63 - 20.45: 1 20.45 - 27.27: 0 27.27 - 34.08: 1 Bond angle restraints: 24845 Sorted by residual: angle pdb=" O PRO D 717 " pdb=" C PRO D 717 " pdb=" N ASP D 719 " ideal model delta sigma weight residual 121.10 87.02 34.08 1.90e+00 2.77e-01 3.22e+02 angle pdb=" N ASP C 590 " pdb=" CA ASP C 590 " pdb=" C ASP C 590 " ideal model delta sigma weight residual 113.88 104.55 9.33 1.23e+00 6.61e-01 5.76e+01 angle pdb=" CA APHE B 623 " pdb=" C APHE B 623 " pdb=" N LEU B 624 " ideal model delta sigma weight residual 117.02 108.28 8.74 1.17e+00 7.31e-01 5.58e+01 angle pdb=" N CYS D 773 " pdb=" CA CYS D 773 " pdb=" C CYS D 773 " ideal model delta sigma weight residual 111.87 102.02 9.85 1.41e+00 5.03e-01 4.88e+01 angle pdb=" C APHE B 623 " pdb=" N LEU B 624 " pdb=" CA LEU B 624 " ideal model delta sigma weight residual 120.63 109.41 11.22 1.61e+00 3.86e-01 4.86e+01 ... (remaining 24840 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.04: 10285 29.04 - 58.09: 431 58.09 - 87.13: 51 87.13 - 116.18: 8 116.18 - 145.22: 2 Dihedral angle restraints: 10777 sinusoidal: 4255 harmonic: 6522 Sorted by residual: dihedral pdb=" CA PRO D 717 " pdb=" C PRO D 717 " pdb=" N ASP D 719 " pdb=" CA ASP D 719 " ideal model delta harmonic sigma weight residual -180.00 -79.07 -100.93 0 5.00e+00 4.00e-02 4.07e+02 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 25.21 67.79 1 1.00e+01 1.00e-02 5.97e+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 36.95 56.05 1 1.00e+01 1.00e-02 4.24e+01 ... (remaining 10774 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 1511 0.088 - 0.177: 1067 0.177 - 0.265: 164 0.265 - 0.354: 20 0.354 - 0.442: 3 Chirality restraints: 2765 Sorted by residual: chirality pdb=" CG LEU D 498 " pdb=" CB LEU D 498 " pdb=" CD1 LEU D 498 " pdb=" CD2 LEU D 498 " both_signs ideal model delta sigma weight residual False -2.59 -2.15 -0.44 2.00e-01 2.50e+01 4.89e+00 chirality pdb=" CG LEU B 498 " pdb=" CB LEU B 498 " pdb=" CD1 LEU B 498 " pdb=" CD2 LEU B 498 " both_signs ideal model delta sigma weight residual False -2.59 -2.19 -0.40 2.00e-01 2.50e+01 3.93e+00 chirality pdb=" CB VAL D 746 " pdb=" CA VAL D 746 " pdb=" CG1 VAL D 746 " pdb=" CG2 VAL D 746 " both_signs ideal model delta sigma weight residual False -2.63 -2.24 -0.39 2.00e-01 2.50e+01 3.88e+00 ... (remaining 2762 not shown) Planarity restraints: 3012 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO D 717 " 0.149 2.00e-02 2.50e+03 1.91e-01 3.63e+02 pdb=" C PRO D 717 " -0.325 2.00e-02 2.50e+03 pdb=" O PRO D 717 " 0.118 2.00e-02 2.50e+03 pdb=" N ASP D 719 " 0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA APHE B 623 " -0.039 2.00e-02 2.50e+03 8.07e-02 6.51e+01 pdb=" C APHE B 623 " 0.139 2.00e-02 2.50e+03 pdb=" O APHE B 623 " -0.055 2.00e-02 2.50e+03 pdb=" N LEU B 624 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA BPHE B 623 " -0.039 2.00e-02 2.50e+03 8.00e-02 6.40e+01 pdb=" C BPHE B 623 " 0.138 2.00e-02 2.50e+03 pdb=" O BPHE B 623 " -0.055 2.00e-02 2.50e+03 pdb=" N LEU B 624 " -0.045 2.00e-02 2.50e+03 ... (remaining 3009 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 432 2.68 - 3.24: 18100 3.24 - 3.79: 28163 3.79 - 4.35: 39663 4.35 - 4.90: 64037 Nonbonded interactions: 150395 Sorted by model distance: nonbonded pdb=" OG SER C 547 " pdb=" OE2 GLU C 550 " model vdw 2.127 3.040 nonbonded pdb=" O LYS E 129 " pdb=" OG1 THR E 130 " model vdw 2.217 3.040 nonbonded pdb=" O SER E 104 " pdb=" N ILE E 106 " model vdw 2.283 3.120 nonbonded pdb=" CZ APHE B 623 " pdb=" O SER C 785 " model vdw 2.285 3.340 nonbonded pdb=" OG SER A 592 " pdb=" OD2 ASP B 590 " model vdw 2.291 3.040 ... (remaining 150390 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 504 or (resid 505 through 506 and (name N or n \ ame CA or name C or name O or name CB )) or resid 510 through 573 or resid 575 t \ hrough 593 or (resid 594 and (name N or name CA or name C or name O or name CB ) \ ) or resid 595 through 622 or resid 624 through 626 or resid 633 or resid 635 or \ resid 637 or resid 639 through 709 or resid 711 through 717 or resid 721 throug \ h 812 or (resid 813 and (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 504 or (resid 505 through 506 and (name N or n \ ame CA or name C or name O or name CB )) or resid 510 or (resid 511 and (name N \ or name CA or name C or name O or name CB )) or resid 512 through 551 or (resid \ 569 and (name N or name CA or name C or name O or name CB )) or resid 570 throug \ h 573 or resid 575 or (resid 576 and (name N or name CA or name C or name O or n \ ame CB )) or resid 577 through 593 or (resid 594 and (name N or name CA or name \ C or name O or name CB )) or resid 595 through 622 or resid 624 through 626 or r \ esid 633 through 635 or resid 637 through 709 or resid 711 through 717 or resid \ 721 through 774 or (resid 784 and (name N or name CA or name C or name O or name \ CB )) or resid 785 through 823)) selection = (chain 'C' and (resid 393 through 504 or (resid 505 through 506 and (name N or n \ ame CA or name C or name O or name CB )) or resid 510 through 573 or resid 575 o \ r (resid 576 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 77 through 622 or resid 624 through 626 or resid 633 or resid 635 or resid 637 o \ r resid 639 through 709 or resid 711 through 717 or resid 721 through 812 or (re \ sid 813 and (name N or name CA or name C or name O or name CB )) or resid 814 th \ rough 818 or (resid 819 through 823 and (name N or name CA or name C or name O o \ r name CB )))) selection = (chain 'D' and (resid 393 through 510 or (resid 511 and (name N or name CA or na \ me C or name O or name CB )) or resid 512 through 551 or (resid 569 and (name N \ or name CA or name C or name O or name CB )) or resid 570 through 573 or resid 5 \ 75 or (resid 576 and (name N or name CA or name C or name O or name CB )) or res \ id 577 through 593 or (resid 594 and (name N or name CA or name C or name O or n \ ame CB )) or resid 595 through 622 or resid 624 through 633 or resid 635 through \ 637 or resid 639 through 717 or resid 721 through 774 or (resid 784 and (name N \ or name CA or name C or name O or name CB )) or resid 785 through 823)) } ncs_group { reference = (chain 'E' and (resid 5 through 69 or (resid 70 and (name N or name CA or name C \ or name O or name CB )) or resid 71 through 84 or resid 93 through 210)) selection = (chain 'F' and (resid 5 through 42 or resid 55 through 69 or (resid 70 and (name \ N or name CA or name C or name O or name CB )) or resid 71 through 84 or resid \ 93 through 210)) selection = (chain 'G' and (resid 5 through 69 or (resid 70 and (name N or name CA or name C \ or name O or name CB )) or resid 71 through 84 or resid 93 through 210)) selection = (chain 'H' and (resid 5 through 42 or resid 55 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.240 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 18.970 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5148 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 : 0.017 1.634 18475 Z= 1.224 Angle : 1.486 34.082 24867 Z= 1.046 Chirality : 0.105 0.442 2765 Planarity : 0.014 0.267 3012 Dihedral : 15.860 145.221 6594 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.62 % Favored : 96.02 % Rotamer: Outliers : 1.59 % Allowed : 3.01 % Favored : 95.40 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.17), residues: 2228 helix: 1.09 (0.14), residues: 1312 sheet: -1.92 (0.39), residues: 93 loop : -1.89 (0.19), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG A 628 TYR 0.045 0.005 TYR B 469 PHE 0.034 0.005 PHE C 517 TRP 0.029 0.006 TRP B 578 HIS 0.011 0.003 HIS G 60 Details of bonding type rmsd covalent geometry : bond 0.01712 (18464) covalent geometry : angle 1.48387 (24845) SS BOND : bond 0.01568 ( 11) SS BOND : angle 2.98649 ( 22) hydrogen bonds : bond 0.13171 ( 1117) hydrogen bonds : angle 5.26290 ( 3220) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 350 time to evaluate : 0.588 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: symmetry clash revert: symmetry clash REVERT: B 523 TYR cc_start: 0.9118 (t80) cc_final: 0.8858 (t80) REVERT: B 585 MET cc_start: 0.9335 (mmt) cc_final: 0.8952 (mmt) REVERT: B 770 LYS cc_start: -0.0146 (OUTLIER) cc_final: -0.0384 (pttm) REVERT: C 585 MET cc_start: 0.9164 (mmt) cc_final: 0.8895 (mmm) REVERT: C 586 ARG cc_start: 0.9228 (mmm-85) cc_final: 0.8832 (tmt170) REVERT: D 585 MET cc_start: 0.9521 (mmt) cc_final: 0.9245 (mmt) REVERT: D 619 ASN cc_start: 0.9187 (t0) cc_final: 0.8705 (t0) REVERT: D 803 LEU cc_start: 0.9380 (mp) cc_final: 0.9080 (mp) REVERT: F 9 GLN cc_start: 0.8512 (mm-40) cc_final: 0.8301 (mt0) REVERT: F 24 MET cc_start: 0.9114 (tpt) cc_final: 0.8804 (tpp) REVERT: F 56 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8340 (mm-30) REVERT: F 92 ASP cc_start: 0.7768 (p0) cc_final: 0.6598 (p0) REVERT: F 191 GLU cc_start: 0.9338 (mm-30) cc_final: 0.9114 (mm-30) REVERT: F 192 MET cc_start: 0.8598 (mtt) cc_final: 0.8096 (tmm) REVERT: F 206 LYS cc_start: 0.9056 (mtpt) cc_final: 0.8782 (mttt) REVERT: H 24 MET cc_start: 0.9153 (tpt) cc_final: 0.8944 (tpp) outliers start: 29 outliers final: 11 residues processed: 373 average time/residue: 0.1571 time to fit residues: 82.6248 Evaluate side-chains 209 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 197 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 770 LYS Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 743 ARG Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain B residue 770 LYS Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 743 ARG Chi-restraints excluded: chain C residue 787 LEU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 746 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 216 optimal weight: 0.6980 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 7.9990 chunk 212 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 619 ASN D 435 HIS E 79 GLN E 160 ASN F 132 HIS F 205 HIS ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.143230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.084243 restraints weight = 137626.909| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 8.14 r_work: 0.2870 rms_B_bonded: 6.40 restraints_weight: 2.0000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2873 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2873 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 18475 Z= 0.141 Angle : 0.629 9.501 24867 Z= 0.325 Chirality : 0.043 0.228 2765 Planarity : 0.004 0.082 3012 Dihedral : 11.712 106.413 2823 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.40 % Favored : 98.37 % Rotamer: Outliers : 1.48 % Allowed : 10.56 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.18), residues: 2230 helix: 2.35 (0.14), residues: 1312 sheet: -1.56 (0.36), residues: 150 loop : -1.26 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 675 TYR 0.020 0.001 TYR A 711 PHE 0.021 0.001 PHE A 495 TRP 0.026 0.001 TRP D 460 HIS 0.011 0.001 HIS G 60 Details of bonding type rmsd covalent geometry : bond 0.00308 (18464) covalent geometry : angle 0.62687 (24845) SS BOND : bond 0.00416 ( 11) SS BOND : angle 1.81304 ( 22) hydrogen bonds : bond 0.04335 ( 1117) hydrogen bonds : angle 4.14593 ( 3220) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4460 Ramachandran restraints generated. 2230 Oldfield, 0 Emsley, 2230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4460 Ramachandran restraints generated. 2230 Oldfield, 0 Emsley, 2230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 241 time to evaluate : 0.553 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: symmetry clash REVERT: A 414 MET cc_start: 0.8251 (mpp) cc_final: 0.7550 (ptp) REVERT: A 463 MET cc_start: 0.8524 (mpp) cc_final: 0.7361 (tpp) REVERT: A 479 LEU cc_start: 0.8280 (tp) cc_final: 0.7814 (mt) REVERT: A 503 MET cc_start: -0.1509 (tmm) cc_final: -0.1929 (ttt) REVERT: A 551 TRP cc_start: 0.6601 (m-10) cc_final: 0.5998 (m-10) REVERT: A 587 GLN cc_start: 0.9095 (tp40) cc_final: 0.8731 (mm-40) REVERT: A 674 MET cc_start: 0.5741 (mtm) cc_final: 0.5032 (ptt) REVERT: B 496 MET cc_start: 0.7140 (mmm) cc_final: 0.6607 (mmm) REVERT: B 585 MET cc_start: 0.9409 (mmt) cc_final: 0.9059 (mmm) REVERT: B 670 MET cc_start: 0.7503 (mmm) cc_final: 0.6959 (mmm) REVERT: C 585 MET cc_start: 0.9122 (mmt) cc_final: 0.8787 (mmm) REVERT: C 586 ARG cc_start: 0.9066 (mmm-85) cc_final: 0.8818 (tmt-80) REVERT: C 619 ASN cc_start: 0.9487 (t0) cc_final: 0.9244 (t0) REVERT: C 670 MET cc_start: 0.6161 (mmm) cc_final: 0.5891 (mmm) REVERT: D 414 MET cc_start: 0.8335 (mpp) cc_final: 0.7749 (mmp) REVERT: D 503 MET cc_start: 0.7194 (mmm) cc_final: 0.6400 (mmm) REVERT: D 551 TRP cc_start: 0.7535 (m100) cc_final: 0.7315 (m100) REVERT: D 619 ASN cc_start: 0.9445 (t0) cc_final: 0.9086 (t0) REVERT: D 639 LEU cc_start: 0.8653 (pt) cc_final: 0.8202 (pt) REVERT: D 670 MET cc_start: 0.6151 (mtt) cc_final: 0.5543 (tpp) REVERT: E 56 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7574 (tp30) REVERT: F 126 GLU cc_start: 0.8948 (tp30) cc_final: 0.8689 (tp30) REVERT: F 192 MET cc_start: 0.8980 (mtt) cc_final: 0.8581 (tmm) REVERT: F 206 LYS cc_start: 0.9154 (mtpt) cc_final: 0.8826 (mttt) REVERT: G 122 ILE cc_start: 0.9237 (tp) cc_final: 0.9000 (tp) REVERT: H 24 MET cc_start: 0.9255 (tpt) cc_final: 0.8958 (mmm) REVERT: H 102 ARG cc_start: 0.9033 (tpt90) cc_final: 0.8623 (tpt170) REVERT: H 203 ASP cc_start: 0.9173 (t0) cc_final: 0.8922 (t0) outliers start: 27 outliers final: 12 residues processed: 260 average time/residue: 0.1430 time to fit residues: 55.2908 Evaluate side-chains 208 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 196 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 787 LEU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain G residue 208 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 7 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 174 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 30 optimal weight: 0.0870 chunk 82 optimal weight: 8.9990 chunk 209 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 overall best weight: 2.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 GLN ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 HIS ** D 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 569 ASN E 160 ASN G 160 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.137714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.077813 restraints weight = 127342.189| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 7.76 r_work: 0.2756 rms_B_bonded: 6.42 restraints_weight: 2.0000 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2755 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2755 r_free = 0.2755 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2755 r_free = 0.2755 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2755 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 18475 Z= 0.246 Angle : 0.672 9.956 24867 Z= 0.347 Chirality : 0.045 0.185 2765 Planarity : 0.004 0.068 3012 Dihedral : 11.023 88.144 2803 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.58 % Favored : 97.24 % Rotamer: Outliers : 2.19 % Allowed : 12.26 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.42 (0.18), residues: 2230 helix: 2.36 (0.14), residues: 1325 sheet: -1.64 (0.38), residues: 136 loop : -1.15 (0.22), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 715 TYR 0.019 0.002 TYR B 673 PHE 0.022 0.002 PHE E 107 TRP 0.040 0.002 TRP A 766 HIS 0.010 0.001 HIS G 60 Details of bonding type rmsd covalent geometry : bond 0.00563 (18464) covalent geometry : angle 0.66886 (24845) SS BOND : bond 0.01369 ( 11) SS BOND : angle 2.13848 ( 22) hydrogen bonds : bond 0.04908 ( 1117) hydrogen bonds : angle 4.31726 ( 3220) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4460 Ramachandran restraints generated. 2230 Oldfield, 0 Emsley, 2230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4460 Ramachandran restraints generated. 2230 Oldfield, 0 Emsley, 2230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 189 time to evaluate : 0.689 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: A 414 MET cc_start: 0.8426 (mpp) cc_final: 0.7663 (ptp) REVERT: A 463 MET cc_start: 0.8723 (mpp) cc_final: 0.7942 (mpp) REVERT: A 496 MET cc_start: 0.4878 (tpt) cc_final: 0.4666 (ttt) REVERT: A 503 MET cc_start: -0.1614 (tmm) cc_final: -0.1961 (ttt) REVERT: A 674 MET cc_start: 0.5785 (mtm) cc_final: 0.4852 (ptp) REVERT: A 708 MET cc_start: 0.4885 (mpp) cc_final: 0.4234 (mmt) REVERT: A 715 ARG cc_start: 0.5996 (mmp-170) cc_final: 0.5374 (mmp-170) REVERT: B 670 MET cc_start: 0.7157 (mmm) cc_final: 0.6612 (mmm) REVERT: C 408 MET cc_start: 0.2244 (mmp) cc_final: 0.2034 (mmp) REVERT: C 585 MET cc_start: 0.9196 (mmt) cc_final: 0.8740 (mmm) REVERT: C 619 ASN cc_start: 0.9541 (t0) cc_final: 0.9246 (t0) REVERT: C 670 MET cc_start: 0.6150 (mmm) cc_final: 0.5908 (mmt) REVERT: D 407 MET cc_start: 0.7992 (pmm) cc_final: 0.7427 (pmm) REVERT: D 503 MET cc_start: 0.6660 (mmm) cc_final: 0.6281 (mmm) REVERT: D 551 TRP cc_start: 0.7954 (m100) cc_final: 0.7709 (m100) REVERT: D 619 ASN cc_start: 0.9541 (t0) cc_final: 0.9181 (t0) REVERT: E 10 MET cc_start: 0.8944 (mmm) cc_final: 0.8471 (tmm) REVERT: E 56 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7639 (tp30) REVERT: E 58 MET cc_start: 0.9172 (mmm) cc_final: 0.8875 (mmp) REVERT: F 81 ASP cc_start: 0.8556 (t0) cc_final: 0.8355 (t0) REVERT: F 117 MET cc_start: 0.8750 (mmm) cc_final: 0.8452 (mmm) REVERT: F 126 GLU cc_start: 0.9006 (tp30) cc_final: 0.8736 (tp30) REVERT: F 192 MET cc_start: 0.9013 (mtt) cc_final: 0.8730 (ttt) REVERT: F 206 LYS cc_start: 0.9276 (mtpt) cc_final: 0.8989 (mttt) REVERT: G 117 MET cc_start: 0.9325 (mmm) cc_final: 0.9079 (mmm) REVERT: H 203 ASP cc_start: 0.9313 (t0) cc_final: 0.9061 (t0) outliers start: 40 outliers final: 29 residues processed: 218 average time/residue: 0.1373 time to fit residues: 45.0211 Evaluate side-chains 196 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 167 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 527 MET Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 787 LEU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 117 MET Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 41 LYS Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 160 ASN Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 150 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 84 optimal weight: 9.9990 chunk 86 optimal weight: 2.9990 chunk 106 optimal weight: 20.0000 chunk 164 optimal weight: 0.5980 chunk 181 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 176 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 412 HIS D 791 ASN ** G 160 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 = 0.4257 r_free = 0.4257 target = 0.140333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.080617 restraints weight = 111977.079| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 6.68 r_work: 0.2872 rms_B_bonded: 5.61 restraints_weight: 2.0000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2878 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2878 r_free = 0.2878 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2878 r_free = 0.2878 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2878 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 18475 Z= 0.155 Angle : 0.589 9.557 24867 Z= 0.301 Chirality : 0.042 0.246 2765 Planarity : 0.004 0.060 3012 Dihedral : 10.239 89.140 2803 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.03 % Favored : 97.78 % Rotamer: Outliers : 2.52 % Allowed : 12.37 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.78 (0.19), residues: 2230 helix: 2.69 (0.14), residues: 1325 sheet: -1.74 (0.36), residues: 149 loop : -1.03 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 715 TYR 0.024 0.001 TYR A 424 PHE 0.016 0.001 PHE A 659 TRP 0.039 0.001 TRP A 551 HIS 0.009 0.001 HIS G 60 Details of bonding type rmsd covalent geometry : bond 0.00348 (18464) covalent geometry : angle 0.58623 (24845) SS BOND : bond 0.01727 ( 11) SS BOND : angle 1.96785 ( 22) hydrogen bonds : bond 0.04049 ( 1117) hydrogen bonds : angle 4.02954 ( 3220) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4460 Ramachandran restraints generated. 2230 Oldfield, 0 Emsley, 2230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4460 Ramachandran restraints generated. 2230 Oldfield, 0 Emsley, 2230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 195 time to evaluate : 0.716 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: symmetry clash REVERT: A 414 MET cc_start: 0.8410 (mpp) cc_final: 0.7727 (ptp) REVERT: A 463 MET cc_start: 0.8573 (mpp) cc_final: 0.7898 (mpp) REVERT: A 503 MET cc_start: -0.1675 (tmm) cc_final: -0.1880 (ttt) REVERT: A 670 MET cc_start: 0.6714 (mmm) cc_final: 0.6391 (mmm) REVERT: A 674 MET cc_start: 0.5574 (mtm) cc_final: 0.4691 (ptp) REVERT: A 708 MET cc_start: 0.4577 (mpp) cc_final: 0.4233 (mmt) REVERT: B 670 MET cc_start: 0.7501 (mmm) cc_final: 0.7062 (mmm) REVERT: C 585 MET cc_start: 0.9044 (mmt) cc_final: 0.8482 (mmm) REVERT: C 619 ASN cc_start: 0.9543 (t0) cc_final: 0.9259 (t0) REVERT: C 670 MET cc_start: 0.6123 (mmm) cc_final: 0.5827 (mmt) REVERT: D 407 MET cc_start: 0.7989 (pmm) cc_final: 0.7441 (pmm) REVERT: D 414 MET cc_start: 0.8461 (ptp) cc_final: 0.8202 (mmp) REVERT: D 503 MET cc_start: 0.7205 (mmm) cc_final: 0.6370 (mmm) REVERT: D 619 ASN cc_start: 0.9478 (t0) cc_final: 0.9035 (t0) REVERT: D 670 MET cc_start: 0.6586 (mtt) cc_final: 0.6341 (mmm) REVERT: E 10 MET cc_start: 0.8921 (mmm) cc_final: 0.8539 (mmm) REVERT: E 56 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7557 (tp30) REVERT: E 69 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8201 (pt) REVERT: F 10 MET cc_start: 0.9452 (tpp) cc_final: 0.9202 (tpp) REVERT: F 117 MET cc_start: 0.8605 (mmm) cc_final: 0.8354 (mmm) REVERT: F 126 GLU cc_start: 0.8948 (tp30) cc_final: 0.8704 (tp30) REVERT: F 192 MET cc_start: 0.8951 (mtt) cc_final: 0.8746 (ttt) REVERT: F 206 LYS cc_start: 0.9250 (mtpt) cc_final: 0.8957 (mttt) REVERT: G 18 PHE cc_start: 0.8482 (t80) cc_final: 0.8252 (t80) REVERT: G 117 MET cc_start: 0.9217 (mmm) cc_final: 0.8946 (mmm) REVERT: G 160 ASN cc_start: 0.8487 (m-40) cc_final: 0.8193 (m110) REVERT: H 203 ASP cc_start: 0.9192 (t0) cc_final: 0.8963 (t0) outliers start: 45 outliers final: 30 residues processed: 224 average time/residue: 0.1392 time to fit residues: 47.0431 Evaluate side-chains 212 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 181 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 527 MET Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 787 LEU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain D residue 784 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 117 MET Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 67 CYS Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 41 LYS Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 66 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 187 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 172 optimal weight: 0.9990 chunk 200 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 198 optimal weight: 0.3980 chunk 154 optimal weight: 0.8980 chunk 118 optimal weight: 8.9990 chunk 6 optimal weight: 0.0470 chunk 93 optimal weight: 4.9990 overall best weight: 0.8682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 HIS ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.141271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.082334 restraints weight = 97197.698| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 6.11 r_work: 0.2922 rms_B_bonded: 5.22 restraints_weight: 2.0000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2927 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2927 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.4087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 18475 Z= 0.121 Angle : 0.568 11.490 24867 Z= 0.288 Chirality : 0.041 0.222 2765 Planarity : 0.004 0.060 3012 Dihedral : 9.566 86.002 2803 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.81 % Favored : 98.01 % Rotamer: Outliers : 2.19 % Allowed : 12.75 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.01 (0.19), residues: 2230 helix: 2.90 (0.14), residues: 1318 sheet: -1.55 (0.39), residues: 140 loop : -1.00 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 715 TYR 0.020 0.001 TYR A 424 PHE 0.024 0.001 PHE A 659 TRP 0.031 0.001 TRP A 551 HIS 0.008 0.001 HIS G 60 Details of bonding type rmsd covalent geometry : bond 0.00265 (18464) covalent geometry : angle 0.56603 (24845) SS BOND : bond 0.00653 ( 11) SS BOND : angle 1.53987 ( 22) hydrogen bonds : bond 0.03736 ( 1117) hydrogen bonds : angle 3.89982 ( 3220) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4460 Ramachandran restraints generated. 2230 Oldfield, 0 Emsley, 2230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4460 Ramachandran restraints generated. 2230 Oldfield, 0 Emsley, 2230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 198 time to evaluate : 0.674 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: A 414 MET cc_start: 0.8411 (mpp) cc_final: 0.7863 (ptp) REVERT: A 479 LEU cc_start: 0.8359 (tp) cc_final: 0.8063 (pt) REVERT: A 503 MET cc_start: -0.2053 (tmm) cc_final: -0.2276 (ttt) REVERT: A 674 MET cc_start: 0.5492 (mtm) cc_final: 0.4600 (ptp) REVERT: A 708 MET cc_start: 0.4875 (mpp) cc_final: 0.4418 (mmt) REVERT: A 715 ARG cc_start: 0.5014 (OUTLIER) cc_final: 0.4807 (mmp-170) REVERT: B 407 MET cc_start: 0.5398 (mpp) cc_final: 0.5113 (mpp) REVERT: B 496 MET cc_start: 0.7321 (mmm) cc_final: 0.6388 (mmm) REVERT: B 670 MET cc_start: 0.7714 (mmm) cc_final: 0.7217 (mmm) REVERT: B 726 ASN cc_start: 0.8080 (m-40) cc_final: 0.7859 (t0) REVERT: C 585 MET cc_start: 0.8976 (mmt) cc_final: 0.8490 (mmt) REVERT: C 619 ASN cc_start: 0.9531 (t0) cc_final: 0.9225 (t0) REVERT: D 407 MET cc_start: 0.7976 (pmm) cc_final: 0.7428 (pmm) REVERT: D 414 MET cc_start: 0.8319 (ptp) cc_final: 0.8077 (mmm) REVERT: D 496 MET cc_start: 0.4903 (mtp) cc_final: 0.4594 (mtp) REVERT: D 503 MET cc_start: 0.7197 (mmm) cc_final: 0.6514 (mmm) REVERT: D 619 ASN cc_start: 0.9485 (t0) cc_final: 0.8997 (t0) REVERT: D 670 MET cc_start: 0.6642 (mtt) cc_final: 0.6440 (mmm) REVERT: E 56 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7606 (tp30) REVERT: F 126 GLU cc_start: 0.8901 (tp30) cc_final: 0.8665 (tp30) REVERT: F 206 LYS cc_start: 0.9259 (mtpt) cc_final: 0.8973 (mttt) REVERT: G 99 ARG cc_start: 0.9352 (mmm-85) cc_final: 0.8770 (mmm-85) REVERT: G 117 MET cc_start: 0.9205 (mmm) cc_final: 0.8849 (mmm) REVERT: H 37 ARG cc_start: 0.8647 (tpp80) cc_final: 0.7580 (tpp80) REVERT: H 200 MET cc_start: 0.9344 (tpp) cc_final: 0.9114 (mtt) REVERT: H 203 ASP cc_start: 0.9110 (t0) cc_final: 0.8901 (t0) outliers start: 39 outliers final: 22 residues processed: 228 average time/residue: 0.1282 time to fit residues: 44.5109 Evaluate side-chains 204 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 181 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 715 ARG Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 117 MET Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 41 LYS Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 66 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 124 optimal weight: 0.1980 chunk 44 optimal weight: 9.9990 chunk 4 optimal weight: 2.9990 chunk 199 optimal weight: 5.9990 chunk 154 optimal weight: 0.7980 chunk 216 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 46 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 chunk 170 optimal weight: 3.9990 chunk 70 optimal weight: 30.0000 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 160 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.138178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.078879 restraints weight = 119052.130| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 6.73 r_work: 0.2825 rms_B_bonded: 5.88 restraints_weight: 2.0000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2826 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2826 r_free = 0.2826 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2826 r_free = 0.2826 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2826 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 18475 Z= 0.227 Angle : 0.650 16.424 24867 Z= 0.328 Chirality : 0.044 0.286 2765 Planarity : 0.004 0.054 3012 Dihedral : 9.733 86.542 2801 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.40 % Favored : 97.42 % Rotamer: Outliers : 2.63 % Allowed : 13.25 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.83 (0.19), residues: 2230 helix: 2.69 (0.14), residues: 1329 sheet: -1.32 (0.43), residues: 113 loop : -1.09 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 715 TYR 0.019 0.001 TYR A 424 PHE 0.028 0.002 PHE A 659 TRP 0.025 0.002 TRP A 551 HIS 0.009 0.001 HIS G 60 Details of bonding type rmsd covalent geometry : bond 0.00526 (18464) covalent geometry : angle 0.64543 (24845) SS BOND : bond 0.00674 ( 11) SS BOND : angle 2.53697 ( 22) hydrogen bonds : bond 0.04454 ( 1117) hydrogen bonds : angle 4.15362 ( 3220) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4460 Ramachandran restraints generated. 2230 Oldfield, 0 Emsley, 2230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4460 Ramachandran restraints generated. 2230 Oldfield, 0 Emsley, 2230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 177 time to evaluate : 0.691 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 414 MET cc_start: 0.8395 (mpp) cc_final: 0.7838 (ptp) REVERT: A 479 LEU cc_start: 0.8332 (tp) cc_final: 0.8021 (pt) REVERT: A 503 MET cc_start: -0.1236 (tmm) cc_final: -0.1601 (ttt) REVERT: A 674 MET cc_start: 0.5401 (mtm) cc_final: 0.4220 (ptm) REVERT: A 708 MET cc_start: 0.4615 (mpp) cc_final: 0.4301 (mmt) REVERT: B 496 MET cc_start: 0.7500 (mmm) cc_final: 0.6799 (mmm) REVERT: B 670 MET cc_start: 0.7679 (mmm) cc_final: 0.7177 (mmm) REVERT: C 585 MET cc_start: 0.9142 (mmt) cc_final: 0.8662 (mmt) REVERT: C 619 ASN cc_start: 0.9571 (t0) cc_final: 0.9231 (t0) REVERT: C 670 MET cc_start: 0.6178 (mmm) cc_final: 0.5937 (mmt) REVERT: D 407 MET cc_start: 0.7925 (pmm) cc_final: 0.7346 (pmm) REVERT: D 414 MET cc_start: 0.8315 (ptp) cc_final: 0.8079 (mmm) REVERT: D 503 MET cc_start: 0.7199 (mmm) cc_final: 0.6372 (mmm) REVERT: D 619 ASN cc_start: 0.9517 (t0) cc_final: 0.9131 (t0) REVERT: D 670 MET cc_start: 0.6755 (mtt) cc_final: 0.6454 (mtt) REVERT: E 56 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7672 (tp30) REVERT: F 126 GLU cc_start: 0.8922 (tp30) cc_final: 0.8659 (tp30) REVERT: F 206 LYS cc_start: 0.9279 (mtpt) cc_final: 0.8962 (mttt) REVERT: G 99 ARG cc_start: 0.9390 (mmm-85) cc_final: 0.8757 (mmm-85) REVERT: G 117 MET cc_start: 0.9258 (mmm) cc_final: 0.8975 (mmm) REVERT: H 37 ARG cc_start: 0.8627 (tpp80) cc_final: 0.8370 (mmm160) REVERT: H 203 ASP cc_start: 0.9208 (t0) cc_final: 0.8988 (t0) outliers start: 47 outliers final: 33 residues processed: 211 average time/residue: 0.1406 time to fit residues: 45.0106 Evaluate side-chains 195 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 162 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 527 MET Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain D residue 529 ILE Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 117 MET Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 67 CYS Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 155 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 11 optimal weight: 9.9990 chunk 198 optimal weight: 0.6980 chunk 151 optimal weight: 0.0970 chunk 191 optimal weight: 0.7980 chunk 25 optimal weight: 6.9990 chunk 154 optimal weight: 0.9980 chunk 142 optimal weight: 3.9990 chunk 106 optimal weight: 9.9990 chunk 165 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 169 optimal weight: 0.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 GLN A 714 GLN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 HIS F 205 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.141126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.082287 restraints weight = 118477.436| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 6.38 r_work: 0.2912 rms_B_bonded: 5.79 restraints_weight: 2.0000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2919 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2919 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.4480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 18475 Z= 0.118 Angle : 0.595 9.883 24867 Z= 0.299 Chirality : 0.041 0.225 2765 Planarity : 0.004 0.057 3012 Dihedral : 9.080 85.211 2801 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.72 % Favored : 98.10 % Rotamer: Outliers : 2.35 % Allowed : 13.96 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.06 (0.19), residues: 2230 helix: 2.95 (0.14), residues: 1312 sheet: -1.13 (0.40), residues: 148 loop : -1.03 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 715 TYR 0.013 0.001 TYR A 405 PHE 0.030 0.001 PHE A 659 TRP 0.023 0.001 TRP A 551 HIS 0.007 0.001 HIS G 60 Details of bonding type rmsd covalent geometry : bond 0.00262 (18464) covalent geometry : angle 0.59197 (24845) SS BOND : bond 0.00674 ( 11) SS BOND : angle 2.14588 ( 22) hydrogen bonds : bond 0.03754 ( 1117) hydrogen bonds : angle 3.96403 ( 3220) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4460 Ramachandran restraints generated. 2230 Oldfield, 0 Emsley, 2230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4460 Ramachandran restraints generated. 2230 Oldfield, 0 Emsley, 2230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 193 time to evaluate : 0.569 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 414 MET cc_start: 0.8459 (mpp) cc_final: 0.8031 (ptp) REVERT: A 463 MET cc_start: 0.6997 (mmp) cc_final: 0.6293 (mmp) REVERT: A 479 LEU cc_start: 0.8243 (tp) cc_final: 0.7937 (pt) REVERT: A 487 GLU cc_start: 0.9209 (mt-10) cc_final: 0.8823 (pp20) REVERT: A 503 MET cc_start: -0.1845 (tmm) cc_final: -0.2094 (ttt) REVERT: A 674 MET cc_start: 0.5268 (mtm) cc_final: 0.4074 (ptm) REVERT: A 708 MET cc_start: 0.4972 (mpp) cc_final: 0.4463 (mmt) REVERT: B 496 MET cc_start: 0.7568 (mmm) cc_final: 0.6795 (mmm) REVERT: B 670 MET cc_start: 0.7627 (mmm) cc_final: 0.7113 (mmm) REVERT: C 585 MET cc_start: 0.9052 (mmt) cc_final: 0.8480 (mmt) REVERT: C 619 ASN cc_start: 0.9547 (t0) cc_final: 0.9297 (t0) REVERT: C 670 MET cc_start: 0.6220 (mmm) cc_final: 0.5990 (mmm) REVERT: D 407 MET cc_start: 0.7854 (pmm) cc_final: 0.6978 (pmm) REVERT: D 414 MET cc_start: 0.8288 (ptp) cc_final: 0.8047 (mmm) REVERT: D 496 MET cc_start: 0.4881 (mtp) cc_final: 0.4624 (mtp) REVERT: D 503 MET cc_start: 0.6957 (mmm) cc_final: 0.6187 (mmm) REVERT: D 619 ASN cc_start: 0.9500 (t0) cc_final: 0.8998 (t0) REVERT: D 670 MET cc_start: 0.6780 (mtt) cc_final: 0.6571 (mtt) REVERT: E 56 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7665 (tp30) REVERT: E 99 ARG cc_start: 0.9296 (mtp180) cc_final: 0.8965 (mtp-110) REVERT: F 126 GLU cc_start: 0.8889 (tp30) cc_final: 0.8667 (tp30) REVERT: F 206 LYS cc_start: 0.9257 (mtpt) cc_final: 0.8921 (mttt) REVERT: G 99 ARG cc_start: 0.9365 (mmm-85) cc_final: 0.8730 (mmm-85) REVERT: G 117 MET cc_start: 0.9169 (mmm) cc_final: 0.8899 (mmm) REVERT: G 205 HIS cc_start: 0.8723 (OUTLIER) cc_final: 0.8289 (m-70) REVERT: H 203 ASP cc_start: 0.9115 (t0) cc_final: 0.8904 (t0) outliers start: 42 outliers final: 30 residues processed: 222 average time/residue: 0.1228 time to fit residues: 41.8346 Evaluate side-chains 214 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 183 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 527 MET Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain E residue 117 MET Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 67 CYS Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 155 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 19 optimal weight: 1.9990 chunk 198 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 27 optimal weight: 30.0000 chunk 143 optimal weight: 6.9990 chunk 102 optimal weight: 30.0000 chunk 220 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 9.9990 chunk 209 optimal weight: 4.9990 chunk 107 optimal weight: 10.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.138763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.079354 restraints weight = 127225.074| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 7.12 r_work: 0.2832 rms_B_bonded: 6.14 restraints_weight: 2.0000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2829 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2829 r_free = 0.2829 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2829 r_free = 0.2829 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2829 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.4609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 18475 Z= 0.183 Angle : 0.646 17.943 24867 Z= 0.321 Chirality : 0.042 0.214 2765 Planarity : 0.004 0.055 3012 Dihedral : 9.275 87.304 2801 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.35 % Favored : 97.47 % Rotamer: Outliers : 2.19 % Allowed : 14.29 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.95 (0.19), residues: 2230 helix: 2.87 (0.14), residues: 1313 sheet: -1.41 (0.43), residues: 124 loop : -1.05 (0.22), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 715 TYR 0.012 0.001 TYR D 647 PHE 0.031 0.001 PHE A 659 TRP 0.020 0.001 TRP A 551 HIS 0.007 0.001 HIS G 60 Details of bonding type rmsd covalent geometry : bond 0.00422 (18464) covalent geometry : angle 0.64364 (24845) SS BOND : bond 0.00786 ( 11) SS BOND : angle 1.84124 ( 22) hydrogen bonds : bond 0.04269 ( 1117) hydrogen bonds : angle 4.10643 ( 3220) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4460 Ramachandran restraints generated. 2230 Oldfield, 0 Emsley, 2230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4460 Ramachandran restraints generated. 2230 Oldfield, 0 Emsley, 2230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 173 time to evaluate : 0.557 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 414 MET cc_start: 0.8440 (mpp) cc_final: 0.8123 (ptp) REVERT: A 463 MET cc_start: 0.7332 (mmp) cc_final: 0.6868 (mmp) REVERT: A 479 LEU cc_start: 0.8298 (tp) cc_final: 0.8028 (pt) REVERT: A 487 GLU cc_start: 0.9290 (mt-10) cc_final: 0.8932 (pp20) REVERT: A 503 MET cc_start: -0.1154 (tmm) cc_final: -0.1520 (ttt) REVERT: A 674 MET cc_start: 0.5322 (mtm) cc_final: 0.4111 (ptm) REVERT: A 708 MET cc_start: 0.4697 (mpp) cc_final: 0.4342 (mmt) REVERT: B 496 MET cc_start: 0.7604 (mmm) cc_final: 0.6861 (mmm) REVERT: B 670 MET cc_start: 0.7716 (mmm) cc_final: 0.7215 (mmm) REVERT: C 585 MET cc_start: 0.9062 (mmt) cc_final: 0.8524 (mmt) REVERT: C 619 ASN cc_start: 0.9591 (t0) cc_final: 0.9242 (t0) REVERT: C 670 MET cc_start: 0.6177 (mmm) cc_final: 0.5958 (mmm) REVERT: D 407 MET cc_start: 0.7945 (pmm) cc_final: 0.7047 (pmm) REVERT: D 414 MET cc_start: 0.8326 (ptp) cc_final: 0.8098 (mmm) REVERT: D 496 MET cc_start: 0.4777 (mtp) cc_final: 0.4450 (mtp) REVERT: D 503 MET cc_start: 0.6679 (mmm) cc_final: 0.6086 (mmm) REVERT: D 619 ASN cc_start: 0.9507 (t0) cc_final: 0.9091 (t0) REVERT: D 670 MET cc_start: 0.7308 (mtt) cc_final: 0.7046 (mmm) REVERT: E 10 MET cc_start: 0.8911 (mmm) cc_final: 0.8558 (mmm) REVERT: E 56 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7538 (tp30) REVERT: F 206 LYS cc_start: 0.9281 (mtpt) cc_final: 0.8923 (mttt) REVERT: G 99 ARG cc_start: 0.9409 (mmm-85) cc_final: 0.8835 (mmm-85) REVERT: G 117 MET cc_start: 0.9240 (mmm) cc_final: 0.8875 (mmm) outliers start: 39 outliers final: 38 residues processed: 202 average time/residue: 0.1184 time to fit residues: 36.7226 Evaluate side-chains 205 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 167 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 527 MET Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain E residue 117 MET Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 67 CYS Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 155 VAL 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 122 ILE Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 155 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 94 optimal weight: 2.9990 chunk 150 optimal weight: 10.0000 chunk 154 optimal weight: 0.7980 chunk 155 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 167 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 160 optimal weight: 6.9990 chunk 157 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 72 optimal weight: 9.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.140338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.081238 restraints weight = 134251.470| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 7.06 r_work: 0.2863 rms_B_bonded: 6.30 restraints_weight: 2.0000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2862 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2862 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.4728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 18475 Z= 0.131 Angle : 0.611 12.896 24867 Z= 0.303 Chirality : 0.041 0.174 2765 Planarity : 0.004 0.059 3012 Dihedral : 8.958 86.321 2801 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.99 % Favored : 97.83 % Rotamer: Outliers : 2.03 % Allowed : 15.22 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.04 (0.19), residues: 2230 helix: 2.93 (0.14), residues: 1319 sheet: -1.31 (0.43), residues: 113 loop : -1.08 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 715 TYR 0.013 0.001 TYR D 647 PHE 0.034 0.001 PHE A 659 TRP 0.020 0.001 TRP A 551 HIS 0.012 0.001 HIS F 205 Details of bonding type rmsd covalent geometry : bond 0.00296 (18464) covalent geometry : angle 0.60814 (24845) SS BOND : bond 0.00747 ( 11) SS BOND : angle 2.04348 ( 22) hydrogen bonds : bond 0.03849 ( 1117) hydrogen bonds : angle 3.96291 ( 3220) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4460 Ramachandran restraints generated. 2230 Oldfield, 0 Emsley, 2230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4460 Ramachandran restraints generated. 2230 Oldfield, 0 Emsley, 2230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 182 time to evaluate : 0.668 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: A 463 MET cc_start: 0.7056 (mmp) cc_final: 0.6523 (mmp) REVERT: A 479 LEU cc_start: 0.8374 (tp) cc_final: 0.8130 (pt) REVERT: A 487 GLU cc_start: 0.9279 (mt-10) cc_final: 0.8911 (pp20) REVERT: A 674 MET cc_start: 0.5277 (mtm) cc_final: 0.3953 (ptm) REVERT: A 721 MET cc_start: 0.4207 (mmm) cc_final: 0.3673 (mmm) REVERT: B 496 MET cc_start: 0.7592 (mmm) cc_final: 0.6846 (mmm) REVERT: B 670 MET cc_start: 0.7791 (mmm) cc_final: 0.7282 (mmm) REVERT: C 585 MET cc_start: 0.8999 (mmt) cc_final: 0.8662 (mmm) REVERT: C 619 ASN cc_start: 0.9577 (t0) cc_final: 0.9321 (t0) REVERT: C 670 MET cc_start: 0.6158 (mmm) cc_final: 0.5925 (mmt) REVERT: D 407 MET cc_start: 0.7901 (pmm) cc_final: 0.7001 (pmm) REVERT: D 496 MET cc_start: 0.5400 (mtp) cc_final: 0.5113 (mtp) REVERT: D 503 MET cc_start: 0.6482 (mmm) cc_final: 0.5900 (mmm) REVERT: D 619 ASN cc_start: 0.9516 (t0) cc_final: 0.9032 (t0) REVERT: D 670 MET cc_start: 0.7567 (mtt) cc_final: 0.7209 (mtt) REVERT: F 58 MET cc_start: 0.8106 (mmm) cc_final: 0.7585 (mmm) REVERT: F 117 MET cc_start: 0.8685 (mmm) cc_final: 0.8469 (mmm) REVERT: F 206 LYS cc_start: 0.9269 (mtpt) cc_final: 0.8901 (mttt) REVERT: G 99 ARG cc_start: 0.9414 (mmm-85) cc_final: 0.8958 (mmm-85) REVERT: G 117 MET cc_start: 0.9218 (mmm) cc_final: 0.8941 (mmm) REVERT: G 205 HIS cc_start: 0.8715 (OUTLIER) cc_final: 0.8260 (m-70) REVERT: H 97 PHE cc_start: 0.9166 (OUTLIER) cc_final: 0.8902 (t80) outliers start: 36 outliers final: 32 residues processed: 210 average time/residue: 0.1237 time to fit residues: 39.7227 Evaluate side-chains 210 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 176 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 527 MET Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain E residue 117 MET Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 67 CYS Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 97 PHE Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 205 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 80 optimal weight: 30.0000 chunk 216 optimal weight: 0.0030 chunk 169 optimal weight: 0.0470 chunk 208 optimal weight: 4.9990 chunk 67 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 15 optimal weight: 0.0270 chunk 47 optimal weight: 30.0000 chunk 45 optimal weight: 9.9990 chunk 180 optimal weight: 7.9990 chunk 81 optimal weight: 20.0000 overall best weight: 2.2150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.138319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.078709 restraints weight = 129965.597| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 6.82 r_work: 0.2824 rms_B_bonded: 6.17 restraints_weight: 2.0000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2829 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2829 r_free = 0.2829 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2829 r_free = 0.2829 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2829 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.4797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 18475 Z= 0.197 Angle : 0.663 17.159 24867 Z= 0.327 Chirality : 0.042 0.181 2765 Planarity : 0.004 0.054 3012 Dihedral : 9.165 88.360 2801 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.58 % Favored : 97.24 % Rotamer: Outliers : 2.03 % Allowed : 15.00 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.95 (0.19), residues: 2230 helix: 2.84 (0.15), residues: 1319 sheet: -1.36 (0.44), residues: 124 loop : -1.05 (0.22), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 204 TYR 0.016 0.001 TYR A 424 PHE 0.035 0.002 PHE A 659 TRP 0.016 0.001 TRP A 551 HIS 0.009 0.001 HIS F 205 Details of bonding type rmsd covalent geometry : bond 0.00456 (18464) covalent geometry : angle 0.66042 (24845) SS BOND : bond 0.00747 ( 11) SS BOND : angle 1.89977 ( 22) hydrogen bonds : bond 0.04298 ( 1117) hydrogen bonds : angle 4.10348 ( 3220) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4460 Ramachandran restraints generated. 2230 Oldfield, 0 Emsley, 2230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4460 Ramachandran restraints generated. 2230 Oldfield, 0 Emsley, 2230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 168 time to evaluate : 0.687 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: A 463 MET cc_start: 0.7178 (mmp) cc_final: 0.6621 (mmp) REVERT: A 479 LEU cc_start: 0.8272 (tp) cc_final: 0.7957 (pt) REVERT: A 487 GLU cc_start: 0.9222 (mt-10) cc_final: 0.8958 (pp20) REVERT: A 674 MET cc_start: 0.5264 (mtm) cc_final: 0.3942 (ptm) REVERT: A 721 MET cc_start: 0.4281 (mmm) cc_final: 0.3928 (mmm) REVERT: B 496 MET cc_start: 0.7637 (mmm) cc_final: 0.6897 (mmm) REVERT: B 670 MET cc_start: 0.7754 (mmm) cc_final: 0.7301 (mmm) REVERT: C 585 MET cc_start: 0.9068 (mmt) cc_final: 0.8751 (mmm) REVERT: C 619 ASN cc_start: 0.9591 (t0) cc_final: 0.9231 (t0) REVERT: C 670 MET cc_start: 0.6209 (mmm) cc_final: 0.5988 (mmm) REVERT: D 407 MET cc_start: 0.8018 (pmm) cc_final: 0.7059 (pmm) REVERT: D 496 MET cc_start: 0.4956 (mtp) cc_final: 0.4709 (mtp) REVERT: D 503 MET cc_start: 0.6464 (mmm) cc_final: 0.5930 (mmm) REVERT: D 619 ASN cc_start: 0.9507 (t0) cc_final: 0.9096 (t0) REVERT: D 670 MET cc_start: 0.7768 (mtt) cc_final: 0.7431 (mtt) REVERT: E 10 MET cc_start: 0.8898 (mmm) cc_final: 0.8552 (mmm) REVERT: F 70 GLU cc_start: 0.8485 (pp20) cc_final: 0.8244 (pp20) REVERT: F 206 LYS cc_start: 0.9288 (mtpt) cc_final: 0.8876 (mttt) REVERT: G 99 ARG cc_start: 0.9416 (mmm-85) cc_final: 0.8871 (mmm-85) REVERT: G 117 MET cc_start: 0.9248 (mmm) cc_final: 0.8975 (mmm) REVERT: G 205 HIS cc_start: 0.8712 (OUTLIER) cc_final: 0.8169 (m-70) REVERT: H 97 PHE cc_start: 0.9156 (OUTLIER) cc_final: 0.8893 (t80) outliers start: 36 outliers final: 33 residues processed: 197 average time/residue: 0.1284 time to fit residues: 39.1096 Evaluate side-chains 199 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 164 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 527 MET Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain E residue 117 MET Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 67 CYS Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 97 PHE Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 205 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 34 optimal weight: 20.0000 chunk 23 optimal weight: 0.2980 chunk 88 optimal weight: 0.0870 chunk 157 optimal weight: 2.9990 chunk 172 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 49 optimal weight: 0.0980 chunk 203 optimal weight: 0.5980 chunk 205 optimal weight: 0.8980 chunk 152 optimal weight: 0.3980 chunk 180 optimal weight: 7.9990 overall best weight: 0.2958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.142220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.083008 restraints weight = 147355.795| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 7.40 r_work: 0.2900 rms_B_bonded: 6.47 restraints_weight: 2.0000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2903 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2903 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.4939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 18475 Z= 0.109 Angle : 0.615 15.288 24867 Z= 0.301 Chirality : 0.041 0.171 2765 Planarity : 0.004 0.059 3012 Dihedral : 8.597 85.518 2801 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.81 % Favored : 98.01 % Rotamer: Outliers : 1.48 % Allowed : 15.65 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.08 (0.19), residues: 2230 helix: 2.96 (0.14), residues: 1326 sheet: -1.15 (0.44), residues: 117 loop : -1.10 (0.22), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 204 TYR 0.014 0.001 TYR D 647 PHE 0.035 0.001 PHE G 73 TRP 0.020 0.001 TRP A 551 HIS 0.005 0.001 HIS G 60 Details of bonding type rmsd covalent geometry : bond 0.00229 (18464) covalent geometry : angle 0.61324 (24845) SS BOND : bond 0.00641 ( 11) SS BOND : angle 1.74576 ( 22) hydrogen bonds : bond 0.03567 ( 1117) hydrogen bonds : angle 3.86925 ( 3220) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5208.36 seconds wall clock time: 89 minutes 50.31 seconds (5390.31 seconds total)