Starting phenix.real_space_refine on Mon Jun 16 10:57:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8piv_17692/06_2025/8piv_17692.cif Found real_map, /net/cci-nas-00/data/ceres_data/8piv_17692/06_2025/8piv_17692.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8piv_17692/06_2025/8piv_17692.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8piv_17692/06_2025/8piv_17692.map" model { file = "/net/cci-nas-00/data/ceres_data/8piv_17692/06_2025/8piv_17692.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8piv_17692/06_2025/8piv_17692.cif" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.045 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): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLU:plan': 4, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 1} 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: {'GLU:plan': 4, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 1} 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: {'GLU:plan': 6, 'ASN:plan1': 1, 'ARG:plan': 3, 'ASP:plan': 1} 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: {'GLU:plan': 6, 'ASN:plan1': 1, 'ARG:plan': 3, 'ASP:plan': 1} 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: {'GLU:plan': 4, 'ASN:plan1': 2, 'ARG:plan': 3, 'ASP:plan': 1} 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: {'GLU:plan': 4, 'ASN:plan1': 2, 'ARG:plan': 3, 'ASP:plan': 1} 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: {'GLU:plan': 6, 'ASN:plan1': 1, 'ARG:plan': 3, 'ASP:plan': 1} 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: {'GLU:plan': 6, 'ASN:plan1': 1, 'ARG:plan': 3, 'ASP:plan': 1} 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: 17.23, per 1000 atoms: 0.95 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: 4.44 Conformation dependent library (CDL) restraints added in 3.9 seconds 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: 1.76 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: 5.93 Time building geometry restraints manager: 5.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.52: 14694 1.52 - 1.88: 3769 1.88 - 2.24: 0 2.24 - 2.61: 0 2.61 - 2.97: 1 Bond restraints: 18464 Sorted by residual: bond pdb=" C PRO D 717 " pdb=" N ASP D 719 " ideal model delta sigma weight residual 1.332 2.966 -1.634 1.40e-02 5.10e+03 1.36e+04 bond pdb=" C SER C 785 " pdb=" O SER C 785 " ideal model delta sigma weight residual 1.235 1.162 0.073 1.26e-02 6.30e+03 3.36e+01 bond pdb=" N LEU B 624 " pdb=" CA LEU B 624 " ideal model delta sigma weight residual 1.458 1.397 0.060 1.29e-02 6.01e+03 2.18e+01 bond pdb=" N VAL B 488 " pdb=" CA VAL B 488 " ideal model delta sigma weight residual 1.456 1.498 -0.042 9.50e-03 1.11e+04 1.91e+01 bond pdb=" N VAL D 488 " pdb=" CA VAL D 488 " ideal model delta sigma weight residual 1.456 1.498 -0.041 9.50e-03 1.11e+04 1.88e+01 ... (remaining 18459 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.82: 24813 6.82 - 13.63: 30 13.63 - 20.45: 1 20.45 - 27.27: 0 27.27 - 34.08: 1 Bond angle restraints: 24845 Sorted by residual: angle pdb=" O PRO D 717 " pdb=" C PRO D 717 " pdb=" N ASP D 719 " ideal model delta sigma weight residual 121.10 87.02 34.08 1.90e+00 2.77e-01 3.22e+02 angle pdb=" N ASP C 590 " pdb=" CA ASP C 590 " pdb=" C ASP C 590 " ideal model delta sigma weight residual 113.88 104.55 9.33 1.23e+00 6.61e-01 5.76e+01 angle pdb=" CA APHE B 623 " pdb=" C APHE B 623 " pdb=" N LEU B 624 " ideal model delta sigma weight residual 117.02 108.28 8.74 1.17e+00 7.31e-01 5.58e+01 angle pdb=" N CYS D 773 " pdb=" CA CYS D 773 " pdb=" C CYS D 773 " ideal model delta sigma weight residual 111.87 102.02 9.85 1.41e+00 5.03e-01 4.88e+01 angle pdb=" C APHE B 623 " pdb=" N LEU B 624 " pdb=" CA LEU B 624 " ideal model delta sigma weight residual 120.63 109.41 11.22 1.61e+00 3.86e-01 4.86e+01 ... (remaining 24840 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.04: 10285 29.04 - 58.09: 431 58.09 - 87.13: 51 87.13 - 116.18: 8 116.18 - 145.22: 2 Dihedral angle restraints: 10777 sinusoidal: 4255 harmonic: 6522 Sorted by residual: dihedral pdb=" CA PRO D 717 " pdb=" C PRO D 717 " pdb=" N ASP D 719 " pdb=" CA ASP D 719 " ideal model delta harmonic sigma weight residual -180.00 -79.07 -100.93 0 5.00e+00 4.00e-02 4.07e+02 dihedral pdb=" CB CYS F 40 " pdb=" SG CYS F 40 " pdb=" SG CYS F 68 " pdb=" CB CYS F 68 " ideal model delta sinusoidal sigma weight residual 93.00 25.21 67.79 1 1.00e+01 1.00e-02 5.97e+01 dihedral pdb=" CB CYS E 40 " pdb=" SG CYS E 40 " pdb=" SG CYS E 68 " pdb=" CB CYS E 68 " ideal model delta sinusoidal sigma weight residual 93.00 36.95 56.05 1 1.00e+01 1.00e-02 4.24e+01 ... (remaining 10774 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 1511 0.088 - 0.177: 1067 0.177 - 0.265: 164 0.265 - 0.354: 20 0.354 - 0.442: 3 Chirality restraints: 2765 Sorted by residual: chirality pdb=" CG LEU D 498 " pdb=" CB LEU D 498 " pdb=" CD1 LEU D 498 " pdb=" CD2 LEU D 498 " both_signs ideal model delta sigma weight residual False -2.59 -2.15 -0.44 2.00e-01 2.50e+01 4.89e+00 chirality pdb=" CG LEU B 498 " pdb=" CB LEU B 498 " pdb=" CD1 LEU B 498 " pdb=" CD2 LEU B 498 " both_signs ideal model delta sigma weight residual False -2.59 -2.19 -0.40 2.00e-01 2.50e+01 3.93e+00 chirality pdb=" CB VAL D 746 " pdb=" CA VAL D 746 " pdb=" CG1 VAL D 746 " pdb=" CG2 VAL D 746 " both_signs ideal model delta sigma weight residual False -2.63 -2.24 -0.39 2.00e-01 2.50e+01 3.88e+00 ... (remaining 2762 not shown) Planarity restraints: 3012 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO D 717 " 0.149 2.00e-02 2.50e+03 1.91e-01 3.63e+02 pdb=" C PRO D 717 " -0.325 2.00e-02 2.50e+03 pdb=" O PRO D 717 " 0.118 2.00e-02 2.50e+03 pdb=" N ASP D 719 " 0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA APHE B 623 " -0.039 2.00e-02 2.50e+03 8.07e-02 6.51e+01 pdb=" C APHE B 623 " 0.139 2.00e-02 2.50e+03 pdb=" O APHE B 623 " -0.055 2.00e-02 2.50e+03 pdb=" N LEU B 624 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA BPHE B 623 " -0.039 2.00e-02 2.50e+03 8.00e-02 6.40e+01 pdb=" C BPHE B 623 " 0.138 2.00e-02 2.50e+03 pdb=" O BPHE B 623 " -0.055 2.00e-02 2.50e+03 pdb=" N LEU B 624 " -0.045 2.00e-02 2.50e+03 ... (remaining 3009 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 432 2.68 - 3.24: 18100 3.24 - 3.79: 28163 3.79 - 4.35: 39663 4.35 - 4.90: 64037 Nonbonded interactions: 150395 Sorted by model distance: nonbonded pdb=" OG SER C 547 " pdb=" OE2 GLU C 550 " model vdw 2.127 3.040 nonbonded pdb=" O LYS E 129 " pdb=" OG1 THR E 130 " model vdw 2.217 3.040 nonbonded pdb=" O SER E 104 " pdb=" N ILE E 106 " model vdw 2.283 3.120 nonbonded pdb=" CZ APHE B 623 " pdb=" O SER C 785 " model vdw 2.285 3.340 nonbonded pdb=" OG SER A 592 " pdb=" OD2 ASP B 590 " model vdw 2.291 3.040 ... (remaining 150390 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 393 through 504 or (resid 505 through 506 and (name N or n \ ame CA or name C or name O or name CB )) or resid 510 through 573 or resid 575 t \ hrough 593 or (resid 594 and (name N or name CA or name C or name O or name CB ) \ ) or resid 595 through 622 or resid 624 through 626 or resid 633 or resid 635 or \ resid 637 or resid 639 through 709 or resid 711 through 717 or resid 721 throug \ h 812 or (resid 813 and (name N or name CA or name C or name O or name CB )) or \ resid 814 through 818 or (resid 819 through 823 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'B' and (resid 393 through 504 or (resid 505 through 506 and (name N or n \ ame CA or name C or name O or name CB )) or resid 510 or (resid 511 and (name N \ or name CA or name C or name O or name CB )) or resid 512 through 551 or (resid \ 569 and (name N or name CA or name C or name O or name CB )) or resid 570 throug \ h 573 or resid 575 or (resid 576 and (name N or name CA or name C or name O or n \ ame CB )) or resid 577 through 593 or (resid 594 and (name N or name CA or name \ C or name O or name CB )) or resid 595 through 622 or resid 624 through 626 or r \ esid 633 through 635 or resid 637 through 709 or resid 711 through 717 or resid \ 721 through 774 or (resid 784 and (name N or name CA or name C or name O or name \ CB )) or resid 785 through 823)) selection = (chain 'C' and (resid 393 through 504 or (resid 505 through 506 and (name N or n \ ame CA or name C or name O or name CB )) or resid 510 through 573 or resid 575 o \ r (resid 576 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 77 through 622 or resid 624 through 626 or resid 633 or resid 635 or resid 637 o \ r resid 639 through 709 or resid 711 through 717 or resid 721 through 812 or (re \ sid 813 and (name N or name CA or name C or name O or name CB )) or resid 814 th \ rough 818 or (resid 819 through 823 and (name N or name CA or name C or name O o \ r name CB )))) selection = (chain 'D' and (resid 393 through 510 or (resid 511 and (name N or name CA or na \ me C or name O or name CB )) or resid 512 through 551 or (resid 569 and (name N \ or name CA or name C or name O or name CB )) or resid 570 through 573 or resid 5 \ 75 or (resid 576 and (name N or name CA or name C or name O or name CB )) or res \ id 577 through 593 or (resid 594 and (name N or name CA or name C or name O or n \ ame CB )) or resid 595 through 622 or resid 624 through 633 or resid 635 through \ 637 or resid 639 through 717 or resid 721 through 774 or (resid 784 and (name N \ or name CA or name C or name O or name CB )) or resid 785 through 823)) } ncs_group { reference = (chain 'E' and (resid 5 through 69 or (resid 70 and (name N or name CA or name C \ or name O or name CB )) or resid 71 through 84 or resid 93 through 210)) selection = (chain 'F' and (resid 5 through 42 or resid 55 through 69 or (resid 70 and (name \ N or name CA or name C or name O or name CB )) or resid 71 through 84 or resid \ 93 through 210)) selection = (chain 'G' and (resid 5 through 69 or (resid 70 and (name N or name CA or name C \ or name O or name CB )) or resid 71 through 84 or resid 93 through 210)) selection = (chain 'H' and (resid 5 through 42 or resid 55 through 210)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.760 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 50.420 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5148 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 1.634 18475 Z= 1.224 Angle : 1.486 34.082 24867 Z= 1.046 Chirality : 0.105 0.442 2765 Planarity : 0.014 0.267 3012 Dihedral : 15.860 145.221 6594 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.62 % Favored : 96.02 % Rotamer: Outliers : 1.59 % Allowed : 3.01 % Favored : 95.40 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (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 TRP 0.029 0.006 TRP B 578 HIS 0.011 0.003 HIS G 60 PHE 0.034 0.005 PHE C 517 TYR 0.045 0.005 TYR B 469 ARG 0.013 0.002 ARG A 628 Details of bonding type rmsd hydrogen bonds : bond 0.13171 ( 1117) hydrogen bonds : angle 5.26290 ( 3220) SS BOND : bond 0.01568 ( 11) SS BOND : angle 2.98649 ( 22) covalent geometry : bond 0.01712 (18464) covalent geometry : angle 1.48387 (24845) *********************** 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 : 1.901 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: symmetry clash REVERT: B 523 TYR cc_start: 0.9118 (t80) cc_final: 0.8857 (t80) REVERT: B 585 MET cc_start: 0.9335 (mmt) cc_final: 0.8953 (mmt) REVERT: B 770 LYS cc_start: -0.0146 (OUTLIER) cc_final: -0.0376 (pttm) REVERT: C 585 MET cc_start: 0.9164 (mmt) cc_final: 0.8896 (mmm) REVERT: C 586 ARG cc_start: 0.9228 (mmm-85) cc_final: 0.8832 (tmt170) REVERT: D 585 MET cc_start: 0.9521 (mmt) cc_final: 0.9245 (mmt) REVERT: D 619 ASN cc_start: 0.9187 (t0) cc_final: 0.8706 (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: 0.8302 (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: 0.8344 (mm-30) REVERT: F 92 ASP cc_start: 0.7768 (p0) cc_final: 0.6673 (p0) REVERT: F 191 GLU cc_start: 0.9338 (mm-30) cc_final: 0.9115 (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: 0.8807 (mttt) REVERT: H 24 MET cc_start: 0.9153 (tpt) cc_final: 0.8943 (tpp) outliers start: 29 outliers final: 11 residues processed: 373 average time/residue: 0.3696 time to fit residues: 193.0640 Evaluate side-chains 211 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 199 time to evaluate : 1.757 ------------------------------------------------------------------------------- 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 189 optimal weight: 0.8980 chunk 169 optimal weight: 0.8980 chunk 94 optimal weight: 0.5980 chunk 57 optimal weight: 0.7980 chunk 114 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 175 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 130 optimal weight: 0.8980 chunk 203 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS A 587 GLN C 435 HIS C 619 ASN D 435 HIS E 79 GLN E 160 ASN F 132 HIS F 205 HIS H 79 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.143481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.083026 restraints weight = 107114.284| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 6.54 r_work: 0.2927 rms_B_bonded: 5.35 restraints_weight: 2.0000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2929 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2929 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2657 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= 0.137 Angle : 0.629 9.554 24867 Z= 0.324 Chirality : 0.042 0.231 2765 Planarity : 0.004 0.080 3012 Dihedral : 11.691 106.559 2823 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.31 % Favored : 98.46 % Rotamer: Outliers : 1.42 % Allowed : 10.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.18), residues: 2230 helix: 2.36 (0.14), residues: 1313 sheet: -1.56 (0.36), residues: 150 loop : -1.26 (0.21), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 460 HIS 0.011 0.001 HIS G 60 PHE 0.022 0.001 PHE A 495 TYR 0.018 0.001 TYR D 647 ARG 0.014 0.001 ARG D 675 Details of bonding type rmsd hydrogen bonds : bond 0.04316 ( 1117) hydrogen bonds : angle 4.13494 ( 3220) SS BOND : bond 0.00323 ( 11) SS BOND : angle 1.84970 ( 22) covalent geometry : bond 0.00297 (18464) covalent geometry : angle 0.62657 (24845) *********************** 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 272 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 246 time to evaluate : 1.940 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: A 414 MET cc_start: 0.8232 (mpp) cc_final: 0.7512 (ptp) REVERT: A 463 MET cc_start: 0.8502 (mpp) cc_final: 0.7346 (tpp) REVERT: A 479 LEU cc_start: 0.8266 (tp) cc_final: 0.7829 (mt) REVERT: A 503 MET cc_start: -0.1546 (tmm) cc_final: -0.1971 (ttt) REVERT: A 551 TRP cc_start: 0.6627 (m-10) cc_final: 0.6030 (m-10) REVERT: A 587 GLN cc_start: 0.8960 (tp-100) cc_final: 0.8560 (mm-40) REVERT: A 674 MET cc_start: 0.5628 (mtm) cc_final: 0.4930 (ptt) REVERT: B 496 MET cc_start: 0.7116 (mmm) cc_final: 0.6566 (mmm) REVERT: B 585 MET cc_start: 0.9392 (mmt) cc_final: 0.9036 (mmm) REVERT: B 670 MET cc_start: 0.7364 (mmm) cc_final: 0.6812 (mmm) REVERT: C 585 MET cc_start: 0.9103 (mmt) cc_final: 0.8785 (mmm) REVERT: C 619 ASN cc_start: 0.9471 (t0) cc_final: 0.9217 (t0) REVERT: C 670 MET cc_start: 0.6155 (mmm) cc_final: 0.5843 (mmm) REVERT: D 414 MET cc_start: 0.8308 (mpp) cc_final: 0.7716 (mmp) REVERT: D 503 MET cc_start: 0.7179 (mmm) cc_final: 0.6397 (mmm) REVERT: D 551 TRP cc_start: 0.7500 (m100) cc_final: 0.7295 (m100) REVERT: D 619 ASN cc_start: 0.9418 (t0) cc_final: 0.9055 (t0) REVERT: D 639 LEU cc_start: 0.8652 (pt) cc_final: 0.8198 (pt) REVERT: D 670 MET cc_start: 0.6074 (mtt) cc_final: 0.5471 (tpp) REVERT: E 56 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7565 (tp30) REVERT: F 24 MET cc_start: 0.9267 (tpt) cc_final: 0.9030 (tpp) REVERT: F 126 GLU cc_start: 0.8881 (tp30) cc_final: 0.8633 (tp30) REVERT: F 192 MET cc_start: 0.8956 (mtt) cc_final: 0.8594 (tmm) REVERT: F 206 LYS cc_start: 0.9202 (mtpt) cc_final: 0.8858 (mttt) REVERT: G 122 ILE cc_start: 0.9245 (tp) cc_final: 0.9008 (tp) REVERT: H 24 MET cc_start: 0.9248 (tpt) cc_final: 0.8952 (mmm) REVERT: H 37 ARG cc_start: 0.8797 (tpp80) cc_final: 0.8554 (tpp80) REVERT: H 102 ARG cc_start: 0.9076 (tpt90) cc_final: 0.8701 (tpt170) REVERT: H 203 ASP cc_start: 0.9148 (t0) cc_final: 0.8883 (t0) outliers start: 26 outliers final: 13 residues processed: 264 average time/residue: 0.3240 time to fit residues: 127.5842 Evaluate side-chains 211 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 198 time to evaluate : 1.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 534 ILE 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 4 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 131 optimal weight: 1.9990 chunk 102 optimal weight: 20.0000 chunk 181 optimal weight: 0.7980 chunk 220 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 204 optimal weight: 2.9990 chunk 219 optimal weight: 0.6980 chunk 114 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 412 HIS E 160 ASN E 205 HIS G 160 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.143803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.084663 restraints weight = 112181.971| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 6.77 r_work: 0.2994 rms_B_bonded: 5.66 restraints_weight: 2.0000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3004 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3004 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18475 Z= 0.162 Angle : 0.600 9.836 24867 Z= 0.310 Chirality : 0.042 0.195 2765 Planarity : 0.004 0.068 3012 Dihedral : 10.474 90.350 2803 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.12 % Favored : 97.69 % Rotamer: Outliers : 1.92 % Allowed : 11.66 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.18), residues: 2230 helix: 2.63 (0.14), residues: 1321 sheet: -1.61 (0.38), residues: 135 loop : -1.08 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP A 766 HIS 0.009 0.001 HIS G 60 PHE 0.014 0.001 PHE E 107 TYR 0.015 0.001 TYR D 647 ARG 0.013 0.001 ARG A 715 Details of bonding type rmsd hydrogen bonds : bond 0.04216 ( 1117) hydrogen bonds : angle 4.05231 ( 3220) SS BOND : bond 0.01077 ( 11) SS BOND : angle 2.07819 ( 22) covalent geometry : bond 0.00360 (18464) covalent geometry : angle 0.59675 (24845) *********************** 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 244 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 209 time to evaluate : 2.088 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: A 414 MET cc_start: 0.8496 (mpp) cc_final: 0.7913 (ptp) REVERT: A 463 MET cc_start: 0.8535 (mpp) cc_final: 0.7798 (mpp) REVERT: A 479 LEU cc_start: 0.8266 (tp) cc_final: 0.8040 (tp) REVERT: A 503 MET cc_start: -0.1395 (tmm) cc_final: -0.1859 (ttt) REVERT: A 674 MET cc_start: 0.5761 (mtm) cc_final: 0.4970 (ptp) REVERT: A 715 ARG cc_start: 0.5480 (mmp-170) cc_final: 0.5031 (mmp-170) REVERT: B 670 MET cc_start: 0.7393 (mmm) cc_final: 0.6864 (mmm) REVERT: C 585 MET cc_start: 0.9222 (mmt) cc_final: 0.8798 (mmm) REVERT: C 619 ASN cc_start: 0.9521 (t0) cc_final: 0.9178 (t0) REVERT: C 670 MET cc_start: 0.6103 (mmm) cc_final: 0.5807 (mmt) REVERT: D 407 MET cc_start: 0.7914 (pmm) cc_final: 0.7334 (pmm) REVERT: D 414 MET cc_start: 0.8366 (mpp) cc_final: 0.7856 (mmp) REVERT: D 463 MET cc_start: 0.5665 (mpp) cc_final: 0.5265 (mpp) REVERT: D 503 MET cc_start: 0.7091 (mmm) cc_final: 0.6439 (mmm) REVERT: D 619 ASN cc_start: 0.9438 (t0) cc_final: 0.8994 (t0) REVERT: D 639 LEU cc_start: 0.8631 (pt) cc_final: 0.8309 (pt) REVERT: D 670 MET cc_start: 0.6371 (mtt) cc_final: 0.5873 (tpp) REVERT: E 56 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7547 (tp30) REVERT: E 160 ASN cc_start: 0.8379 (t0) cc_final: 0.8157 (t0) REVERT: F 117 MET cc_start: 0.8752 (mmm) cc_final: 0.8487 (mmm) REVERT: F 126 GLU cc_start: 0.8957 (tp30) cc_final: 0.8713 (tp30) REVERT: F 192 MET cc_start: 0.8945 (mtt) cc_final: 0.8689 (tmm) REVERT: F 206 LYS cc_start: 0.9282 (mtpt) cc_final: 0.9028 (mttt) REVERT: G 99 ARG cc_start: 0.9343 (mmm-85) cc_final: 0.8790 (mmm-85) REVERT: G 117 MET cc_start: 0.9307 (mmm) cc_final: 0.9087 (mmm) REVERT: H 203 ASP cc_start: 0.9164 (t0) cc_final: 0.8935 (t0) outliers start: 35 outliers final: 24 residues processed: 232 average time/residue: 0.3274 time to fit residues: 113.4282 Evaluate side-chains 208 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 184 time to evaluate : 1.995 ------------------------------------------------------------------------------- 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 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 591 ILE 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 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 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 G residue 185 LEU Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain H residue 153 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 108 optimal weight: 30.0000 chunk 111 optimal weight: 10.0000 chunk 158 optimal weight: 0.9990 chunk 183 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 chunk 123 optimal weight: 0.0010 chunk 50 optimal weight: 10.0000 chunk 127 optimal weight: 3.9990 chunk 84 optimal weight: 10.0000 chunk 143 optimal weight: 10.0000 chunk 214 optimal weight: 10.0000 overall best weight: 4.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 HIS D 569 ASN ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 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 = 0.4197 r_free = 0.4197 target = 0.135868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.075848 restraints weight = 108190.031| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 5.96 r_work: 0.2791 rms_B_bonded: 5.53 restraints_weight: 2.0000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2795 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2795 r_free = 0.2795 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2795 r_free = 0.2795 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2795 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.4090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.060 18475 Z= 0.373 Angle : 0.767 9.624 24867 Z= 0.395 Chirality : 0.048 0.269 2765 Planarity : 0.005 0.055 3012 Dihedral : 11.141 86.734 2803 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.30 % Favored : 96.52 % Rotamer: Outliers : 2.90 % Allowed : 12.81 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.18), residues: 2230 helix: 2.13 (0.14), residues: 1335 sheet: -1.83 (0.38), residues: 129 loop : -1.08 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 551 HIS 0.029 0.002 HIS E 205 PHE 0.027 0.003 PHE E 107 TYR 0.020 0.002 TYR B 673 ARG 0.006 0.001 ARG A 715 Details of bonding type rmsd hydrogen bonds : bond 0.05343 ( 1117) hydrogen bonds : angle 4.56946 ( 3220) SS BOND : bond 0.00844 ( 11) SS BOND : angle 1.87785 ( 22) covalent geometry : bond 0.00858 (18464) covalent geometry : angle 0.76517 (24845) *********************** 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 228 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 176 time to evaluate : 2.016 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: 0.8406 (mpp) cc_final: 0.7699 (ptp) REVERT: A 674 MET cc_start: 0.5352 (mtm) cc_final: 0.4500 (ptp) REVERT: A 708 MET cc_start: 0.5149 (mpp) cc_final: 0.4590 (mmt) REVERT: A 715 ARG cc_start: 0.5761 (OUTLIER) cc_final: 0.4757 (mmp-170) REVERT: B 670 MET cc_start: 0.7137 (mmm) cc_final: 0.6686 (mmm) REVERT: C 585 MET cc_start: 0.9233 (mmt) cc_final: 0.8823 (mmm) REVERT: C 670 MET cc_start: 0.6196 (mmm) cc_final: 0.5869 (mmt) REVERT: D 407 MET cc_start: 0.7932 (pmm) cc_final: 0.7265 (pmm) REVERT: D 414 MET cc_start: 0.8216 (mpp) cc_final: 0.7682 (mmp) REVERT: D 483 LEU cc_start: 0.9029 (tt) cc_final: 0.8812 (mp) REVERT: D 503 MET cc_start: 0.6400 (mmm) cc_final: 0.6157 (mmm) REVERT: D 619 ASN cc_start: 0.9492 (t0) cc_final: 0.9179 (t0) REVERT: D 670 MET cc_start: 0.6699 (mtt) cc_final: 0.6305 (mtt) REVERT: E 10 MET cc_start: 0.8755 (mmm) cc_final: 0.8468 (tmm) REVERT: E 56 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7552 (tp30) REVERT: F 10 MET cc_start: 0.9479 (tpp) cc_final: 0.9223 (tpp) REVERT: F 81 ASP cc_start: 0.8792 (t0) cc_final: 0.8516 (t0) REVERT: F 192 MET cc_start: 0.9015 (mtt) cc_final: 0.8701 (ttt) REVERT: F 206 LYS cc_start: 0.9305 (mtpt) cc_final: 0.9009 (mttt) REVERT: G 117 MET cc_start: 0.9285 (mmm) cc_final: 0.9023 (mmm) REVERT: H 160 ASN cc_start: 0.8401 (m-40) cc_final: 0.8113 (m110) REVERT: H 203 ASP cc_start: 0.9193 (t0) cc_final: 0.8947 (t0) outliers start: 52 outliers final: 38 residues processed: 213 average time/residue: 0.3108 time to fit residues: 100.0784 Evaluate side-chains 199 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 160 time to evaluate : 2.003 ------------------------------------------------------------------------------- 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 715 ARG Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 592 SER 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 529 ILE Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain E residue 59 THR 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 66 THR Chi-restraints excluded: chain F residue 67 CYS Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 200 MET Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 41 LYS Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 153 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 129 optimal weight: 0.9980 chunk 139 optimal weight: 20.0000 chunk 173 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 212 optimal weight: 2.9990 chunk 156 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 122 optimal weight: 8.9990 chunk 178 optimal weight: 2.9990 chunk 113 optimal weight: 10.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.138233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.079077 restraints weight = 98207.325| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 6.18 r_work: 0.2858 rms_B_bonded: 5.38 restraints_weight: 2.0000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2858 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2858 r_free = 0.2858 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2858 r_free = 0.2858 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2858 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.4262 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= 0.193 Angle : 0.637 17.109 24867 Z= 0.323 Chirality : 0.042 0.215 2765 Planarity : 0.004 0.058 3012 Dihedral : 10.312 89.896 2803 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.31 % Favored : 97.51 % Rotamer: Outliers : 2.79 % Allowed : 13.25 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.18), residues: 2230 helix: 2.54 (0.14), residues: 1331 sheet: -1.69 (0.42), residues: 118 loop : -1.08 (0.22), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 551 HIS 0.008 0.001 HIS G 60 PHE 0.016 0.001 PHE G 18 TYR 0.041 0.001 TYR A 424 ARG 0.005 0.001 ARG B 715 Details of bonding type rmsd hydrogen bonds : bond 0.04348 ( 1117) hydrogen bonds : angle 4.16582 ( 3220) SS BOND : bond 0.00621 ( 11) SS BOND : angle 1.71652 ( 22) covalent geometry : bond 0.00446 (18464) covalent geometry : angle 0.63508 (24845) *********************** 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 232 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 182 time to evaluate : 1.783 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: 0.8296 (mpp) cc_final: 0.7709 (ptp) REVERT: A 463 MET cc_start: 0.8532 (mpp) cc_final: 0.7516 (mpp) REVERT: A 487 GLU cc_start: 0.9156 (mt-10) cc_final: 0.8874 (pp20) REVERT: A 674 MET cc_start: 0.5307 (mtm) cc_final: 0.4048 (ptm) REVERT: A 715 ARG cc_start: 0.5598 (OUTLIER) cc_final: 0.5015 (mmp-170) REVERT: B 496 MET cc_start: 0.7327 (mmm) cc_final: 0.6397 (mmm) REVERT: B 670 MET cc_start: 0.7673 (mmm) cc_final: 0.7178 (mmm) REVERT: B 714 GLN cc_start: 0.8537 (mm-40) cc_final: 0.7624 (tp-100) REVERT: C 585 MET cc_start: 0.9141 (mmt) cc_final: 0.8733 (mmt) REVERT: D 407 MET cc_start: 0.7960 (pmm) cc_final: 0.7332 (pmm) REVERT: D 414 MET cc_start: 0.8187 (mpp) cc_final: 0.7923 (mmp) REVERT: D 503 MET cc_start: 0.6699 (mmm) cc_final: 0.6266 (mmm) REVERT: D 619 ASN cc_start: 0.9498 (t0) cc_final: 0.9127 (t0) REVERT: D 670 MET cc_start: 0.6832 (mtt) cc_final: 0.6451 (mtt) REVERT: E 10 MET cc_start: 0.8748 (mmm) cc_final: 0.8432 (mmm) REVERT: E 56 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7351 (tp30) REVERT: F 10 MET cc_start: 0.9479 (tpp) cc_final: 0.9222 (tpp) REVERT: F 117 MET cc_start: 0.8627 (mmm) cc_final: 0.8350 (mmm) REVERT: F 126 GLU cc_start: 0.8830 (tp30) cc_final: 0.8569 (tp30) REVERT: F 192 MET cc_start: 0.8994 (mtt) cc_final: 0.8722 (ttt) REVERT: F 206 LYS cc_start: 0.9291 (mtpt) cc_final: 0.8972 (mttt) REVERT: G 99 ARG cc_start: 0.9337 (mmm-85) cc_final: 0.8632 (mmm-85) REVERT: G 117 MET cc_start: 0.9239 (mmm) cc_final: 0.9001 (mmm) REVERT: H 203 ASP cc_start: 0.9192 (t0) cc_final: 0.8952 (t0) outliers start: 50 outliers final: 38 residues processed: 220 average time/residue: 0.3268 time to fit residues: 111.0924 Evaluate side-chains 200 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 161 time to evaluate : 1.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 LEU 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 715 ARG Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 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 66 THR Chi-restraints excluded: chain F residue 67 CYS Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain 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 H residue 26 ILE Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 205 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 96 optimal weight: 0.9990 chunk 219 optimal weight: 0.6980 chunk 168 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 chunk 216 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 218 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 120 optimal weight: 9.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 791 ASN E 132 HIS E 205 HIS G 160 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.140211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.081765 restraints weight = 115868.446| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 6.95 r_work: 0.2870 rms_B_bonded: 5.98 restraints_weight: 2.0000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2874 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2874 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 18475 Z= 0.126 Angle : 0.597 16.153 24867 Z= 0.299 Chirality : 0.041 0.256 2765 Planarity : 0.004 0.055 3012 Dihedral : 9.566 86.162 2801 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.08 % Favored : 97.74 % Rotamer: Outliers : 2.19 % Allowed : 14.40 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.19), residues: 2230 helix: 2.84 (0.14), residues: 1329 sheet: -1.49 (0.40), residues: 137 loop : -1.06 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 551 HIS 0.025 0.002 HIS E 205 PHE 0.021 0.001 PHE A 659 TYR 0.029 0.001 TYR A 424 ARG 0.005 0.000 ARG A 715 Details of bonding type rmsd hydrogen bonds : bond 0.03851 ( 1117) hydrogen bonds : angle 3.98075 ( 3220) SS BOND : bond 0.00749 ( 11) SS BOND : angle 2.53547 ( 22) covalent geometry : bond 0.00285 (18464) covalent geometry : angle 0.59235 (24845) *********************** 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 229 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 190 time to evaluate : 2.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 MET cc_start: 0.8299 (mpp) cc_final: 0.7794 (ptp) REVERT: A 463 MET cc_start: 0.8285 (mpp) cc_final: 0.7129 (mmt) REVERT: A 485 ARG cc_start: 0.7841 (mtt180) cc_final: 0.6763 (ptm160) REVERT: A 487 GLU cc_start: 0.9225 (mt-10) cc_final: 0.8939 (pp20) REVERT: A 674 MET cc_start: 0.5282 (mtm) cc_final: 0.3980 (ptm) REVERT: A 715 ARG cc_start: 0.5357 (OUTLIER) cc_final: 0.4843 (mmp-170) REVERT: B 496 MET cc_start: 0.7363 (mmm) cc_final: 0.6428 (mmm) REVERT: B 670 MET cc_start: 0.7687 (mmm) cc_final: 0.7278 (mmm) REVERT: C 414 MET cc_start: 0.6657 (mpp) cc_final: 0.6346 (ppp) REVERT: C 585 MET cc_start: 0.9062 (mmt) cc_final: 0.8630 (mmt) REVERT: C 670 MET cc_start: 0.6182 (mmm) cc_final: 0.5926 (mmm) REVERT: D 407 MET cc_start: 0.7881 (pmm) cc_final: 0.7312 (pmm) REVERT: D 414 MET cc_start: 0.8417 (mpp) cc_final: 0.8208 (mmp) REVERT: D 503 MET cc_start: 0.7009 (mmm) cc_final: 0.6444 (mmm) REVERT: D 619 ASN cc_start: 0.9494 (t0) cc_final: 0.9007 (t0) REVERT: D 670 MET cc_start: 0.6794 (mtt) cc_final: 0.6523 (mtt) REVERT: E 56 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7593 (tp30) REVERT: F 117 MET cc_start: 0.8706 (mmm) cc_final: 0.8391 (mmm) REVERT: F 126 GLU cc_start: 0.8899 (tp30) cc_final: 0.8682 (tp30) REVERT: F 192 MET cc_start: 0.8995 (mtt) cc_final: 0.8741 (ttt) REVERT: F 206 LYS cc_start: 0.9284 (mtpt) cc_final: 0.8942 (mttt) REVERT: G 99 ARG cc_start: 0.9351 (mmm-85) cc_final: 0.8692 (mmm-85) REVERT: G 117 MET cc_start: 0.9213 (mmm) cc_final: 0.8970 (mmm) REVERT: G 205 HIS cc_start: 0.8746 (OUTLIER) cc_final: 0.8149 (m-70) REVERT: H 66 THR cc_start: 0.9036 (OUTLIER) cc_final: 0.8811 (p) REVERT: H 160 ASN cc_start: 0.8671 (m-40) cc_final: 0.8388 (m110) REVERT: H 203 ASP cc_start: 0.9205 (t0) cc_final: 0.8997 (t0) outliers start: 39 outliers final: 26 residues processed: 217 average time/residue: 0.3062 time to fit residues: 102.0863 Evaluate side-chains 202 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 173 time to evaluate : 1.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 LEU 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 715 ARG Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain E residue 66 THR 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 28 VAL Chi-restraints excluded: chain F residue 67 CYS 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 G residue 205 HIS Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 66 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 95 optimal weight: 0.0980 chunk 85 optimal weight: 20.0000 chunk 30 optimal weight: 2.9990 chunk 222 optimal weight: 4.9990 chunk 161 optimal weight: 10.0000 chunk 60 optimal weight: 8.9990 chunk 174 optimal weight: 6.9990 chunk 219 optimal weight: 0.9990 chunk 112 optimal weight: 8.9990 chunk 218 optimal weight: 0.8980 chunk 135 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 619 ASN E 205 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.140182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.081818 restraints weight = 113293.269| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 6.86 r_work: 0.2874 rms_B_bonded: 5.86 restraints_weight: 2.0000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2877 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 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 = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2877 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.4591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 18475 Z= 0.138 Angle : 0.619 15.437 24867 Z= 0.306 Chirality : 0.042 0.270 2765 Planarity : 0.004 0.055 3012 Dihedral : 9.305 86.490 2801 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.94 % Favored : 97.88 % Rotamer: Outliers : 2.03 % Allowed : 15.22 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.19), residues: 2230 helix: 2.84 (0.14), residues: 1330 sheet: -1.43 (0.42), residues: 120 loop : -1.13 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 551 HIS 0.007 0.001 HIS E 205 PHE 0.020 0.001 PHE A 659 TYR 0.026 0.001 TYR A 424 ARG 0.005 0.000 ARG D 743 Details of bonding type rmsd hydrogen bonds : bond 0.03921 ( 1117) hydrogen bonds : angle 3.98226 ( 3220) SS BOND : bond 0.00605 ( 11) SS BOND : angle 2.28216 ( 22) covalent geometry : bond 0.00316 (18464) covalent geometry : angle 0.61533 (24845) *********************** 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 214 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 178 time to evaluate : 1.858 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: 0.8401 (mpp) cc_final: 0.8049 (ptp) REVERT: A 463 MET cc_start: 0.8256 (mpp) cc_final: 0.7125 (mmt) REVERT: A 485 ARG cc_start: 0.7834 (mtt180) cc_final: 0.6748 (ptm160) REVERT: A 487 GLU cc_start: 0.9211 (mt-10) cc_final: 0.8921 (pp20) REVERT: A 674 MET cc_start: 0.5179 (mtm) cc_final: 0.3883 (ptm) REVERT: A 715 ARG cc_start: 0.4966 (mmp-170) cc_final: 0.4436 (mmp-170) REVERT: B 496 MET cc_start: 0.7568 (mmm) cc_final: 0.6825 (mmm) REVERT: B 670 MET cc_start: 0.7743 (mmm) cc_final: 0.7207 (mmm) REVERT: C 585 MET cc_start: 0.9011 (mmt) cc_final: 0.8577 (mmt) REVERT: D 407 MET cc_start: 0.7900 (pmm) cc_final: 0.7289 (pmm) REVERT: D 503 MET cc_start: 0.7037 (mmm) cc_final: 0.6575 (mmm) REVERT: D 619 ASN cc_start: 0.9500 (t0) cc_final: 0.9016 (t0) REVERT: E 56 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7614 (tp30) REVERT: F 117 MET cc_start: 0.8675 (mmm) cc_final: 0.8428 (mmm) REVERT: F 126 GLU cc_start: 0.8895 (tp30) cc_final: 0.8673 (tp30) REVERT: F 192 MET cc_start: 0.9020 (mtt) cc_final: 0.8765 (ttt) REVERT: F 206 LYS cc_start: 0.9284 (mtpt) cc_final: 0.8939 (mttt) REVERT: G 99 ARG cc_start: 0.9343 (mmm-85) cc_final: 0.8724 (mmm-85) REVERT: G 117 MET cc_start: 0.9163 (mmm) cc_final: 0.8900 (mmm) REVERT: H 160 ASN cc_start: 0.8648 (m-40) cc_final: 0.8340 (m110) REVERT: H 203 ASP cc_start: 0.9191 (t0) cc_final: 0.8981 (t0) outliers start: 36 outliers final: 31 residues processed: 204 average time/residue: 0.2994 time to fit residues: 94.1804 Evaluate side-chains 203 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 172 time to evaluate : 1.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 LEU 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 589 CYS Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain E residue 117 MET Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain 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 12 LEU Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 66 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 199 optimal weight: 5.9990 chunk 121 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 110 optimal weight: 20.0000 chunk 7 optimal weight: 4.9990 chunk 125 optimal weight: 0.3980 chunk 208 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 163 optimal weight: 1.9990 chunk 145 optimal weight: 8.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 GLN ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.139950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.080832 restraints weight = 114330.735| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 6.48 r_work: 0.2923 rms_B_bonded: 5.47 restraints_weight: 2.0000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2929 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2929 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.4760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 18475 Z= 0.233 Angle : 0.675 15.757 24867 Z= 0.336 Chirality : 0.043 0.220 2765 Planarity : 0.004 0.051 3012 Dihedral : 9.722 88.703 2801 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.89 % Favored : 96.93 % Rotamer: Outliers : 2.41 % Allowed : 15.16 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.19), residues: 2230 helix: 2.73 (0.14), residues: 1325 sheet: -1.64 (0.42), residues: 123 loop : -1.07 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 551 HIS 0.021 0.002 HIS E 205 PHE 0.020 0.002 PHE A 659 TYR 0.028 0.002 TYR A 424 ARG 0.005 0.001 ARG A 715 Details of bonding type rmsd hydrogen bonds : bond 0.04527 ( 1117) hydrogen bonds : angle 4.22744 ( 3220) SS BOND : bond 0.00722 ( 11) SS BOND : angle 2.22453 ( 22) covalent geometry : bond 0.00540 (18464) covalent geometry : angle 0.67184 (24845) *********************** 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 207 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 164 time to evaluate : 2.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 MET cc_start: 0.8339 (mpp) cc_final: 0.7936 (ptp) REVERT: A 463 MET cc_start: 0.8484 (mpp) cc_final: 0.7655 (mmt) REVERT: A 485 ARG cc_start: 0.7866 (mtt180) cc_final: 0.7604 (mtt180) REVERT: A 487 GLU cc_start: 0.9167 (mt-10) cc_final: 0.8851 (pp20) REVERT: A 674 MET cc_start: 0.5086 (mtm) cc_final: 0.3843 (ptm) REVERT: A 715 ARG cc_start: 0.5152 (OUTLIER) cc_final: 0.4582 (mmp-170) REVERT: A 721 MET cc_start: 0.4432 (mmm) cc_final: 0.4148 (mmm) REVERT: B 496 MET cc_start: 0.7566 (mmm) cc_final: 0.6805 (mmm) REVERT: B 670 MET cc_start: 0.7636 (mmm) cc_final: 0.7192 (mmm) REVERT: D 407 MET cc_start: 0.8046 (pmm) cc_final: 0.7400 (pmm) REVERT: D 619 ASN cc_start: 0.9481 (t0) cc_final: 0.9124 (t0) REVERT: D 721 MET cc_start: 0.8834 (ttm) cc_final: 0.8525 (tmm) REVERT: E 10 MET cc_start: 0.8741 (mmm) cc_final: 0.8468 (mmm) REVERT: E 56 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7405 (tp30) REVERT: F 117 MET cc_start: 0.8734 (mmm) cc_final: 0.8514 (mmm) REVERT: F 206 LYS cc_start: 0.9273 (mtpt) cc_final: 0.8917 (mttt) REVERT: G 99 ARG cc_start: 0.9304 (mmm-85) cc_final: 0.8714 (mmm-85) REVERT: G 117 MET cc_start: 0.9297 (mmm) cc_final: 0.9076 (mmm) REVERT: G 205 HIS cc_start: 0.8852 (OUTLIER) cc_final: 0.8280 (m-70) REVERT: H 203 ASP cc_start: 0.9210 (t0) cc_final: 0.8999 (t0) outliers start: 43 outliers final: 36 residues processed: 195 average time/residue: 0.2999 time to fit residues: 90.8712 Evaluate side-chains 199 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 161 time to evaluate : 2.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 LEU 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 587 GLN Chi-restraints excluded: chain A residue 715 ARG Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain E residue 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 66 THR Chi-restraints excluded: chain F residue 67 CYS Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain 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 40 CYS Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 153 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 96 optimal weight: 0.6980 chunk 161 optimal weight: 3.9990 chunk 201 optimal weight: 0.9990 chunk 211 optimal weight: 0.0000 chunk 98 optimal weight: 0.7980 chunk 121 optimal weight: 0.8980 chunk 176 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 142 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 159 optimal weight: 6.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 HIS G 160 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.143581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.084786 restraints weight = 116214.261| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 6.47 r_work: 0.2984 rms_B_bonded: 5.62 restraints_weight: 2.0000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2989 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2989 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.4860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 18475 Z= 0.120 Angle : 0.631 15.023 24867 Z= 0.309 Chirality : 0.041 0.265 2765 Planarity : 0.004 0.054 3012 Dihedral : 9.105 87.417 2801 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.99 % Favored : 97.83 % Rotamer: Outliers : 1.92 % Allowed : 15.87 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.19), residues: 2230 helix: 2.95 (0.14), residues: 1322 sheet: -1.24 (0.45), residues: 106 loop : -1.18 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 551 HIS 0.008 0.001 HIS E 205 PHE 0.025 0.001 PHE B 659 TYR 0.023 0.001 TYR A 424 ARG 0.004 0.000 ARG A 715 Details of bonding type rmsd hydrogen bonds : bond 0.03874 ( 1117) hydrogen bonds : angle 3.95855 ( 3220) SS BOND : bond 0.00833 ( 11) SS BOND : angle 2.15654 ( 22) covalent geometry : bond 0.00265 (18464) covalent geometry : angle 0.62751 (24845) *********************** 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 224 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 190 time to evaluate : 1.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 MET cc_start: 0.8124 (mpp) cc_final: 0.7877 (ptp) REVERT: A 463 MET cc_start: 0.8240 (mpp) cc_final: 0.7087 (mmt) REVERT: A 485 ARG cc_start: 0.7855 (mtt180) cc_final: 0.6765 (ptm160) REVERT: A 487 GLU cc_start: 0.9290 (mt-10) cc_final: 0.8931 (pp20) REVERT: A 674 MET cc_start: 0.5062 (mtm) cc_final: 0.3819 (ptm) REVERT: A 715 ARG cc_start: 0.4917 (OUTLIER) cc_final: 0.4447 (mmp-170) REVERT: A 721 MET cc_start: 0.4184 (mmm) cc_final: 0.3945 (mmm) REVERT: B 496 MET cc_start: 0.7559 (mmm) cc_final: 0.6790 (mmm) REVERT: B 670 MET cc_start: 0.7800 (mmm) cc_final: 0.7320 (mmm) REVERT: D 407 MET cc_start: 0.7997 (pmm) cc_final: 0.7067 (pmm) REVERT: D 619 ASN cc_start: 0.9480 (t0) cc_final: 0.8991 (t0) REVERT: D 670 MET cc_start: 0.7564 (mtt) cc_final: 0.7344 (mmm) REVERT: D 674 MET cc_start: 0.2994 (pmm) cc_final: 0.2785 (pmm) REVERT: E 56 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7560 (tp30) REVERT: F 56 GLU cc_start: 0.8297 (mm-30) cc_final: 0.7641 (mm-30) REVERT: F 117 MET cc_start: 0.8712 (mmm) cc_final: 0.8500 (mmm) REVERT: F 206 LYS cc_start: 0.9263 (mtpt) cc_final: 0.8889 (mttt) REVERT: G 99 ARG cc_start: 0.9345 (mmm-85) cc_final: 0.8758 (mmm-85) REVERT: G 117 MET cc_start: 0.9212 (mmm) cc_final: 0.8950 (mmm) REVERT: G 205 HIS cc_start: 0.8809 (OUTLIER) cc_final: 0.8327 (m-70) REVERT: H 203 ASP cc_start: 0.9128 (t0) cc_final: 0.8920 (t0) outliers start: 34 outliers final: 28 residues processed: 212 average time/residue: 0.3158 time to fit residues: 104.8084 Evaluate side-chains 211 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 181 time to evaluate : 1.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 LEU 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 715 ARG Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain E residue 117 MET Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 67 CYS Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 200 MET Chi-restraints excluded: chain F residue 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 157 optimal weight: 4.9990 chunk 188 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 140 optimal weight: 20.0000 chunk 187 optimal weight: 2.9990 chunk 178 optimal weight: 0.9980 chunk 141 optimal weight: 4.9990 chunk 149 optimal weight: 0.8980 chunk 174 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.142149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.082687 restraints weight = 135570.352| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 6.92 r_work: 0.2951 rms_B_bonded: 5.85 restraints_weight: 2.0000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2949 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2949 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.4909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 18475 Z= 0.145 Angle : 0.628 14.448 24867 Z= 0.310 Chirality : 0.042 0.266 2765 Planarity : 0.004 0.056 3012 Dihedral : 9.042 89.139 2801 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.31 % Favored : 97.51 % Rotamer: Outliers : 1.97 % Allowed : 15.65 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.19), residues: 2230 helix: 2.95 (0.14), residues: 1322 sheet: -1.34 (0.43), residues: 123 loop : -1.11 (0.22), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 551 HIS 0.009 0.001 HIS E 205 PHE 0.032 0.001 PHE B 659 TYR 0.022 0.001 TYR A 424 ARG 0.004 0.000 ARG A 715 Details of bonding type rmsd hydrogen bonds : bond 0.03944 ( 1117) hydrogen bonds : angle 3.99804 ( 3220) SS BOND : bond 0.00770 ( 11) SS BOND : angle 2.16537 ( 22) covalent geometry : bond 0.00333 (18464) covalent geometry : angle 0.62536 (24845) ********************** 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 212 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 177 time to evaluate : 2.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 MET cc_start: 0.8052 (mpp) cc_final: 0.7778 (ptp) REVERT: A 463 MET cc_start: 0.8271 (mpp) cc_final: 0.7166 (mmt) REVERT: A 485 ARG cc_start: 0.7831 (mtt180) cc_final: 0.7543 (mtt180) REVERT: A 487 GLU cc_start: 0.9297 (mt-10) cc_final: 0.8938 (pp20) REVERT: A 674 MET cc_start: 0.5063 (mtm) cc_final: 0.3834 (ptm) REVERT: A 715 ARG cc_start: 0.4994 (OUTLIER) cc_final: 0.4457 (mmp-170) REVERT: A 721 MET cc_start: 0.4270 (mmm) cc_final: 0.4010 (mmm) REVERT: B 496 MET cc_start: 0.7594 (mmm) cc_final: 0.6801 (mmm) REVERT: B 670 MET cc_start: 0.7657 (mmm) cc_final: 0.7202 (mmm) REVERT: D 407 MET cc_start: 0.8054 (pmm) cc_final: 0.7121 (pmm) REVERT: D 619 ASN cc_start: 0.9501 (t0) cc_final: 0.9046 (t0) REVERT: D 674 MET cc_start: 0.2969 (pmm) cc_final: 0.2746 (pmm) REVERT: D 742 LEU cc_start: 0.7643 (mp) cc_final: 0.7287 (tt) REVERT: E 56 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7580 (tp30) REVERT: F 56 GLU cc_start: 0.8350 (mm-30) cc_final: 0.7665 (mm-30) REVERT: F 117 MET cc_start: 0.8733 (mmm) cc_final: 0.8523 (mmm) REVERT: F 206 LYS cc_start: 0.9267 (mtpt) cc_final: 0.8889 (mttt) REVERT: G 99 ARG cc_start: 0.9337 (mmm-85) cc_final: 0.9006 (mmt90) REVERT: G 117 MET cc_start: 0.9254 (mmm) cc_final: 0.9001 (mmm) REVERT: G 205 HIS cc_start: 0.8818 (OUTLIER) cc_final: 0.8385 (m-70) REVERT: H 203 ASP cc_start: 0.9156 (t0) cc_final: 0.8954 (t0) outliers start: 35 outliers final: 28 residues processed: 199 average time/residue: 0.3166 time to fit residues: 98.6936 Evaluate side-chains 203 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 173 time to evaluate : 1.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 LEU 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 715 ARG Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain E residue 117 MET Chi-restraints excluded: chain E residue 195 VAL 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 212 optimal weight: 9.9990 chunk 53 optimal weight: 0.7980 chunk 193 optimal weight: 9.9990 chunk 79 optimal weight: 6.9990 chunk 11 optimal weight: 0.0170 chunk 191 optimal weight: 2.9990 chunk 39 optimal weight: 30.0000 chunk 92 optimal weight: 1.9990 chunk 32 optimal weight: 0.0570 chunk 121 optimal weight: 9.9990 chunk 194 optimal weight: 0.7980 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 GLN ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.143628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.084157 restraints weight = 121485.236| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 6.55 r_work: 0.3001 rms_B_bonded: 5.59 restraints_weight: 2.0000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3007 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3007 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.5040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18475 Z= 0.116 Angle : 0.617 14.896 24867 Z= 0.302 Chirality : 0.041 0.245 2765 Planarity : 0.004 0.058 3012 Dihedral : 8.729 89.602 2801 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.99 % Favored : 97.83 % Rotamer: Outliers : 1.86 % Allowed : 16.09 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.19), residues: 2230 helix: 3.02 (0.14), residues: 1320 sheet: -1.28 (0.43), residues: 129 loop : -1.10 (0.22), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 671 HIS 0.005 0.001 HIS G 60 PHE 0.022 0.001 PHE G 18 TYR 0.024 0.001 TYR D 647 ARG 0.005 0.000 ARG G 204 Details of bonding type rmsd hydrogen bonds : bond 0.03719 ( 1117) hydrogen bonds : angle 3.93180 ( 3220) SS BOND : bond 0.00679 ( 11) SS BOND : angle 1.98945 ( 22) covalent geometry : bond 0.00255 (18464) covalent geometry : angle 0.61490 (24845) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11392.53 seconds wall clock time: 196 minutes 58.00 seconds (11818.00 seconds total)