Starting phenix.real_space_refine on Tue Nov 19 05:01:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8piv_17692/11_2024/8piv_17692.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8piv_17692/11_2024/8piv_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8piv_17692/11_2024/8piv_17692.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8piv_17692/11_2024/8piv_17692.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8piv_17692/11_2024/8piv_17692.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8piv_17692/11_2024/8piv_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 16.31, per 1000 atoms: 0.90 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: 4.52 Conformation dependent library (CDL) restraints added in 3.8 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: 1.86 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: 5.57 Time building geometry restraints manager: 5.21 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: 0.700 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: 0.680 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 47.800 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.100 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.390 ------------------------------------------------------------------------------- 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 18464 Z= 0.970 Angle : 1.484 34.082 24845 Z= 1.045 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 *********************** 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 : 1.926 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: 0.3990 time to fit residues: 207.8160 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 : 2.104 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5181 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 18464 Z= 0.196 Angle : 0.627 9.554 24845 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 *********************** 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 : 1.949 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: 0.5077 (mpp) cc_final: 0.4805 (ptp) REVERT: A 503 MET cc_start: 0.0456 (tmm) cc_final: -0.0029 (ttt) REVERT: A 551 TRP cc_start: 0.6348 (m-10) cc_final: 0.5622 (m-10) REVERT: A 587 GLN cc_start: 0.8383 (tp-100) cc_final: 0.8020 (mm-40) REVERT: B 585 MET cc_start: 0.9291 (mmt) cc_final: 0.8890 (mmm) REVERT: C 585 MET cc_start: 0.9224 (mmt) cc_final: 0.8852 (mmm) REVERT: C 586 ARG cc_start: 0.9382 (mmm-85) cc_final: 0.8885 (tmt-80) REVERT: C 619 ASN cc_start: 0.9256 (t0) cc_final: 0.8962 (t0) REVERT: D 551 TRP cc_start: 0.7076 (m100) cc_final: 0.6864 (m100) REVERT: D 619 ASN cc_start: 0.9228 (t0) cc_final: 0.8929 (t0) REVERT: E 56 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8304 (tp30) REVERT: F 24 MET cc_start: 0.9061 (tpt) cc_final: 0.8840 (tpp) REVERT: F 56 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8411 (mm-30) REVERT: F 192 MET cc_start: 0.8518 (mtt) cc_final: 0.8202 (tmm) REVERT: F 206 LYS cc_start: 0.9085 (mtpt) cc_final: 0.8792 (mttt) REVERT: H 102 ARG cc_start: 0.9081 (tpt90) cc_final: 0.8700 (tpt170) REVERT: H 203 ASP cc_start: 0.9107 (t0) cc_final: 0.8877 (t0) outliers start: 26 outliers final: 13 residues processed: 264 average time/residue: 0.3391 time to fit residues: 132.3901 Evaluate side-chains 210 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 197 time to evaluate : 2.218 ------------------------------------------------------------------------------- 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 113 optimal weight: 0.0060 chunk 63 optimal weight: 8.9990 chunk 169 optimal weight: 1.9990 chunk 138 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 chunk 203 optimal weight: 2.9990 chunk 220 optimal weight: 3.9990 chunk 181 optimal weight: 0.7980 chunk 202 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 163 optimal weight: 5.9990 overall best weight: 1.3602 ------------------------------------------------------------------------------- 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 160 ASN E 205 HIS G 160 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5239 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18464 Z= 0.221 Angle : 0.597 9.850 24845 Z= 0.308 Chirality : 0.042 0.200 2765 Planarity : 0.004 0.068 3012 Dihedral : 10.512 91.655 2803 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.85 % Favored : 97.97 % Rotamer: Outliers : 1.92 % Allowed : 11.38 % Favored : 86.70 % 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: 1.70 (0.18), residues: 2230 helix: 2.62 (0.14), residues: 1318 sheet: -1.42 (0.39), residues: 123 loop : -1.13 (0.21), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP A 766 HIS 0.009 0.001 HIS G 60 PHE 0.019 0.001 PHE A 659 TYR 0.016 0.001 TYR B 673 ARG 0.013 0.001 ARG A 715 *********************** 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 245 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 210 time to evaluate : 1.972 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: A 414 MET cc_start: 0.5243 (mpp) cc_final: 0.4956 (ptp) REVERT: A 503 MET cc_start: 0.0635 (tmm) cc_final: 0.0009 (ttt) REVERT: B 463 MET cc_start: 0.1391 (mtm) cc_final: 0.1188 (mtt) REVERT: C 585 MET cc_start: 0.9255 (mmt) cc_final: 0.8766 (mmm) REVERT: C 586 ARG cc_start: 0.9339 (mmm-85) cc_final: 0.8973 (tmt-80) REVERT: C 619 ASN cc_start: 0.9277 (t0) cc_final: 0.9033 (t0) REVERT: D 619 ASN cc_start: 0.9217 (t0) cc_final: 0.8957 (t0) REVERT: E 56 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8335 (tp30) REVERT: E 70 GLU cc_start: 0.8509 (pp20) cc_final: 0.8295 (pp20) REVERT: E 160 ASN cc_start: 0.8635 (t0) cc_final: 0.8411 (t0) REVERT: F 56 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8349 (mm-30) REVERT: F 117 MET cc_start: 0.8300 (mmm) cc_final: 0.8058 (mmm) REVERT: F 192 MET cc_start: 0.8622 (mtt) cc_final: 0.8282 (tmm) REVERT: F 206 LYS cc_start: 0.9093 (mtpt) cc_final: 0.8887 (mttt) REVERT: G 117 MET cc_start: 0.9343 (mmm) cc_final: 0.9131 (mmm) REVERT: G 129 LYS cc_start: 0.9310 (mtmm) cc_final: 0.9088 (mtpp) outliers start: 35 outliers final: 23 residues processed: 232 average time/residue: 0.3314 time to fit residues: 115.0163 Evaluate side-chains 214 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 191 time to evaluate : 2.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 527 MET Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 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 117 MET Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 201 optimal weight: 0.8980 chunk 153 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 204 optimal weight: 2.9990 chunk 216 optimal weight: 3.9990 chunk 106 optimal weight: 10.0000 chunk 193 optimal weight: 7.9990 chunk 58 optimal weight: 0.6980 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 569 ASN ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 HIS ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5258 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 18464 Z= 0.231 Angle : 0.591 9.629 24845 Z= 0.300 Chirality : 0.042 0.236 2765 Planarity : 0.004 0.060 3012 Dihedral : 10.060 89.385 2803 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.81 % Favored : 98.01 % Rotamer: Outliers : 2.35 % Allowed : 11.93 % Favored : 85.71 % 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: 1.86 (0.18), residues: 2230 helix: 2.76 (0.14), residues: 1322 sheet: -1.34 (0.40), residues: 122 loop : -1.10 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A 551 HIS 0.022 0.001 HIS E 205 PHE 0.016 0.001 PHE A 659 TYR 0.016 0.001 TYR D 647 ARG 0.011 0.000 ARG A 715 *********************** 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 242 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 199 time to evaluate : 1.908 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 503 MET cc_start: 0.0042 (tmm) cc_final: -0.0296 (ttt) REVERT: C 585 MET cc_start: 0.9264 (mmt) cc_final: 0.8780 (mmt) REVERT: C 586 ARG cc_start: 0.9367 (mmm-85) cc_final: 0.8943 (tmt-80) REVERT: C 619 ASN cc_start: 0.9231 (t0) cc_final: 0.8966 (t0) REVERT: D 407 MET cc_start: 0.1664 (pmm) cc_final: 0.1273 (pmm) REVERT: D 619 ASN cc_start: 0.9255 (t0) cc_final: 0.8899 (t0) REVERT: E 74 LYS cc_start: 0.8840 (tmmt) cc_final: 0.8381 (tttt) REVERT: F 56 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8233 (mm-30) REVERT: F 117 MET cc_start: 0.8306 (mmm) cc_final: 0.8082 (mmm) REVERT: F 192 MET cc_start: 0.8568 (mtt) cc_final: 0.8280 (tmm) REVERT: F 206 LYS cc_start: 0.9092 (mtpt) cc_final: 0.8867 (mttt) REVERT: G 99 ARG cc_start: 0.9629 (mmm-85) cc_final: 0.9238 (mmm-85) REVERT: G 117 MET cc_start: 0.9371 (mmm) cc_final: 0.9136 (mmm) REVERT: H 43 LYS cc_start: 0.7352 (mmtt) cc_final: 0.7059 (mmmm) outliers start: 43 outliers final: 35 residues processed: 227 average time/residue: 0.3308 time to fit residues: 112.8801 Evaluate side-chains 217 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 182 time to evaluate : 1.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 527 MET Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 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 D residue 784 THR Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 117 MET Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 67 CYS Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 150 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 40 CYS Chi-restraints excluded: chain G residue 41 LYS Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 153 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 180 optimal weight: 6.9990 chunk 122 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 161 optimal weight: 2.9990 chunk 89 optimal weight: 9.9990 chunk 184 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 0 optimal weight: 40.0000 chunk 110 optimal weight: 8.9990 chunk 194 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 GLN ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 HIS ** D 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5398 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.061 18464 Z= 0.498 Angle : 0.752 11.964 24845 Z= 0.385 Chirality : 0.047 0.312 2765 Planarity : 0.005 0.057 3012 Dihedral : 10.779 87.968 2803 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.16 % Favored : 96.65 % Rotamer: Outliers : 3.01 % Allowed : 12.37 % Favored : 84.62 % 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: 1.45 (0.18), residues: 2230 helix: 2.33 (0.14), residues: 1329 sheet: -1.42 (0.42), residues: 121 loop : -1.12 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 551 HIS 0.030 0.002 HIS F 205 PHE 0.025 0.002 PHE E 107 TYR 0.020 0.002 TYR B 673 ARG 0.012 0.001 ARG A 715 *********************** 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 230 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 176 time to evaluate : 2.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 708 MET cc_start: 0.4220 (mpp) cc_final: 0.4005 (mmt) REVERT: C 585 MET cc_start: 0.9347 (mmt) cc_final: 0.8943 (mmt) REVERT: C 586 ARG cc_start: 0.9345 (mmm-85) cc_final: 0.8978 (tmt170) REVERT: C 619 ASN cc_start: 0.9381 (t0) cc_final: 0.9120 (t0) REVERT: D 407 MET cc_start: 0.2134 (pmm) cc_final: 0.1787 (pmm) REVERT: D 619 ASN cc_start: 0.9332 (t0) cc_final: 0.9043 (t0) REVERT: E 10 MET cc_start: 0.8634 (mmm) cc_final: 0.8364 (tmm) REVERT: E 30 THR cc_start: 0.9324 (OUTLIER) cc_final: 0.9087 (p) REVERT: E 56 GLU cc_start: 0.9099 (tp30) cc_final: 0.8811 (tp30) REVERT: F 10 MET cc_start: 0.9621 (tpp) cc_final: 0.9323 (tpp) REVERT: F 192 MET cc_start: 0.8578 (mtt) cc_final: 0.8285 (ttt) REVERT: F 206 LYS cc_start: 0.9049 (mtpt) cc_final: 0.8837 (mttt) REVERT: G 117 MET cc_start: 0.9465 (mmm) cc_final: 0.9221 (mmm) REVERT: H 37 ARG cc_start: 0.8907 (tpp80) cc_final: 0.8559 (tpp80) REVERT: H 56 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7814 (mm-30) outliers start: 54 outliers final: 38 residues processed: 214 average time/residue: 0.3387 time to fit residues: 107.5574 Evaluate side-chains 204 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 165 time to evaluate : 2.331 ------------------------------------------------------------------------------- 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 587 GLN Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain B residue 708 MET 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 E residue 30 THR Chi-restraints excluded: chain E residue 40 CYS 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 150 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 41 LYS Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 153 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 72 optimal weight: 5.9990 chunk 194 optimal weight: 0.8980 chunk 42 optimal weight: 30.0000 chunk 127 optimal weight: 8.9990 chunk 53 optimal weight: 0.7980 chunk 216 optimal weight: 0.3980 chunk 179 optimal weight: 0.0370 chunk 100 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 113 optimal weight: 7.9990 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 791 ASN E 132 HIS F 205 HIS G 160 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5288 moved from start: 0.4339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18464 Z= 0.178 Angle : 0.603 14.289 24845 Z= 0.303 Chirality : 0.041 0.195 2765 Planarity : 0.004 0.056 3012 Dihedral : 9.794 87.639 2803 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.72 % Favored : 98.10 % Rotamer: Outliers : 2.24 % Allowed : 13.63 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.87 (0.14), residues: 1318 sheet: -1.03 (0.43), residues: 124 loop : -1.19 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 551 HIS 0.006 0.001 HIS G 60 PHE 0.018 0.001 PHE A 659 TYR 0.042 0.001 TYR A 424 ARG 0.010 0.000 ARG A 715 *********************** 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 236 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 196 time to evaluate : 2.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 708 MET cc_start: 0.4179 (mpp) cc_final: 0.3891 (mmt) REVERT: C 585 MET cc_start: 0.9229 (mmt) cc_final: 0.8718 (mmt) REVERT: C 586 ARG cc_start: 0.9365 (mmm-85) cc_final: 0.8905 (tmt-80) REVERT: C 619 ASN cc_start: 0.9275 (t0) cc_final: 0.9054 (t0) REVERT: D 619 ASN cc_start: 0.9294 (t0) cc_final: 0.8864 (t0) REVERT: E 10 MET cc_start: 0.8605 (mmm) cc_final: 0.8291 (mmm) REVERT: E 56 GLU cc_start: 0.9008 (tp30) cc_final: 0.8498 (tp30) REVERT: F 10 MET cc_start: 0.9635 (tpp) cc_final: 0.9323 (tpp) REVERT: F 117 MET cc_start: 0.8313 (mmm) cc_final: 0.8108 (mmm) REVERT: F 192 MET cc_start: 0.8482 (mtt) cc_final: 0.8258 (ttt) REVERT: F 206 LYS cc_start: 0.9081 (mtpt) cc_final: 0.8811 (mttt) REVERT: G 99 ARG cc_start: 0.9573 (mmm-85) cc_final: 0.9201 (mmm-85) REVERT: G 117 MET cc_start: 0.9402 (mmm) cc_final: 0.9188 (mmm) REVERT: G 160 ASN cc_start: 0.8755 (OUTLIER) cc_final: 0.8502 (m110) REVERT: G 205 HIS cc_start: 0.8644 (OUTLIER) cc_final: 0.8240 (m-70) outliers start: 40 outliers final: 25 residues processed: 224 average time/residue: 0.3224 time to fit residues: 108.9962 Evaluate side-chains 205 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 178 time to evaluate : 2.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 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 66 THR 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 160 ASN Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain H residue 57 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 208 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 123 optimal weight: 0.0000 chunk 158 optimal weight: 4.9990 chunk 122 optimal weight: 9.9990 chunk 182 optimal weight: 2.9990 chunk 121 optimal weight: 7.9990 chunk 215 optimal weight: 0.6980 chunk 135 optimal weight: 0.9990 chunk 131 optimal weight: 0.6980 chunk 99 optimal weight: 5.9990 overall best weight: 1.0788 ------------------------------------------------------------------------------- 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** F 205 HIS G 160 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5293 moved from start: 0.4531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 18464 Z= 0.195 Angle : 0.637 15.391 24845 Z= 0.314 Chirality : 0.041 0.177 2765 Planarity : 0.004 0.059 3012 Dihedral : 9.440 88.776 2801 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.12 % Favored : 97.69 % Rotamer: Outliers : 2.35 % Allowed : 13.90 % Favored : 83.74 % 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: 2.00 (0.19), residues: 2230 helix: 2.91 (0.14), residues: 1321 sheet: -1.15 (0.42), residues: 126 loop : -1.13 (0.22), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 551 HIS 0.019 0.001 HIS F 205 PHE 0.021 0.001 PHE A 659 TYR 0.029 0.001 TYR A 424 ARG 0.009 0.001 ARG A 715 *********************** 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 226 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 184 time to evaluate : 1.984 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 708 MET cc_start: 0.4228 (mpp) cc_final: 0.3781 (mmt) REVERT: C 585 MET cc_start: 0.9284 (mmt) cc_final: 0.8936 (mmm) REVERT: C 586 ARG cc_start: 0.9404 (mmm-85) cc_final: 0.8976 (tmt-80) REVERT: C 619 ASN cc_start: 0.9281 (t0) cc_final: 0.8947 (t0) REVERT: D 619 ASN cc_start: 0.9296 (t0) cc_final: 0.8877 (t0) REVERT: E 30 THR cc_start: 0.9282 (OUTLIER) cc_final: 0.9073 (p) REVERT: E 56 GLU cc_start: 0.9002 (tp30) cc_final: 0.8459 (tp30) REVERT: F 117 MET cc_start: 0.8349 (mmm) cc_final: 0.8110 (mmm) REVERT: F 192 MET cc_start: 0.8485 (mtt) cc_final: 0.8258 (ttt) REVERT: F 206 LYS cc_start: 0.9064 (mtpt) cc_final: 0.8777 (mttt) REVERT: G 99 ARG cc_start: 0.9607 (mmm-85) cc_final: 0.9239 (mmm-85) REVERT: G 117 MET cc_start: 0.9395 (mmm) cc_final: 0.9188 (mmm) REVERT: G 160 ASN cc_start: 0.8728 (OUTLIER) cc_final: 0.8501 (m110) REVERT: G 205 HIS cc_start: 0.8686 (OUTLIER) cc_final: 0.8357 (m-70) outliers start: 42 outliers final: 28 residues processed: 213 average time/residue: 0.3262 time to fit residues: 105.6846 Evaluate side-chains 209 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 178 time to evaluate : 2.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 66 THR 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 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 G residue 40 CYS Chi-restraints excluded: chain G residue 41 LYS Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 160 ASN Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 57 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 133 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 chunk 128 optimal weight: 0.9980 chunk 65 optimal weight: 20.0000 chunk 42 optimal weight: 20.0000 chunk 41 optimal weight: 20.0000 chunk 137 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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** F 205 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5321 moved from start: 0.4674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18464 Z= 0.243 Angle : 0.630 11.954 24845 Z= 0.313 Chirality : 0.041 0.179 2765 Planarity : 0.004 0.058 3012 Dihedral : 9.396 89.851 2801 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.49 % Favored : 97.33 % Rotamer: Outliers : 2.24 % Allowed : 14.07 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.97 (0.19), residues: 2230 helix: 2.88 (0.14), residues: 1326 sheet: -1.11 (0.41), residues: 131 loop : -1.17 (0.22), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 551 HIS 0.007 0.001 HIS G 60 PHE 0.021 0.001 PHE G 18 TYR 0.028 0.001 TYR A 424 ARG 0.008 0.001 ARG A 715 *********************** 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 217 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 177 time to evaluate : 2.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 708 MET cc_start: 0.4249 (mpp) cc_final: 0.3909 (mmt) REVERT: C 585 MET cc_start: 0.9280 (mmt) cc_final: 0.8781 (mmt) REVERT: C 586 ARG cc_start: 0.9382 (mmm-85) cc_final: 0.8966 (tmt-80) REVERT: C 619 ASN cc_start: 0.9310 (t0) cc_final: 0.8993 (t0) REVERT: D 407 MET cc_start: 0.2421 (pmm) cc_final: 0.1850 (pmm) REVERT: D 619 ASN cc_start: 0.9302 (t0) cc_final: 0.8956 (t0) REVERT: E 10 MET cc_start: 0.8672 (mmm) cc_final: 0.8357 (mmm) REVERT: E 30 THR cc_start: 0.9283 (OUTLIER) cc_final: 0.9073 (p) REVERT: E 56 GLU cc_start: 0.9021 (tp30) cc_final: 0.8499 (tp30) REVERT: F 117 MET cc_start: 0.8356 (mmm) cc_final: 0.8102 (mmm) REVERT: F 192 MET cc_start: 0.8521 (mtt) cc_final: 0.8256 (ttt) REVERT: F 206 LYS cc_start: 0.9092 (mtpt) cc_final: 0.8810 (mttt) REVERT: G 99 ARG cc_start: 0.9600 (mmm-85) cc_final: 0.9254 (mmm-85) REVERT: G 117 MET cc_start: 0.9379 (mmm) cc_final: 0.9160 (mmm) outliers start: 40 outliers final: 35 residues processed: 206 average time/residue: 0.3435 time to fit residues: 110.1968 Evaluate side-chains 205 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 169 time to evaluate : 2.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 117 MET Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 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 12 LEU Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 205 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 196 optimal weight: 0.7980 chunk 206 optimal weight: 0.7980 chunk 188 optimal weight: 3.9990 chunk 201 optimal weight: 0.7980 chunk 121 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 157 optimal weight: 3.9990 chunk 61 optimal weight: 30.0000 chunk 181 optimal weight: 2.9990 chunk 190 optimal weight: 0.7980 chunk 200 optimal weight: 4.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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** G 160 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5300 moved from start: 0.4783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18464 Z= 0.204 Angle : 0.632 17.708 24845 Z= 0.310 Chirality : 0.041 0.178 2765 Planarity : 0.004 0.057 3012 Dihedral : 9.159 89.331 2801 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.08 % Favored : 97.74 % Rotamer: Outliers : 2.30 % Allowed : 14.56 % Favored : 83.14 % 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: 2.91 (0.14), residues: 1326 sheet: -1.06 (0.41), residues: 141 loop : -1.13 (0.22), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 551 HIS 0.009 0.001 HIS F 205 PHE 0.024 0.001 PHE H 73 TYR 0.025 0.001 TYR A 424 ARG 0.010 0.001 ARG D 743 *********************** 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 223 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 182 time to evaluate : 1.946 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: A 481 ILE cc_start: 0.4766 (mp) cc_final: 0.4507 (mm) REVERT: C 585 MET cc_start: 0.9247 (mmt) cc_final: 0.8919 (mmm) REVERT: C 586 ARG cc_start: 0.9356 (mmm-85) cc_final: 0.8933 (tmt-80) REVERT: C 619 ASN cc_start: 0.9288 (t0) cc_final: 0.8940 (t0) REVERT: C 670 MET cc_start: 0.3730 (mmt) cc_final: 0.3514 (mmt) REVERT: D 619 ASN cc_start: 0.9299 (t0) cc_final: 0.8877 (t0) REVERT: E 56 GLU cc_start: 0.9116 (tp30) cc_final: 0.8604 (tp30) REVERT: F 58 MET cc_start: 0.7831 (mmp) cc_final: 0.7560 (mmm) REVERT: F 117 MET cc_start: 0.8354 (mmm) cc_final: 0.8142 (mmm) REVERT: F 192 MET cc_start: 0.8492 (mtt) cc_final: 0.8260 (ttt) REVERT: F 206 LYS cc_start: 0.9087 (mtpt) cc_final: 0.8772 (mttt) REVERT: G 99 ARG cc_start: 0.9605 (mmm-85) cc_final: 0.9233 (mmt90) REVERT: G 117 MET cc_start: 0.9375 (mmm) cc_final: 0.9149 (mmm) REVERT: G 205 HIS cc_start: 0.8635 (OUTLIER) cc_final: 0.8296 (m-70) REVERT: H 160 ASN cc_start: 0.8334 (m-40) cc_final: 0.8078 (m110) outliers start: 41 outliers final: 33 residues processed: 211 average time/residue: 0.3139 time to fit residues: 101.8305 Evaluate side-chains 209 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 175 time to evaluate : 1.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain E residue 40 CYS 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 40 CYS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 67 CYS Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 40 CYS 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 12 LEU Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 155 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 132 optimal weight: 2.9990 chunk 212 optimal weight: 7.9990 chunk 129 optimal weight: 2.9990 chunk 100 optimal weight: 20.0000 chunk 147 optimal weight: 7.9990 chunk 223 optimal weight: 0.9990 chunk 205 optimal weight: 4.9990 chunk 177 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 137 optimal weight: 0.9980 chunk 108 optimal weight: 8.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 GLN ** D 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5325 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 : 0.004 0.039 18464 Z= 0.254 Angle : 0.641 11.520 24845 Z= 0.319 Chirality : 0.042 0.177 2765 Planarity : 0.004 0.057 3012 Dihedral : 9.169 87.871 2801 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.62 % Favored : 97.20 % Rotamer: Outliers : 2.08 % Allowed : 14.78 % Favored : 83.14 % 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: 1.99 (0.19), residues: 2230 helix: 2.86 (0.14), residues: 1326 sheet: -0.77 (0.43), residues: 134 loop : -1.17 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 551 HIS 0.006 0.001 HIS G 60 PHE 0.024 0.001 PHE G 18 TYR 0.026 0.001 TYR A 424 ARG 0.008 0.001 ARG A 715 ********************** 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 205 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 168 time to evaluate : 1.827 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: A 481 ILE cc_start: 0.4764 (mp) cc_final: 0.4467 (mm) REVERT: A 708 MET cc_start: 0.4433 (mpp) cc_final: 0.3974 (mmm) REVERT: C 585 MET cc_start: 0.9279 (mmt) cc_final: 0.8934 (mmm) REVERT: C 586 ARG cc_start: 0.9382 (mmm-85) cc_final: 0.8944 (tmt-80) REVERT: C 619 ASN cc_start: 0.9316 (t0) cc_final: 0.8984 (t0) REVERT: D 619 ASN cc_start: 0.9303 (t0) cc_final: 0.8955 (t0) REVERT: E 56 GLU cc_start: 0.9125 (tp30) cc_final: 0.8616 (tp30) REVERT: F 58 MET cc_start: 0.7845 (mmp) cc_final: 0.7585 (mmm) REVERT: F 117 MET cc_start: 0.8351 (mmm) cc_final: 0.8133 (mmm) REVERT: F 192 MET cc_start: 0.8519 (mtt) cc_final: 0.8256 (ttt) REVERT: F 206 LYS cc_start: 0.9092 (mtpt) cc_final: 0.8864 (mttt) REVERT: G 99 ARG cc_start: 0.9604 (mmm-85) cc_final: 0.9244 (mmt90) REVERT: G 117 MET cc_start: 0.9386 (mmm) cc_final: 0.9160 (mmm) REVERT: G 205 HIS cc_start: 0.8648 (OUTLIER) cc_final: 0.8310 (m-70) REVERT: H 160 ASN cc_start: 0.8340 (m-40) cc_final: 0.8036 (m110) outliers start: 37 outliers final: 35 residues processed: 198 average time/residue: 0.3109 time to fit residues: 95.4348 Evaluate side-chains 203 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 167 time to evaluate : 1.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain E residue 117 MET Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 67 CYS Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 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 G residue 205 HIS Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 155 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 141 optimal weight: 4.9990 chunk 189 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 163 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 chunk 177 optimal weight: 5.9990 chunk 74 optimal weight: 0.2980 chunk 182 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 32 optimal weight: 8.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 GLN ** D 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.142936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.083977 restraints weight = 118065.075| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 6.88 r_work: 0.2967 rms_B_bonded: 5.63 restraints_weight: 2.0000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2972 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 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 = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2972 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.4941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18464 Z= 0.185 Angle : 0.643 17.177 24845 Z= 0.313 Chirality : 0.041 0.179 2765 Planarity : 0.004 0.056 3012 Dihedral : 8.928 88.088 2801 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.17 % Favored : 97.65 % Rotamer: Outliers : 2.03 % Allowed : 15.00 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.06 (0.19), residues: 2230 helix: 2.94 (0.14), residues: 1326 sheet: -0.97 (0.44), residues: 120 loop : -1.15 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 551 HIS 0.006 0.001 HIS G 60 PHE 0.020 0.001 PHE H 73 TYR 0.024 0.001 TYR A 424 ARG 0.009 0.001 ARG F 204 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3884.84 seconds wall clock time: 72 minutes 57.26 seconds (4377.26 seconds total)