Starting phenix.real_space_refine on Sat Jul 4 05:08:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8piv_17692/07_2026/8piv_17692.cif Found real_map, /net/cci-nas-00/data/ceres_data/8piv_17692/07_2026/8piv_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8piv_17692/07_2026/8piv_17692.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8piv_17692/07_2026/8piv_17692.map" model { file = "/net/cci-nas-00/data/ceres_data/8piv_17692/07_2026/8piv_17692.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8piv_17692/07_2026/8piv_17692.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8piv_17692/07_2026/8piv_17692.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8piv_17692/07_2026/8piv_17692.cif" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: 5.42, per 1000 atoms: 0.30 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: 1.12 Conformation dependent library (CDL) restraints added in 948.1 milliseconds 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: 0.39 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: 3.36 Time building geometry restraints manager: 1.50 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 - 20.19: 9751 20.19 - 40.37: 770 40.37 - 60.56: 160 60.56 - 80.75: 29 80.75 - 100.93: 13 Dihedral angle restraints: 10723 sinusoidal: 4201 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 10720 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: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.730 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5099 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 : 15.285 100.932 6540 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 are 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/Z covalent geometry : bond 0.01712 / 1.22 (18464) covalent geometry : angle 1.48387 / 1.05 (24845) SS BOND : bond 0.01568 / 1.21 ( 11) SS BOND : angle 2.98649 / 1.91 ( 22) hydrogen bonds : bond 0.13171 / 8.83 ( 1117) hydrogen bonds : angle 5.26290 / 3.72 ( 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 : 0.707 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: 0.9229 (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: 0.1505 time to fit residues: 79.8186 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 : 0.575 ------------------------------------------------------------------------------- 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... 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 = 0.143242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.084300 restraints weight = 137624.161| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 8.45 r_work: 0.2873 rms_B_bonded: 6.26 restraints_weight: 2.0000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2876 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2876 r_free = 0.2876 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 = 0.2876 r_free = 0.2876 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2876 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 18475 Z= 0.142 Angle : 0.629 9.552 24867 Z= 0.326 Chirality : 0.042 0.226 2765 Planarity : 0.004 0.079 3012 Dihedral : 10.596 88.137 2769 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.40 % Favored : 98.37 % Rotamer: Outliers : 1.48 % Allowed : 10.62 % Favored : 87.90 % 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 are not related in a simple way. whole: 1.32 (0.18), residues: 2230 helix: 2.34 (0.14), residues: 1314 sheet: -1.71 (0.36), residues: 141 loop : -1.25 (0.21), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 675 TYR 0.019 0.001 TYR A 711 PHE 0.022 0.001 PHE A 495 TRP 0.024 0.001 TRP D 460 HIS 0.010 0.001 HIS G 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (18464) covalent geometry : angle 0.62707 / 0.32 (24845) SS BOND : bond 0.00531 / 0.28 ( 11) SS BOND : angle 1.84055 / 1.36 ( 22) hydrogen bonds : bond 0.04318 / 2.85 ( 1117) hydrogen bonds : angle 4.14045 / 2.94 ( 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 267 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 240 time to evaluate : 0.615 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: 0.8241 (mpp) cc_final: 0.7544 (ptp) REVERT: A 463 MET cc_start: 0.8520 (mpp) cc_final: 0.7336 (tpp) REVERT: A 479 LEU cc_start: 0.8281 (tp) cc_final: 0.7837 (mt) REVERT: A 503 MET cc_start: -0.1517 (tmm) cc_final: -0.1942 (ttt) REVERT: A 551 TRP cc_start: 0.6616 (m-10) cc_final: 0.6020 (m-10) REVERT: A 587 GLN cc_start: 0.9096 (tp40) cc_final: 0.8745 (mm-40) REVERT: A 674 MET cc_start: 0.5716 (mtm) cc_final: 0.4999 (ptt) REVERT: B 496 MET cc_start: 0.7135 (mmm) cc_final: 0.6601 (mmm) REVERT: B 585 MET cc_start: 0.9394 (mmt) cc_final: 0.9048 (mmm) REVERT: B 670 MET cc_start: 0.7507 (mmm) cc_final: 0.6851 (mmm) REVERT: C 585 MET cc_start: 0.9117 (mmt) cc_final: 0.8776 (mmm) REVERT: C 619 ASN cc_start: 0.9495 (t0) cc_final: 0.9244 (t0) REVERT: C 670 MET cc_start: 0.6159 (mmm) cc_final: 0.5878 (mmm) REVERT: D 414 MET cc_start: 0.8451 (mpp) cc_final: 0.7936 (mmp) REVERT: D 503 MET cc_start: 0.7192 (mmm) cc_final: 0.6389 (mmm) REVERT: D 551 TRP cc_start: 0.7550 (m100) cc_final: 0.7333 (m100) REVERT: D 619 ASN cc_start: 0.9439 (t0) cc_final: 0.9080 (t0) REVERT: D 639 LEU cc_start: 0.8644 (pt) cc_final: 0.8193 (pt) REVERT: D 670 MET cc_start: 0.6131 (mtt) cc_final: 0.5522 (tpp) REVERT: E 56 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7567 (tp30) REVERT: F 126 GLU cc_start: 0.8940 (tp30) cc_final: 0.8686 (tp30) REVERT: F 192 MET cc_start: 0.8998 (mtt) cc_final: 0.8613 (tmm) REVERT: F 206 LYS cc_start: 0.9173 (mtpt) cc_final: 0.8850 (mttt) REVERT: G 122 ILE cc_start: 0.9246 (tp) cc_final: 0.9008 (tp) REVERT: H 24 MET cc_start: 0.9272 (tpt) cc_final: 0.8977 (mmm) REVERT: H 102 ARG cc_start: 0.9041 (tpt90) cc_final: 0.8632 (tpt170) REVERT: H 203 ASP cc_start: 0.9191 (t0) cc_final: 0.8940 (t0) outliers start: 27 outliers final: 12 residues processed: 259 average time/residue: 0.1260 time to fit residues: 49.2463 Evaluate side-chains 207 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 195 time to evaluate : 0.583 ------------------------------------------------------------------------------- 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: 5.9990 chunk 36 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 174 optimal weight: 4.9990 chunk 74 optimal weight: 7.9990 chunk 62 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 82 optimal weight: 9.9990 chunk 209 optimal weight: 5.9990 chunk 58 optimal weight: 0.7980 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4209 r_free = 0.4209 target = 0.137114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.076914 restraints weight = 125439.494| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 6.51 r_work: 0.2788 rms_B_bonded: 5.72 restraints_weight: 2.0000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2790 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2790 r_free = 0.2790 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2790 r_free = 0.2790 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2790 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 18475 Z= 0.288 Angle : 0.697 9.885 24867 Z= 0.361 Chirality : 0.046 0.190 2765 Planarity : 0.005 0.066 3012 Dihedral : 10.523 88.384 2749 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.76 % Favored : 97.06 % Rotamer: Outliers : 2.41 % Allowed : 12.15 % Favored : 85.44 % 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 are not related in a simple way. whole: 1.34 (0.18), residues: 2230 helix: 2.25 (0.14), residues: 1330 sheet: -1.74 (0.39), residues: 133 loop : -1.12 (0.22), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 715 TYR 0.019 0.002 TYR B 673 PHE 0.024 0.002 PHE E 73 TRP 0.049 0.002 TRP A 766 HIS 0.010 0.002 HIS G 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00665 / 0.29 (18464) covalent geometry : angle 0.69446 / 0.36 (24845) SS BOND : bond 0.00522 / 0.38 ( 11) SS BOND : angle 1.95118 / 1.52 ( 22) hydrogen bonds : bond 0.05040 / 3.30 ( 1117) hydrogen bonds : angle 4.39102 / 3.12 ( 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: 44 poor density : 185 time to evaluate : 0.559 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: 0.7617 (ptp) REVERT: A 463 MET cc_start: 0.8731 (mpp) cc_final: 0.7950 (mpp) REVERT: A 496 MET cc_start: 0.4836 (tpt) cc_final: 0.4536 (ttt) REVERT: A 503 MET cc_start: -0.1650 (tmm) cc_final: -0.1980 (ttt) REVERT: A 674 MET cc_start: 0.5609 (mtm) cc_final: 0.4719 (ptp) REVERT: A 708 MET cc_start: 0.4863 (mpp) cc_final: 0.4229 (mmt) REVERT: A 715 ARG cc_start: 0.4793 (mmp-170) cc_final: 0.4195 (mmp-170) REVERT: B 670 MET cc_start: 0.7050 (mmm) cc_final: 0.6506 (mmm) REVERT: C 408 MET cc_start: 0.2134 (mmp) cc_final: 0.1905 (mmp) REVERT: C 585 MET cc_start: 0.9232 (mmt) cc_final: 0.8815 (mmm) REVERT: C 619 ASN cc_start: 0.9525 (t0) cc_final: 0.9219 (t0) REVERT: D 407 MET cc_start: 0.7876 (pmm) cc_final: 0.7303 (pmm) REVERT: D 503 MET cc_start: 0.6686 (mmm) cc_final: 0.6327 (mmm) REVERT: D 551 TRP cc_start: 0.7999 (m100) cc_final: 0.7757 (m100) REVERT: D 619 ASN cc_start: 0.9496 (t0) cc_final: 0.9110 (t0) REVERT: D 639 LEU cc_start: 0.8517 (pt) cc_final: 0.8295 (pt) REVERT: D 670 MET cc_start: 0.6533 (mtt) cc_final: 0.6252 (mtt) REVERT: E 10 MET cc_start: 0.8961 (mmm) cc_final: 0.8442 (tmm) REVERT: E 56 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7633 (tp30) REVERT: F 117 MET cc_start: 0.8684 (mmm) cc_final: 0.8385 (mmm) REVERT: F 126 GLU cc_start: 0.8952 (tp30) cc_final: 0.8679 (tp30) REVERT: F 192 MET cc_start: 0.8995 (mtt) cc_final: 0.8703 (ttt) REVERT: F 206 LYS cc_start: 0.9247 (mtpt) cc_final: 0.8941 (mttt) REVERT: G 117 MET cc_start: 0.9300 (mmm) cc_final: 0.9043 (mmm) REVERT: H 203 ASP cc_start: 0.9266 (t0) cc_final: 0.8996 (t0) outliers start: 44 outliers final: 29 residues processed: 216 average time/residue: 0.1231 time to fit residues: 40.4820 Evaluate side-chains 193 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 164 time to evaluate : 0.594 ------------------------------------------------------------------------------- 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 629 MET Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 534 ILE 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 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 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: 20.0000 chunk 84 optimal weight: 7.9990 chunk 86 optimal weight: 30.0000 chunk 106 optimal weight: 8.9990 chunk 164 optimal weight: 0.9990 chunk 181 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 chunk 105 optimal weight: 5.9990 chunk 176 optimal weight: 3.9990 chunk 4 optimal weight: 0.0570 overall best weight: 0.9504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 412 HIS D 791 ASN E 132 HIS ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.140346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.080058 restraints weight = 111818.275| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 6.58 r_work: 0.2862 rms_B_bonded: 5.85 restraints_weight: 2.0000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2862 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 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 = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2862 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3815 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= 0.128 Angle : 0.578 9.580 24867 Z= 0.295 Chirality : 0.041 0.240 2765 Planarity : 0.004 0.060 3012 Dihedral : 9.524 89.229 2749 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.81 % Favored : 98.01 % Rotamer: Outliers : 2.03 % Allowed : 12.86 % 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 are not related in a simple way. whole: 1.79 (0.19), residues: 2230 helix: 2.68 (0.14), residues: 1330 sheet: -1.43 (0.37), residues: 156 loop : -1.08 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 743 TYR 0.033 0.001 TYR A 424 PHE 0.019 0.001 PHE E 73 TRP 0.038 0.001 TRP A 551 HIS 0.009 0.001 HIS G 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (18464) covalent geometry : angle 0.57551 / 0.29 (24845) SS BOND : bond 0.00928 / 0.44 ( 11) SS BOND : angle 1.99320 / 1.55 ( 22) hydrogen bonds : bond 0.03922 / 2.60 ( 1117) hydrogen bonds : angle 3.99829 / 2.84 ( 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 234 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 198 time to evaluate : 0.715 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: 0.8446 (mpp) cc_final: 0.7836 (ptp) REVERT: A 503 MET cc_start: -0.1973 (tmm) cc_final: -0.2192 (ttt) REVERT: A 674 MET cc_start: 0.5610 (mtm) cc_final: 0.4700 (ptp) REVERT: A 708 MET cc_start: 0.4545 (mpp) cc_final: 0.4195 (mmt) REVERT: A 715 ARG cc_start: 0.4387 (mmp-170) cc_final: 0.3974 (mmp-170) REVERT: B 670 MET cc_start: 0.7459 (mmm) cc_final: 0.7102 (mmm) REVERT: C 585 MET cc_start: 0.9041 (mmt) cc_final: 0.8521 (mmm) REVERT: C 619 ASN cc_start: 0.9530 (t0) cc_final: 0.9262 (t0) REVERT: D 407 MET cc_start: 0.7972 (pmm) cc_final: 0.7409 (pmm) REVERT: D 414 MET cc_start: 0.8443 (ptp) cc_final: 0.8190 (mmp) REVERT: D 496 MET cc_start: 0.4997 (mtt) cc_final: 0.4530 (mtp) REVERT: D 503 MET cc_start: 0.7159 (mmm) cc_final: 0.6323 (mmm) REVERT: D 585 MET cc_start: 0.9300 (mmt) cc_final: 0.9092 (mmt) REVERT: D 619 ASN cc_start: 0.9485 (t0) cc_final: 0.8992 (t0) REVERT: D 639 LEU cc_start: 0.8326 (pt) cc_final: 0.8029 (pt) REVERT: D 670 MET cc_start: 0.6517 (mtt) cc_final: 0.5870 (tpp) REVERT: E 10 MET cc_start: 0.8988 (mmm) cc_final: 0.8610 (mmm) REVERT: E 56 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7517 (tp30) REVERT: E 69 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8160 (pt) REVERT: F 10 MET cc_start: 0.9470 (tpp) cc_final: 0.9235 (tpp) REVERT: F 30 THR cc_start: 0.9491 (m) cc_final: 0.9283 (p) REVERT: F 117 MET cc_start: 0.8663 (mmm) cc_final: 0.8418 (mmm) REVERT: F 126 GLU cc_start: 0.9013 (tp30) cc_final: 0.8780 (tp30) REVERT: F 192 MET cc_start: 0.8980 (mtt) cc_final: 0.8756 (ttt) REVERT: F 206 LYS cc_start: 0.9257 (mtpt) cc_final: 0.8978 (mttt) REVERT: G 117 MET cc_start: 0.9230 (mmm) cc_final: 0.8961 (mmm) REVERT: G 160 ASN cc_start: 0.8451 (m-40) cc_final: 0.8146 (m110) REVERT: H 144 SER cc_start: 0.9467 (m) cc_final: 0.9238 (t) outliers start: 36 outliers final: 26 residues processed: 222 average time/residue: 0.1196 time to fit residues: 40.8470 Evaluate side-chains 206 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 179 time to evaluate : 0.644 ------------------------------------------------------------------------------- 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 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 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 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 66 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 187 optimal weight: 2.9990 chunk 106 optimal weight: 9.9990 chunk 172 optimal weight: 0.6980 chunk 200 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 144 optimal weight: 10.0000 chunk 198 optimal weight: 0.6980 chunk 154 optimal weight: 0.7980 chunk 118 optimal weight: 9.9990 chunk 6 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 587 GLN ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 160 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.140518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.081292 restraints weight = 96830.250| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 6.31 r_work: 0.2873 rms_B_bonded: 5.78 restraints_weight: 2.0000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2872 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2872 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.4054 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= 0.150 Angle : 0.576 10.812 24867 Z= 0.294 Chirality : 0.041 0.241 2765 Planarity : 0.004 0.059 3012 Dihedral : 9.174 89.457 2749 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.08 % Favored : 97.74 % Rotamer: Outliers : 2.35 % Allowed : 12.86 % Favored : 84.78 % 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 are not related in a simple way. whole: 1.88 (0.19), residues: 2230 helix: 2.77 (0.14), residues: 1329 sheet: -1.45 (0.38), residues: 154 loop : -1.04 (0.23), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 586 TYR 0.025 0.001 TYR A 424 PHE 0.024 0.001 PHE A 659 TRP 0.030 0.001 TRP A 551 HIS 0.008 0.001 HIS G 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (18464) covalent geometry : angle 0.57423 / 0.29 (24845) SS BOND : bond 0.00700 / 0.37 ( 11) SS BOND : angle 1.72149 / 1.30 ( 22) hydrogen bonds : bond 0.04021 / 2.65 ( 1117) hydrogen bonds : angle 4.02068 / 2.86 ( 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 228 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 186 time to evaluate : 0.480 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: 0.8455 (mpp) cc_final: 0.7888 (ptp) REVERT: A 479 LEU cc_start: 0.8352 (tp) cc_final: 0.8052 (pt) REVERT: A 503 MET cc_start: -0.1677 (tmm) cc_final: -0.1884 (ttt) REVERT: A 674 MET cc_start: 0.5515 (mtm) cc_final: 0.4356 (ptm) REVERT: A 708 MET cc_start: 0.4857 (mpp) cc_final: 0.4453 (mmt) REVERT: A 715 ARG cc_start: 0.4221 (mmp-170) cc_final: 0.3565 (mmp-170) REVERT: B 496 MET cc_start: 0.7321 (mmm) cc_final: 0.6408 (mmm) REVERT: B 670 MET cc_start: 0.7690 (mmm) cc_final: 0.7163 (mmm) REVERT: B 726 ASN cc_start: 0.7925 (m-40) cc_final: 0.7711 (t0) REVERT: C 585 MET cc_start: 0.9050 (mmt) cc_final: 0.8624 (mmt) REVERT: C 619 ASN cc_start: 0.9552 (t0) cc_final: 0.9234 (t0) REVERT: D 407 MET cc_start: 0.7992 (pmm) cc_final: 0.7431 (pmm) REVERT: D 414 MET cc_start: 0.8433 (ptp) cc_final: 0.8171 (mmm) REVERT: D 496 MET cc_start: 0.4973 (mtt) cc_final: 0.4562 (mtp) REVERT: D 503 MET cc_start: 0.7246 (mmm) cc_final: 0.6504 (mmm) REVERT: D 551 TRP cc_start: 0.8072 (m100) cc_final: 0.7870 (m100) REVERT: D 619 ASN cc_start: 0.9492 (t0) cc_final: 0.9073 (t0) REVERT: D 670 MET cc_start: 0.6664 (mtt) cc_final: 0.6438 (mmm) REVERT: D 721 MET cc_start: 0.8785 (ttm) cc_final: 0.8581 (tmm) REVERT: E 10 MET cc_start: 0.8860 (mmm) cc_final: 0.8533 (mmm) REVERT: E 56 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7619 (tp30) REVERT: E 58 MET cc_start: 0.9169 (mmm) cc_final: 0.8915 (mmp) REVERT: E 205 HIS cc_start: 0.9002 (OUTLIER) cc_final: 0.8570 (t-90) REVERT: F 117 MET cc_start: 0.8622 (mmm) cc_final: 0.8366 (mmm) REVERT: F 126 GLU cc_start: 0.8953 (tp30) cc_final: 0.8706 (tp30) REVERT: F 192 MET cc_start: 0.8958 (mtt) cc_final: 0.8752 (ttt) REVERT: F 206 LYS cc_start: 0.9252 (mtpt) cc_final: 0.8968 (mttt) REVERT: G 117 MET cc_start: 0.9270 (mmm) cc_final: 0.8988 (mmm) REVERT: H 37 ARG cc_start: 0.8655 (tpp80) cc_final: 0.7664 (tpp80) REVERT: H 144 SER cc_start: 0.9478 (m) cc_final: 0.9240 (t) outliers start: 42 outliers final: 26 residues processed: 215 average time/residue: 0.1164 time to fit residues: 38.5408 Evaluate side-chains 203 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 176 time to evaluate : 0.551 ------------------------------------------------------------------------------- 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 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 591 ILE 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 205 HIS Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 66 THR 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 185 LEU Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain H residue 57 VAL 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: 0.5980 chunk 44 optimal weight: 20.0000 chunk 4 optimal weight: 6.9990 chunk 199 optimal weight: 5.9990 chunk 154 optimal weight: 0.9980 chunk 216 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 170 optimal weight: 0.7980 chunk 70 optimal weight: 30.0000 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 587 GLN ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 HIS G 160 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.140176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.081255 restraints weight = 121468.064| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 7.20 r_work: 0.2865 rms_B_bonded: 5.91 restraints_weight: 2.0000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2866 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2866 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.4288 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= 0.152 Angle : 0.612 17.372 24867 Z= 0.306 Chirality : 0.042 0.268 2765 Planarity : 0.004 0.055 3012 Dihedral : 8.828 86.710 2747 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.90 % Favored : 97.92 % Rotamer: Outliers : 2.63 % Allowed : 13.30 % Favored : 84.07 % 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 are not related in a simple way. whole: 1.93 (0.19), residues: 2230 helix: 2.79 (0.14), residues: 1328 sheet: -1.68 (0.40), residues: 139 loop : -0.95 (0.22), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 586 TYR 0.018 0.001 TYR A 424 PHE 0.027 0.001 PHE A 659 TRP 0.026 0.001 TRP A 551 HIS 0.010 0.001 HIS G 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (18464) covalent geometry : angle 0.60739 / 0.30 (24845) SS BOND : bond 0.00922 / 0.68 ( 11) SS BOND : angle 2.56074 / 1.55 ( 22) hydrogen bonds : bond 0.04064 / 2.70 ( 1117) hydrogen bonds : angle 4.02183 / 2.88 ( 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 227 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 180 time to evaluate : 0.698 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: 0.8519 (mpp) cc_final: 0.8038 (ptp) REVERT: A 463 MET cc_start: 0.7198 (mmp) cc_final: 0.6530 (mmp) REVERT: A 479 LEU cc_start: 0.8306 (tp) cc_final: 0.8016 (pt) REVERT: A 503 MET cc_start: -0.1623 (tmm) cc_final: -0.1845 (ttt) REVERT: A 674 MET cc_start: 0.5372 (mtm) cc_final: 0.4164 (ptm) REVERT: A 708 MET cc_start: 0.4925 (mpp) cc_final: 0.4481 (mmt) REVERT: B 407 MET cc_start: 0.5427 (mpp) cc_final: 0.5147 (mpp) REVERT: B 496 MET cc_start: 0.7487 (mmm) cc_final: 0.6749 (mmm) REVERT: B 670 MET cc_start: 0.7664 (mmm) cc_final: 0.7159 (mmm) REVERT: C 585 MET cc_start: 0.9059 (mmt) cc_final: 0.8606 (mmt) REVERT: C 619 ASN cc_start: 0.9575 (t0) cc_final: 0.9259 (t0) REVERT: D 407 MET cc_start: 0.7959 (pmm) cc_final: 0.7397 (pmm) REVERT: D 414 MET cc_start: 0.8301 (ptp) cc_final: 0.8084 (mmm) REVERT: D 496 MET cc_start: 0.5202 (mtt) cc_final: 0.4735 (mtp) REVERT: D 503 MET cc_start: 0.6970 (mmm) cc_final: 0.6485 (mmm) REVERT: D 619 ASN cc_start: 0.9508 (t0) cc_final: 0.9095 (t0) REVERT: D 670 MET cc_start: 0.6782 (mtt) cc_final: 0.6516 (mtt) REVERT: D 721 MET cc_start: 0.8773 (ttm) cc_final: 0.8555 (tmm) REVERT: E 10 MET cc_start: 0.8846 (mmm) cc_final: 0.8561 (mmm) REVERT: E 56 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7636 (tp30) REVERT: E 58 MET cc_start: 0.9164 (mmm) cc_final: 0.8569 (mmp) REVERT: E 98 LEU cc_start: 0.9165 (tt) cc_final: 0.8945 (tp) REVERT: F 126 GLU cc_start: 0.8931 (tp30) cc_final: 0.8690 (tp30) REVERT: F 192 MET cc_start: 0.8992 (mtt) cc_final: 0.8750 (ttt) REVERT: F 206 LYS cc_start: 0.9281 (mtpt) cc_final: 0.8986 (mttt) REVERT: G 99 ARG cc_start: 0.9370 (mmm-85) cc_final: 0.8717 (mmm-85) REVERT: G 117 MET cc_start: 0.9260 (mmm) cc_final: 0.8936 (mmm) REVERT: H 144 SER cc_start: 0.9480 (m) cc_final: 0.9241 (t) outliers start: 47 outliers final: 31 residues processed: 214 average time/residue: 0.1227 time to fit residues: 40.5265 Evaluate side-chains 200 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 169 time to evaluate : 0.608 ------------------------------------------------------------------------------- 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 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 807 MET 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 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 80 ILE 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 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 205 HIS 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: 2.9990 chunk 151 optimal weight: 4.9990 chunk 191 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 154 optimal weight: 0.8980 chunk 142 optimal weight: 6.9990 chunk 106 optimal weight: 10.0000 chunk 165 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 169 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 587 GLN ** A 714 GLN ** 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 = 0.4246 r_free = 0.4246 target = 0.139175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.079868 restraints weight = 115459.822| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 6.68 r_work: 0.2846 rms_B_bonded: 5.90 restraints_weight: 2.0000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2846 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2846 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.4489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 18475 Z= 0.181 Angle : 0.635 14.718 24867 Z= 0.317 Chirality : 0.042 0.231 2765 Planarity : 0.004 0.056 3012 Dihedral : 8.878 85.758 2747 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.12 % Favored : 97.69 % Rotamer: Outliers : 2.30 % Allowed : 13.90 % Favored : 83.80 % 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 are not related in a simple way. whole: 1.94 (0.19), residues: 2230 helix: 2.83 (0.14), residues: 1316 sheet: -1.46 (0.40), residues: 140 loop : -1.00 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 586 TYR 0.018 0.001 TYR A 424 PHE 0.028 0.002 PHE A 659 TRP 0.023 0.001 TRP A 551 HIS 0.007 0.001 HIS G 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 (18464) covalent geometry : angle 0.63184 / 0.32 (24845) SS BOND : bond 0.01027 / 0.62 ( 11) SS BOND : angle 2.22868 / 1.41 ( 22) hydrogen bonds : bond 0.04247 / 2.81 ( 1117) hydrogen bonds : angle 4.11165 / 2.94 ( 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 211 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 170 time to evaluate : 0.564 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 414 MET cc_start: 0.8417 (mpp) cc_final: 0.8018 (ptp) REVERT: A 463 MET cc_start: 0.7279 (mmp) cc_final: 0.6768 (mmp) REVERT: A 479 LEU cc_start: 0.8320 (tp) cc_final: 0.8011 (pt) REVERT: A 503 MET cc_start: -0.1190 (tmm) cc_final: -0.1580 (ttt) REVERT: A 674 MET cc_start: 0.5275 (mtm) cc_final: 0.4097 (ptm) REVERT: A 708 MET cc_start: 0.4629 (mpp) cc_final: 0.4305 (mmt) REVERT: B 496 MET cc_start: 0.7541 (mmm) cc_final: 0.6844 (mmm) REVERT: B 670 MET cc_start: 0.7660 (mmm) cc_final: 0.7164 (mmm) REVERT: C 585 MET cc_start: 0.9094 (mmt) cc_final: 0.8606 (mmt) REVERT: C 619 ASN cc_start: 0.9580 (t0) cc_final: 0.9245 (t0) REVERT: D 407 MET cc_start: 0.7936 (pmm) cc_final: 0.7346 (pmm) REVERT: D 414 MET cc_start: 0.8289 (ptp) cc_final: 0.8071 (mmm) REVERT: D 496 MET cc_start: 0.5482 (mtt) cc_final: 0.5018 (mtp) REVERT: D 503 MET cc_start: 0.6795 (mmm) cc_final: 0.6543 (mmm) REVERT: D 619 ASN cc_start: 0.9489 (t0) cc_final: 0.9078 (t0) REVERT: D 674 MET cc_start: 0.3282 (pmm) cc_final: 0.2850 (pmm) REVERT: D 721 MET cc_start: 0.8775 (ttm) cc_final: 0.8553 (tmm) REVERT: E 10 MET cc_start: 0.8832 (mmm) cc_final: 0.8549 (mmm) REVERT: E 56 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7630 (tp30) REVERT: F 126 GLU cc_start: 0.8886 (tp30) cc_final: 0.8628 (tp30) REVERT: F 192 MET cc_start: 0.8995 (mtt) cc_final: 0.8700 (ttt) REVERT: F 206 LYS cc_start: 0.9284 (mtpt) cc_final: 0.8969 (mttt) REVERT: G 99 ARG cc_start: 0.9401 (mmm-85) cc_final: 0.8806 (mmm-85) REVERT: G 117 MET cc_start: 0.9224 (mmm) cc_final: 0.8875 (mmm) REVERT: G 205 HIS cc_start: 0.8711 (OUTLIER) cc_final: 0.8181 (m-70) REVERT: H 144 SER cc_start: 0.9477 (m) cc_final: 0.9274 (t) REVERT: H 160 ASN cc_start: 0.8498 (m-40) cc_final: 0.8200 (m110) outliers start: 41 outliers final: 31 residues processed: 205 average time/residue: 0.1144 time to fit residues: 37.0080 Evaluate side-chains 196 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 164 time to evaluate : 0.475 ------------------------------------------------------------------------------- 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 807 MET 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 77 CYS 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 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 80 ILE 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 66 THR Chi-restraints excluded: chain H residue 205 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 19 optimal weight: 0.9980 chunk 198 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 27 optimal weight: 20.0000 chunk 143 optimal weight: 20.0000 chunk 102 optimal weight: 20.0000 chunk 220 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 11 optimal weight: 10.0000 chunk 209 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 587 GLN ** A 714 GLN ** 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 = 0.4236 r_free = 0.4236 target = 0.138544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.079000 restraints weight = 127384.138| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 6.74 r_work: 0.2826 rms_B_bonded: 6.07 restraints_weight: 2.0000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2825 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2825 r_free = 0.2825 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 = 0.2825 r_free = 0.2825 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2825 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.4709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 18475 Z= 0.197 Angle : 0.639 12.041 24867 Z= 0.321 Chirality : 0.043 0.245 2765 Planarity : 0.004 0.051 3012 Dihedral : 8.935 85.056 2747 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.58 % Favored : 97.24 % Rotamer: Outliers : 2.19 % Allowed : 14.56 % Favored : 83.25 % 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 are not related in a simple way. whole: 1.88 (0.19), residues: 2230 helix: 2.78 (0.14), residues: 1323 sheet: -1.52 (0.42), residues: 136 loop : -1.04 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 586 TYR 0.019 0.001 TYR A 424 PHE 0.032 0.002 PHE A 659 TRP 0.020 0.001 TRP A 551 HIS 0.006 0.001 HIS G 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.20 (18464) covalent geometry : angle 0.63641 / 0.32 (24845) SS BOND : bond 0.00721 / 0.48 ( 11) SS BOND : angle 1.90838 / 1.44 ( 22) hydrogen bonds : bond 0.04346 / 2.87 ( 1117) hydrogen bonds : angle 4.17944 / 2.99 ( 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 208 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 169 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 MET cc_start: 0.8197 (mpp) cc_final: 0.7922 (ptp) REVERT: A 463 MET cc_start: 0.7303 (mmp) cc_final: 0.6807 (mmp) REVERT: A 479 LEU cc_start: 0.8268 (tp) cc_final: 0.7969 (pt) REVERT: A 485 ARG cc_start: 0.7749 (mtt180) cc_final: 0.6499 (ptm160) REVERT: A 674 MET cc_start: 0.5285 (mtm) cc_final: 0.3997 (ptm) REVERT: A 708 MET cc_start: 0.4793 (mpp) cc_final: 0.4423 (mmt) REVERT: A 715 ARG cc_start: 0.4219 (mmp-170) cc_final: 0.3823 (mmp-170) REVERT: B 496 MET cc_start: 0.7599 (mmm) cc_final: 0.6880 (mmm) REVERT: B 670 MET cc_start: 0.7744 (mmm) cc_final: 0.7338 (mmm) REVERT: C 585 MET cc_start: 0.9086 (mmt) cc_final: 0.8633 (mmt) REVERT: C 619 ASN cc_start: 0.9590 (t0) cc_final: 0.9258 (t0) REVERT: D 407 MET cc_start: 0.8058 (pmm) cc_final: 0.7398 (pmm) REVERT: D 496 MET cc_start: 0.5602 (mtt) cc_final: 0.5118 (mtp) REVERT: D 619 ASN cc_start: 0.9498 (t0) cc_final: 0.9084 (t0) REVERT: D 674 MET cc_start: 0.3584 (pmm) cc_final: 0.3352 (pmm) REVERT: D 721 MET cc_start: 0.8843 (ttm) cc_final: 0.8533 (tmm) REVERT: E 10 MET cc_start: 0.8864 (mmm) cc_final: 0.8581 (mmm) REVERT: E 56 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7686 (tp30) REVERT: F 58 MET cc_start: 0.8092 (mmp) cc_final: 0.7622 (mmm) REVERT: F 117 MET cc_start: 0.8728 (mmm) cc_final: 0.8507 (mmm) REVERT: F 192 MET cc_start: 0.8984 (mtt) cc_final: 0.8676 (ttt) REVERT: F 206 LYS cc_start: 0.9298 (mtpt) cc_final: 0.8962 (mttt) REVERT: G 99 ARG cc_start: 0.9385 (mmm-85) cc_final: 0.8808 (mmm-85) REVERT: G 117 MET cc_start: 0.9303 (mmm) cc_final: 0.9055 (mmm) REVERT: H 97 PHE cc_start: 0.9143 (OUTLIER) cc_final: 0.8867 (t80) REVERT: H 160 ASN cc_start: 0.8502 (m-40) cc_final: 0.8197 (m110) outliers start: 39 outliers final: 34 residues processed: 199 average time/residue: 0.1160 time to fit residues: 35.9347 Evaluate side-chains 195 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 160 time to evaluate : 0.576 ------------------------------------------------------------------------------- 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 807 MET 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 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 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 40 CYS Chi-restraints excluded: chain F residue 66 THR 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 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 H residue 26 ILE Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 97 PHE Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 205 HIS 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: 1.9990 chunk 55 optimal weight: 1.9990 chunk 167 optimal weight: 0.7980 chunk 68 optimal weight: 8.9990 chunk 160 optimal weight: 4.9990 chunk 157 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 587 GLN ** A 714 GLN ** 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 = 0.4254 r_free = 0.4254 target = 0.139694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.080273 restraints weight = 134248.995| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 6.94 r_work: 0.2861 rms_B_bonded: 6.10 restraints_weight: 2.0000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2861 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2861 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.4834 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= 0.145 Angle : 0.635 15.055 24867 Z= 0.313 Chirality : 0.042 0.303 2765 Planarity : 0.004 0.057 3012 Dihedral : 8.599 81.598 2747 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.99 % Favored : 97.83 % Rotamer: Outliers : 2.13 % Allowed : 15.05 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.19), residues: 2230 helix: 2.86 (0.14), residues: 1323 sheet: -1.25 (0.45), residues: 107 loop : -1.08 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 37 TYR 0.015 0.001 TYR A 424 PHE 0.031 0.001 PHE A 659 TRP 0.019 0.001 TRP A 551 HIS 0.006 0.001 HIS G 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (18464) covalent geometry : angle 0.63187 / 0.31 (24845) SS BOND : bond 0.00796 / 0.57 ( 11) SS BOND : angle 2.16810 / 1.60 ( 22) hydrogen bonds : bond 0.04051 / 2.69 ( 1117) hydrogen bonds : angle 4.05493 / 2.91 ( 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 217 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 179 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 MET cc_start: 0.7078 (mmp) cc_final: 0.6507 (mmp) REVERT: A 479 LEU cc_start: 0.8297 (tp) cc_final: 0.7837 (pt) REVERT: A 485 ARG cc_start: 0.7738 (mtt180) cc_final: 0.7354 (mtt180) REVERT: A 487 GLU cc_start: 0.9214 (mt-10) cc_final: 0.8851 (pp20) REVERT: A 674 MET cc_start: 0.5233 (mtm) cc_final: 0.3945 (ptm) REVERT: A 708 MET cc_start: 0.4767 (mpp) cc_final: 0.4300 (mmm) REVERT: B 496 MET cc_start: 0.7596 (mmm) cc_final: 0.6854 (mmm) REVERT: B 670 MET cc_start: 0.7749 (mmm) cc_final: 0.7207 (mmm) REVERT: C 585 MET cc_start: 0.9043 (mmt) cc_final: 0.8567 (mmt) REVERT: C 619 ASN cc_start: 0.9574 (t0) cc_final: 0.9257 (t0) REVERT: D 407 MET cc_start: 0.8033 (pmm) cc_final: 0.7060 (pmm) REVERT: D 496 MET cc_start: 0.5621 (mtt) cc_final: 0.5151 (mtp) REVERT: D 619 ASN cc_start: 0.9503 (t0) cc_final: 0.9022 (t0) REVERT: D 670 MET cc_start: 0.7592 (mtt) cc_final: 0.6960 (tpp) REVERT: E 10 MET cc_start: 0.8881 (mmm) cc_final: 0.8591 (mmm) REVERT: E 56 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7678 (tp30) REVERT: F 192 MET cc_start: 0.9009 (mtt) cc_final: 0.8746 (ttt) REVERT: F 206 LYS cc_start: 0.9301 (mtpt) cc_final: 0.8950 (mttt) REVERT: G 99 ARG cc_start: 0.9388 (mmm-85) cc_final: 0.8825 (mmm-85) REVERT: G 117 MET cc_start: 0.9246 (mmm) cc_final: 0.8976 (mmm) REVERT: G 205 HIS cc_start: 0.8729 (OUTLIER) cc_final: 0.8202 (m-70) REVERT: H 97 PHE cc_start: 0.9157 (OUTLIER) cc_final: 0.8889 (t80) outliers start: 38 outliers final: 31 residues processed: 207 average time/residue: 0.1137 time to fit residues: 36.7832 Evaluate side-chains 199 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 166 time to evaluate : 0.511 ------------------------------------------------------------------------------- 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 807 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 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 66 THR 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 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 66 THR Chi-restraints excluded: chain H residue 97 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 80 optimal weight: 9.9990 chunk 216 optimal weight: 2.9990 chunk 169 optimal weight: 0.0030 chunk 208 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 15 optimal weight: 0.0270 chunk 47 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 180 optimal weight: 7.9990 chunk 81 optimal weight: 20.0000 overall best weight: 1.6052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 587 GLN ** A 714 GLN ** 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 = 0.4292 r_free = 0.4292 target = 0.141814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.081892 restraints weight = 128876.232| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 6.59 r_work: 0.2939 rms_B_bonded: 5.57 restraints_weight: 2.0000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2944 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 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 = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2943 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.4950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18475 Z= 0.160 Angle : 0.646 11.790 24867 Z= 0.320 Chirality : 0.042 0.266 2765 Planarity : 0.004 0.052 3012 Dihedral : 8.532 80.328 2747 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.26 % Favored : 97.56 % Rotamer: Outliers : 2.03 % Allowed : 15.27 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.19), residues: 2230 helix: 2.82 (0.14), residues: 1329 sheet: -1.19 (0.46), residues: 104 loop : -1.14 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 586 TYR 0.019 0.001 TYR C 673 PHE 0.032 0.001 PHE A 659 TRP 0.019 0.001 TRP C 460 HIS 0.006 0.001 HIS A 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (18464) covalent geometry : angle 0.64388 / 0.32 (24845) SS BOND : bond 0.00650 / 0.43 ( 11) SS BOND : angle 2.03999 / 1.52 ( 22) hydrogen bonds : bond 0.04101 / 2.72 ( 1117) hydrogen bonds : angle 4.07628 / 2.93 ( 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 206 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 170 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 MET cc_start: 0.7092 (mmp) cc_final: 0.6484 (mmp) REVERT: A 479 LEU cc_start: 0.8190 (tp) cc_final: 0.7691 (pt) REVERT: A 485 ARG cc_start: 0.7683 (mtt180) cc_final: 0.7168 (mtt180) REVERT: A 487 GLU cc_start: 0.9120 (mt-10) cc_final: 0.8826 (pp20) REVERT: A 674 MET cc_start: 0.5189 (mtm) cc_final: 0.3923 (ptm) REVERT: A 708 MET cc_start: 0.4780 (mpp) cc_final: 0.4368 (mmm) REVERT: B 496 MET cc_start: 0.7583 (mmm) cc_final: 0.6834 (mmm) REVERT: B 670 MET cc_start: 0.7582 (mmm) cc_final: 0.7138 (mmm) REVERT: C 585 MET cc_start: 0.9124 (mmt) cc_final: 0.8700 (mmt) REVERT: C 619 ASN cc_start: 0.9559 (t0) cc_final: 0.9292 (t0) REVERT: D 407 MET cc_start: 0.8079 (pmm) cc_final: 0.7144 (pmm) REVERT: D 496 MET cc_start: 0.5668 (mtt) cc_final: 0.5070 (mtp) REVERT: D 619 ASN cc_start: 0.9493 (t0) cc_final: 0.9047 (t0) REVERT: D 742 LEU cc_start: 0.7742 (mm) cc_final: 0.7502 (tt) REVERT: E 10 MET cc_start: 0.8770 (mmm) cc_final: 0.8489 (mmm) REVERT: E 56 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7739 (tp30) REVERT: F 206 LYS cc_start: 0.9275 (mtpt) cc_final: 0.8906 (mttt) REVERT: G 99 ARG cc_start: 0.9362 (mmm-85) cc_final: 0.8797 (mmm-85) REVERT: G 117 MET cc_start: 0.9262 (mmm) cc_final: 0.9010 (mmm) REVERT: G 205 HIS cc_start: 0.8751 (OUTLIER) cc_final: 0.8258 (m-70) REVERT: H 97 PHE cc_start: 0.9119 (OUTLIER) cc_final: 0.8837 (t80) outliers start: 36 outliers final: 31 residues processed: 197 average time/residue: 0.1127 time to fit residues: 35.2445 Evaluate side-chains 200 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 167 time to evaluate : 0.590 ------------------------------------------------------------------------------- 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 807 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 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 40 CYS Chi-restraints excluded: chain F residue 66 THR 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 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 66 THR Chi-restraints excluded: chain H residue 97 PHE 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: 3.9990 chunk 88 optimal weight: 30.0000 chunk 157 optimal weight: 6.9990 chunk 172 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 49 optimal weight: 20.0000 chunk 203 optimal weight: 1.9990 chunk 205 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 180 optimal weight: 7.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 412 HIS A 587 GLN ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.140857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.081651 restraints weight = 135998.455| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 6.91 r_work: 0.2901 rms_B_bonded: 6.14 restraints_weight: 2.0000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2900 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2900 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.5055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 18475 Z= 0.195 Angle : 0.663 11.897 24867 Z= 0.329 Chirality : 0.043 0.253 2765 Planarity : 0.004 0.054 3012 Dihedral : 8.594 80.032 2747 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.53 % Favored : 97.29 % Rotamer: Outliers : 1.97 % Allowed : 15.44 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.19), residues: 2230 helix: 2.80 (0.14), residues: 1323 sheet: -1.48 (0.43), residues: 129 loop : -1.10 (0.22), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 586 TYR 0.019 0.001 TYR C 673 PHE 0.034 0.002 PHE A 659 TRP 0.017 0.001 TRP A 551 HIS 0.005 0.001 HIS G 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.19 (18464) covalent geometry : angle 0.66046 / 0.33 (24845) SS BOND : bond 0.00645 / 0.43 ( 11) SS BOND : angle 2.06879 / 1.54 ( 22) hydrogen bonds : bond 0.04287 / 2.83 ( 1117) hydrogen bonds : angle 4.15910 / 2.98 ( 3220) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4488.61 seconds wall clock time: 77 minutes 33.73 seconds (4653.73 seconds total)