Starting phenix.real_space_refine on Sun Aug 24 09:05:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p3s_17393/08_2025/8p3s_17393.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p3s_17393/08_2025/8p3s_17393.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8p3s_17393/08_2025/8p3s_17393.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p3s_17393/08_2025/8p3s_17393.map" model { file = "/net/cci-nas-00/data/ceres_data/8p3s_17393/08_2025/8p3s_17393.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p3s_17393/08_2025/8p3s_17393.cif" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.049 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 127 5.16 5 C 11954 2.51 5 N 2866 2.21 5 O 3243 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18195 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 3103 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 404, 3081 Classifications: {'peptide': 404} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 15} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 390} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 6, 'ASP:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 47 Conformer: "B" Number of residues, atoms: 404, 3081 Classifications: {'peptide': 404} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 15} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 390} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 6, 'ASP:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 47 bond proxies already assigned to first conformer: 3125 Chain: "B" Number of atoms: 3077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3077 Classifications: {'peptide': 404} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 14} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 390} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 7, 'ASP:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 53 Chain: "C" Number of atoms: 3015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3015 Classifications: {'peptide': 395} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 12} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 383} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 5, 'ASP:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 44 Chain: "D" Number of atoms: 3100 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 404, 3078 Classifications: {'peptide': 404} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 14} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 390} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 7, 'ASP:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 49 Conformer: "B" Number of residues, atoms: 404, 3078 Classifications: {'peptide': 404} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 14} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 390} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 7, 'ASP:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 49 bond proxies already assigned to first conformer: 3122 Chain: "E" Number of atoms: 1368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1368 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 174} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 1373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1373 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 3 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "G" Number of atoms: 1372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1372 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 174} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1359 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 174} Chain breaks: 3 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 14 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 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: 4 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 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: 4.82, per 1000 atoms: 0.26 Number of scatterers: 18195 At special positions: 0 Unit cell: (118.531, 127.204, 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 127 16.00 P 5 15.00 O 3243 8.00 N 2866 7.00 C 11954 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.02 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.02 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 68 " distance=2.05 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=2.03 Simple disulfide: pdb=" SG CYS G 67 " - pdb=" SG CYS G 77 " distance=2.06 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 68 " distance=2.02 Simple disulfide: pdb=" SG CYS H 67 " - pdb=" SG CYS H 77 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.19 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 476.8 nanoseconds 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4208 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 26 sheets defined 60.5% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 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: 3.727A 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: 3.678A 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: 3.531A 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: 3.599A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 415 Processing helix chain 'B' and resid 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: 3.665A 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 629 removed outlier: 3.735A pdb=" N ARG B 628 " --> pdb=" O LEU B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 641 Processing helix chain 'B' and resid 653 through 662 Processing helix chain 'B' and resid 664 through 677 removed outlier: 3.675A 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: 3.542A 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: 3.590A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) removed outlier: 4.113A 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: 3.686A pdb=" N GLU C 550 " --> pdb=" O SER C 547 " (cutoff:3.500A) removed outlier: 3.784A 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: 3.732A 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: 3.539A 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: 3.765A 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: 3.743A 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: 3.619A 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 635 through 641 Processing helix chain 'D' and resid 653 through 662 Processing helix chain 'D' and resid 664 through 677 removed outlier: 3.678A 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 706 through 714 removed outlier: 3.545A pdb=" N GLN D 714 " --> pdb=" O GLU D 710 " (cutoff:3.500A) 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: 3.539A 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 161 removed outlier: 3.728A pdb=" N SER E 137 " --> pdb=" O ASN E 133 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA E 161 " --> pdb=" O ILE E 157 " (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: 3.506A pdb=" N LEU F 98 " --> pdb=" O ALA F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 127 removed outlier: 3.900A pdb=" N GLU F 126 " --> pdb=" O ILE F 122 " (cutoff:3.500A) removed outlier: 3.876A 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: 3.740A 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: 4.091A pdb=" N GLU G 126 " --> pdb=" O ILE G 122 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N PHE G 127 " --> pdb=" O ALA G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 134 through 162 Processing helix chain 'G' and resid 177 through 210 Processing helix chain 'H' and resid 6 through 30 removed outlier: 3.944A pdb=" N MET H 10 " --> pdb=" O ARG H 6 " (cutoff:3.500A) removed outlier: 3.981A 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 Processing helix chain 'H' and resid 177 through 210 removed outlier: 4.030A 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: 3.847A 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: 6.338A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 4.099A 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: 3.823A 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: 6.316A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 8.779A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.036A 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: 3.847A 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: 6.352A 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: 6.461A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 8.828A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.036A 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: 3.833A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.327A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 8.798A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 34 through 38 Processing sheet with id=AC4, first strand: chain 'F' and resid 37 through 38 Processing sheet with id=AC5, first strand: chain 'F' and resid 65 through 67 removed outlier: 3.794A pdb=" N LYS F 78 " --> pdb=" O THR F 66 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 34 through 38 Processing sheet with id=AC7, first strand: chain 'H' and resid 36 through 38 Processing sheet with id=AC8, first strand: chain 'H' and resid 65 through 67 1131 hydrogen bonds defined for protein. 3272 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.12 Time building geometry restraints manager: 1.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2816 1.31 - 1.44: 5174 1.44 - 1.57: 10374 1.57 - 1.71: 10 1.71 - 1.84: 206 Bond restraints: 18580 Sorted by residual: bond pdb=" C PRO B 512 " pdb=" O PRO B 512 " ideal model delta sigma weight residual 1.233 1.178 0.055 1.13e-02 7.83e+03 2.34e+01 bond pdb=" N VAL D 488 " pdb=" CA VAL D 488 " ideal model delta sigma weight residual 1.456 1.498 -0.042 9.50e-03 1.11e+04 1.94e+01 bond pdb=" N VAL C 488 " pdb=" CA VAL C 488 " ideal model delta sigma weight residual 1.456 1.497 -0.041 9.50e-03 1.11e+04 1.86e+01 bond pdb=" C LYS A 506 " pdb=" O LYS A 506 " ideal model delta sigma weight residual 1.238 1.183 0.055 1.28e-02 6.10e+03 1.84e+01 bond pdb=" N VAL B 488 " pdb=" CA VAL B 488 " ideal model delta sigma weight residual 1.456 1.497 -0.041 9.50e-03 1.11e+04 1.83e+01 ... (remaining 18575 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 22193 2.24 - 4.48: 2617 4.48 - 6.71: 193 6.71 - 8.95: 27 8.95 - 11.19: 8 Bond angle restraints: 25038 Sorted by residual: angle pdb=" O LYS A 506 " pdb=" C LYS A 506 " pdb=" N PRO A 507 " ideal model delta sigma weight residual 121.32 110.49 10.83 1.15e+00 7.56e-01 8.88e+01 angle pdb=" N ASP C 590 " pdb=" CA ASP C 590 " pdb=" C ASP C 590 " ideal model delta sigma weight residual 113.88 104.62 9.26 1.23e+00 6.61e-01 5.67e+01 angle pdb=" N PRO B 512 " pdb=" CA PRO B 512 " pdb=" C PRO B 512 " ideal model delta sigma weight residual 110.80 100.86 9.94 1.51e+00 4.39e-01 4.33e+01 angle pdb=" C LYS A 506 " pdb=" N PRO A 507 " pdb=" CA PRO A 507 " ideal model delta sigma weight residual 119.84 111.94 7.90 1.25e+00 6.40e-01 4.00e+01 angle pdb=" N PRO B 632 " pdb=" CA PRO B 632 " pdb=" CB PRO B 632 " ideal model delta sigma weight residual 103.25 96.64 6.61 1.05e+00 9.07e-01 3.97e+01 ... (remaining 25033 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.03: 10376 29.03 - 58.07: 435 58.07 - 87.10: 52 87.10 - 116.14: 8 116.14 - 145.17: 2 Dihedral angle restraints: 10873 sinusoidal: 4263 harmonic: 6610 Sorted by residual: dihedral pdb=" CB CYS F 40 " pdb=" SG CYS F 40 " pdb=" SG CYS F 68 " pdb=" CB CYS F 68 " ideal model delta sinusoidal sigma weight residual 93.00 23.57 69.43 1 1.00e+01 1.00e-02 6.23e+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 35.60 57.40 1 1.00e+01 1.00e-02 4.43e+01 dihedral pdb=" CB CYS G 40 " pdb=" SG CYS G 40 " pdb=" SG CYS G 68 " pdb=" CB CYS G 68 " ideal model delta sinusoidal sigma weight residual 93.00 43.29 49.71 1 1.00e+01 1.00e-02 3.39e+01 ... (remaining 10870 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.173: 2587 0.173 - 0.347: 197 0.347 - 0.520: 8 0.520 - 0.693: 0 0.693 - 0.866: 1 Chirality restraints: 2793 Sorted by residual: chirality pdb=" CB VAL A 626 " pdb=" CA VAL A 626 " pdb=" CG1 VAL A 626 " pdb=" CG2 VAL A 626 " both_signs ideal model delta sigma weight residual False -2.63 -1.76 -0.87 2.00e-01 2.50e+01 1.88e+01 chirality pdb=" CG LEU A 483 " pdb=" CB LEU A 483 " pdb=" CD1 LEU A 483 " pdb=" CD2 LEU A 483 " both_signs ideal model delta sigma weight residual False -2.59 -2.10 -0.49 2.00e-01 2.50e+01 6.04e+00 chirality pdb=" CG LEU D 483 " pdb=" CB LEU D 483 " pdb=" CD1 LEU D 483 " pdb=" CD2 LEU D 483 " both_signs ideal model delta sigma weight residual False -2.59 -2.16 -0.43 2.00e-01 2.50e+01 4.64e+00 ... (remaining 2790 not shown) Planarity restraints: 3050 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 628 " 0.693 9.50e-02 1.11e+02 3.11e-01 5.88e+01 pdb=" NE ARG B 628 " -0.042 2.00e-02 2.50e+03 pdb=" CZ ARG B 628 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG B 628 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 628 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA BPHE D 574 " 0.033 2.00e-02 2.50e+03 6.76e-02 4.56e+01 pdb=" C BPHE D 574 " -0.117 2.00e-02 2.50e+03 pdb=" O BPHE D 574 " 0.044 2.00e-02 2.50e+03 pdb=" N ASN D 575 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 675 " -0.601 9.50e-02 1.11e+02 2.70e-01 4.44e+01 pdb=" NE ARG D 675 " 0.034 2.00e-02 2.50e+03 pdb=" CZ ARG D 675 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG D 675 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG D 675 " -0.021 2.00e-02 2.50e+03 ... (remaining 3047 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2409 2.75 - 3.29: 18613 3.29 - 3.83: 29986 3.83 - 4.36: 37700 4.36 - 4.90: 62814 Nonbonded interactions: 151522 Sorted by model distance: nonbonded pdb=" O LYS E 129 " pdb=" OG1 THR E 130 " model vdw 2.216 3.040 nonbonded pdb=" O GLU B 627 " pdb=" N MET B 629 " model vdw 2.254 3.120 nonbonded pdb=" O SER E 104 " pdb=" N ILE E 106 " model vdw 2.271 3.120 nonbonded pdb=" O GLU H 70 " pdb=" OE1 GLU H 70 " model vdw 2.279 3.040 nonbonded pdb=" OG SER A 592 " pdb=" OD2 ASP B 590 " model vdw 2.287 3.040 ... (remaining 151517 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 506 or resid 510 through 573 or resid 575 thro \ ugh 593 or (resid 594 and (name N or name CA or name C or name O or name CB )) o \ r resid 595 through 622 or resid 624 through 626 or (resid 633 through 634 and ( \ name N or name CA or name C or name O or name CB )) or resid 635 through 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 506 or resid 510 through 549 or (resid 550 and \ (name N or name CA or name C or name O or name CB )) or resid 551 or (resid 569 \ and (name N or name CA or name C or name O or name CB )) or resid 570 through 5 \ 73 or resid 575 or (resid 576 and (name N or name CA or name C or name O or name \ CB )) or resid 577 through 593 or (resid 594 and (name N or name CA or name C o \ r name O or name CB )) or resid 595 through 622 or resid 624 through 626 or (res \ id 633 through 634 and (name N or name CA or name C or name O or name CB )) or r \ esid 635 through 773 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 573 or resid 575 or (resid 576 and (name N or \ name CA or name C or name O or name CB )) or resid 577 through 622 or resid 624 \ through 626 or (resid 633 through 634 and (name N or name CA or name C or name O \ or name CB )) or resid 635 through 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 82 \ 3 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'D' and (resid 393 through 506 or resid 510 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 o \ r resid 575 or (resid 576 and (name N or name CA or name C or name O or name CB \ )) or resid 577 through 593 or (resid 594 and (name N or name CA or name C or na \ me O or name CB )) or resid 595 through 622 or resid 624 through 626 or resid 63 \ 3 through 773 or (resid 784 and (name N or name CA or name C or name O or name C \ B )) or resid 785 through 823)) } ncs_group { reference = (chain 'E' and (resid 5 through 84 or resid 93 through 94 or (resid 95 and (name \ N or name CA or name C or name O or name CB )) or resid 96 through 203 or (resi \ d 204 and (name N or name CA or name C or name O or name CB )) or resid 205 thro \ ugh 206 or (resid 207 and (name N or name CA or name C or name O or name CB )) o \ r resid 208 through 210)) selection = (chain 'F' and (resid 5 through 42 or resid 55 through 84 or resid 93 through 20 \ 3 or (resid 204 and (name N or name CA or name C or name O or name CB )) or resi \ d 205 through 206 or (resid 207 and (name N or name CA or name C or name O or na \ me CB )) or resid 208 through 210)) selection = (chain 'G' and (resid 5 through 84 or resid 93 through 94 or (resid 95 and (name \ N or name CA or name C or name O or name CB )) or resid 96 through 203 or (resi \ d 204 and (name N or name CA or name C or name O or name CB )) or resid 205 or ( \ resid 206 through 207 and (name N or name CA or name C or name O or name CB )) o \ r resid 208 through 210)) selection = (chain 'H' and (resid 5 through 42 or resid 55 through 94 or (resid 95 and (name \ N or name CA or name C or name O or name CB )) or resid 96 through 210)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 17.580 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4965 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 : 0.012 0.064 18592 Z= 0.893 Angle : 1.461 11.189 25062 Z= 1.037 Chirality : 0.107 0.866 2793 Planarity : 0.015 0.311 3050 Dihedral : 15.799 145.169 6629 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.53 % Allowed : 4.26 % Favored : 95.21 % Rotamer: Outliers : 1.80 % Allowed : 3.66 % Favored : 94.54 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.17), residues: 2268 helix: 0.97 (0.14), residues: 1332 sheet: -1.68 (0.37), residues: 107 loop : -1.98 (0.19), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.002 ARG A 628 TYR 0.034 0.005 TYR B 469 PHE 0.021 0.005 PHE A 517 TRP 0.032 0.006 TRP B 578 HIS 0.011 0.003 HIS E 60 Details of bonding type rmsd covalent geometry : bond 0.01250 (18580) covalent geometry : angle 1.45848 (25038) SS BOND : bond 0.01439 ( 12) SS BOND : angle 3.08345 ( 24) hydrogen bonds : bond 0.13525 ( 1131) hydrogen bonds : angle 5.28407 ( 3272) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 365 time to evaluate : 0.570 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 591 ILE cc_start: 0.8820 (tp) cc_final: 0.8550 (pt) REVERT: B 585 MET cc_start: 0.8907 (mmt) cc_final: 0.8298 (mmt) REVERT: E 81 ASP cc_start: 0.8323 (t0) cc_final: 0.7959 (p0) REVERT: E 92 ASP cc_start: 0.7509 (t0) cc_final: 0.7061 (p0) REVERT: E 207 GLN cc_start: 0.8904 (mm110) cc_final: 0.8650 (tm-30) REVERT: F 24 MET cc_start: 0.9162 (tpt) cc_final: 0.8905 (tpt) REVERT: F 61 SER cc_start: 0.9389 (t) cc_final: 0.9060 (p) REVERT: F 65 ARG cc_start: 0.8441 (mtm-85) cc_final: 0.7950 (mtm110) REVERT: F 81 ASP cc_start: 0.8811 (t0) cc_final: 0.8585 (t70) REVERT: F 98 LEU cc_start: 0.8486 (tt) cc_final: 0.8236 (mm) REVERT: F 126 GLU cc_start: 0.9529 (mt-10) cc_final: 0.9194 (tm-30) REVERT: G 13 THR cc_start: 0.9374 (t) cc_final: 0.9026 (p) REVERT: G 81 ASP cc_start: 0.9230 (p0) cc_final: 0.8842 (t0) REVERT: H 6 ARG cc_start: 0.8404 (tmt-80) cc_final: 0.8176 (tmm160) REVERT: H 10 MET cc_start: 0.9034 (tpp) cc_final: 0.8705 (tpp) REVERT: H 13 THR cc_start: 0.9102 (m) cc_final: 0.8698 (t) REVERT: H 35 TYR cc_start: 0.8828 (m-80) cc_final: 0.8552 (m-80) REVERT: H 61 SER cc_start: 0.9502 (t) cc_final: 0.8935 (p) REVERT: H 70 GLU cc_start: 0.8706 (tm-30) cc_final: 0.8495 (pp20) REVERT: H 74 LYS cc_start: 0.9234 (ttpp) cc_final: 0.8998 (ttmm) outliers start: 33 outliers final: 8 residues processed: 392 average time/residue: 0.6567 time to fit residues: 283.6725 Evaluate side-chains 202 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 194 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain D residue 628 ARG Chi-restraints excluded: chain D residue 743 ARG Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain E residue 12 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 216 optimal weight: 0.6980 chunk 98 optimal weight: 0.5980 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 0.8980 chunk 212 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 GLN E 160 ASN F 205 HIS H 79 GLN H 133 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.153771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.085970 restraints weight = 87604.122| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 5.50 r_work: 0.2949 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2946 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 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 = 0.2944 r_free = 0.2944 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2944 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 18592 Z= 0.157 Angle : 0.670 18.103 25062 Z= 0.347 Chirality : 0.044 0.233 2793 Planarity : 0.004 0.040 3050 Dihedral : 11.468 101.628 2841 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.26 % Favored : 97.56 % Rotamer: Outliers : 2.35 % Allowed : 13.44 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.18), residues: 2268 helix: 2.21 (0.14), residues: 1342 sheet: -1.52 (0.36), residues: 156 loop : -1.39 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 594 TYR 0.016 0.002 TYR H 128 PHE 0.031 0.002 PHE A 658 TRP 0.015 0.001 TRP D 766 HIS 0.006 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00358 (18580) covalent geometry : angle 0.66632 (25038) SS BOND : bond 0.01099 ( 12) SS BOND : angle 2.47901 ( 24) hydrogen bonds : bond 0.04554 ( 1131) hydrogen bonds : angle 4.16082 ( 3272) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 232 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 674 MET cc_start: 0.8020 (mtp) cc_final: 0.7817 (mtp) REVERT: A 762 LEU cc_start: 0.6302 (OUTLIER) cc_final: 0.6072 (tp) REVERT: B 496 MET cc_start: 0.7175 (mtp) cc_final: 0.6954 (mtt) REVERT: B 674 MET cc_start: 0.8624 (ptp) cc_final: 0.8116 (ptp) REVERT: C 407 MET cc_start: 0.6363 (OUTLIER) cc_final: 0.6106 (mpp) REVERT: C 414 MET cc_start: 0.1726 (mtm) cc_final: 0.1387 (mtp) REVERT: C 460 TRP cc_start: 0.4518 (OUTLIER) cc_final: 0.3655 (t-100) REVERT: C 674 MET cc_start: -0.4892 (ptm) cc_final: -0.5143 (ptp) REVERT: C 695 LYS cc_start: 0.7109 (mmtt) cc_final: 0.6410 (pptt) REVERT: D 407 MET cc_start: 0.7653 (mpp) cc_final: 0.7401 (mpp) REVERT: D 414 MET cc_start: 0.5872 (mpt) cc_final: 0.5086 (tmt) REVERT: D 503 MET cc_start: 0.5355 (tpt) cc_final: 0.4116 (tpt) REVERT: E 58 MET cc_start: 0.8164 (mmp) cc_final: 0.7926 (tpt) REVERT: E 95 GLU cc_start: 0.8667 (mp0) cc_final: 0.8383 (mp0) REVERT: F 24 MET cc_start: 0.9220 (tpt) cc_final: 0.8954 (tpt) REVERT: F 61 SER cc_start: 0.9162 (t) cc_final: 0.8706 (p) REVERT: F 65 ARG cc_start: 0.8390 (mtm-85) cc_final: 0.7755 (mtm110) REVERT: F 67 CYS cc_start: 0.7262 (m) cc_final: 0.6580 (m) REVERT: F 81 ASP cc_start: 0.8495 (t0) cc_final: 0.8129 (t70) REVERT: F 126 GLU cc_start: 0.9387 (mt-10) cc_final: 0.9031 (tm-30) REVERT: G 13 THR cc_start: 0.9172 (t) cc_final: 0.8883 (p) REVERT: G 81 ASP cc_start: 0.8963 (p0) cc_final: 0.8618 (t0) REVERT: G 203 ASP cc_start: 0.8473 (m-30) cc_final: 0.7824 (m-30) REVERT: H 34 LEU cc_start: 0.9054 (tp) cc_final: 0.8583 (tp) REVERT: H 35 TYR cc_start: 0.8816 (m-80) cc_final: 0.8496 (m-80) REVERT: H 61 SER cc_start: 0.9160 (t) cc_final: 0.8260 (p) REVERT: H 74 LYS cc_start: 0.8965 (ttpp) cc_final: 0.8545 (mtpt) REVERT: H 81 ASP cc_start: 0.9202 (t0) cc_final: 0.8851 (t0) REVERT: H 115 LEU cc_start: 0.9335 (mt) cc_final: 0.9014 (mt) outliers start: 43 outliers final: 7 residues processed: 255 average time/residue: 0.6791 time to fit residues: 191.2083 Evaluate side-chains 187 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 177 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 460 TRP Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 125 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 174 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 189 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 chunk 146 optimal weight: 2.9990 chunk 129 optimal weight: 7.9990 chunk 177 optimal weight: 4.9990 chunk 84 optimal weight: 30.0000 chunk 71 optimal weight: 4.9990 chunk 115 optimal weight: 7.9990 chunk 187 optimal weight: 0.6980 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN E 205 HIS ** F 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.149941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.082069 restraints weight = 76072.160| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 5.63 r_work: 0.2919 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2913 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2913 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 18592 Z= 0.304 Angle : 0.719 14.163 25062 Z= 0.374 Chirality : 0.047 0.216 2793 Planarity : 0.005 0.081 3050 Dihedral : 11.277 84.190 2828 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.24 % Favored : 96.59 % Rotamer: Outliers : 2.95 % Allowed : 15.57 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.18), residues: 2268 helix: 2.06 (0.14), residues: 1345 sheet: -1.18 (0.37), residues: 165 loop : -1.14 (0.22), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 743 TYR 0.031 0.002 TYR A 405 PHE 0.025 0.002 PHE H 73 TRP 0.011 0.002 TRP D 671 HIS 0.007 0.002 HIS E 60 Details of bonding type rmsd covalent geometry : bond 0.00711 (18580) covalent geometry : angle 0.71649 (25038) SS BOND : bond 0.00790 ( 12) SS BOND : angle 2.17222 ( 24) hydrogen bonds : bond 0.05208 ( 1131) hydrogen bonds : angle 4.37792 ( 3272) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 187 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.7641 (mpt) cc_final: 0.6071 (mmt) REVERT: A 463 MET cc_start: 0.5355 (mtm) cc_final: 0.4951 (mmm) REVERT: A 486 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7468 (tp30) REVERT: A 721 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.8026 (pmt) REVERT: A 762 LEU cc_start: 0.6486 (OUTLIER) cc_final: 0.6205 (mm) REVERT: B 407 MET cc_start: 0.7364 (OUTLIER) cc_final: 0.7054 (mpp) REVERT: B 496 MET cc_start: 0.7698 (mtp) cc_final: 0.7315 (mtp) REVERT: B 659 PHE cc_start: 0.8287 (OUTLIER) cc_final: 0.7962 (t80) REVERT: B 674 MET cc_start: 0.8727 (ptp) cc_final: 0.8277 (ptp) REVERT: B 714 GLN cc_start: 0.9091 (mm-40) cc_final: 0.8571 (pm20) REVERT: C 414 MET cc_start: 0.2398 (mtm) cc_final: 0.2135 (mtp) REVERT: C 674 MET cc_start: -0.4506 (ptm) cc_final: -0.4841 (ptp) REVERT: C 695 LYS cc_start: 0.6947 (mmtt) cc_final: 0.6382 (pptt) REVERT: D 503 MET cc_start: 0.4979 (tpt) cc_final: 0.4699 (tpt) REVERT: E 11 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.9021 (pp) REVERT: E 58 MET cc_start: 0.8031 (mmp) cc_final: 0.7766 (tpt) REVERT: E 95 GLU cc_start: 0.8447 (mp0) cc_final: 0.8203 (mp0) REVERT: E 207 GLN cc_start: 0.8956 (tm-30) cc_final: 0.8741 (tm-30) REVERT: F 61 SER cc_start: 0.9124 (t) cc_final: 0.8667 (p) REVERT: F 65 ARG cc_start: 0.8512 (mtm-85) cc_final: 0.7841 (mtm180) REVERT: F 67 CYS cc_start: 0.7745 (m) cc_final: 0.7507 (m) REVERT: F 81 ASP cc_start: 0.8556 (t0) cc_final: 0.8295 (t70) REVERT: G 81 ASP cc_start: 0.9022 (p0) cc_final: 0.8630 (t0) REVERT: G 140 ILE cc_start: 0.9122 (mm) cc_final: 0.8905 (mm) REVERT: H 35 TYR cc_start: 0.8923 (m-80) cc_final: 0.8640 (m-80) REVERT: H 74 LYS cc_start: 0.9100 (ttpp) cc_final: 0.8867 (ttmt) REVERT: H 81 ASP cc_start: 0.9200 (t0) cc_final: 0.8908 (t0) outliers start: 54 outliers final: 20 residues processed: 223 average time/residue: 0.5900 time to fit residues: 147.0832 Evaluate side-chains 191 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 166 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 659 PHE Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 544 SER Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 784 THR Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain H residue 150 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 149 optimal weight: 0.9990 chunk 208 optimal weight: 0.7980 chunk 85 optimal weight: 30.0000 chunk 139 optimal weight: 0.6980 chunk 164 optimal weight: 4.9990 chunk 69 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 chunk 147 optimal weight: 0.9980 chunk 88 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 A 709 ASN E 205 HIS F 205 HIS ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 149 ASN G 205 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.152704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.087182 restraints weight = 89040.782| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 6.08 r_work: 0.2960 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2960 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2960 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 18592 Z= 0.154 Angle : 0.621 14.289 25062 Z= 0.315 Chirality : 0.042 0.279 2793 Planarity : 0.004 0.047 3050 Dihedral : 10.447 87.963 2828 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.99 % Favored : 97.83 % Rotamer: Outliers : 3.06 % Allowed : 16.49 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.18), residues: 2268 helix: 2.47 (0.14), residues: 1344 sheet: -0.75 (0.41), residues: 139 loop : -1.12 (0.22), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 743 TYR 0.022 0.001 TYR A 405 PHE 0.014 0.001 PHE H 73 TRP 0.011 0.001 TRP E 178 HIS 0.006 0.001 HIS G 60 Details of bonding type rmsd covalent geometry : bond 0.00359 (18580) covalent geometry : angle 0.61806 (25038) SS BOND : bond 0.00849 ( 12) SS BOND : angle 2.04031 ( 24) hydrogen bonds : bond 0.04157 ( 1131) hydrogen bonds : angle 4.04860 ( 3272) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 191 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.7914 (mpt) cc_final: 0.6399 (mmt) REVERT: A 463 MET cc_start: 0.5255 (mtm) cc_final: 0.4710 (mmm) REVERT: A 486 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7603 (tp30) REVERT: A 496 MET cc_start: 0.6919 (tmm) cc_final: 0.5920 (tmm) REVERT: A 721 MET cc_start: 0.8198 (OUTLIER) cc_final: 0.7981 (pmt) REVERT: B 407 MET cc_start: 0.7269 (OUTLIER) cc_final: 0.6957 (mpp) REVERT: B 496 MET cc_start: 0.7420 (mtp) cc_final: 0.7200 (mtp) REVERT: B 659 PHE cc_start: 0.7962 (t80) cc_final: 0.7684 (t80) REVERT: B 674 MET cc_start: 0.8561 (ptp) cc_final: 0.8113 (ptp) REVERT: B 714 GLN cc_start: 0.8970 (mm-40) cc_final: 0.8646 (mm-40) REVERT: C 414 MET cc_start: 0.2437 (mtm) cc_final: 0.2203 (mtp) REVERT: C 674 MET cc_start: -0.4552 (ptm) cc_final: -0.4955 (ptp) REVERT: C 695 LYS cc_start: 0.7134 (mmtt) cc_final: 0.6622 (pptt) REVERT: D 401 LEU cc_start: 0.6808 (OUTLIER) cc_final: 0.6386 (mp) REVERT: D 408 MET cc_start: 0.6333 (mpm) cc_final: 0.5829 (mpm) REVERT: D 463 MET cc_start: 0.5786 (mmt) cc_final: 0.5552 (mmm) REVERT: D 503 MET cc_start: 0.5364 (tpt) cc_final: 0.5020 (tpt) REVERT: D 629 MET cc_start: 0.6873 (ppp) cc_final: 0.6402 (ppp) REVERT: D 755 GLU cc_start: 0.5890 (mt-10) cc_final: 0.5510 (pp20) REVERT: E 58 MET cc_start: 0.8271 (mmp) cc_final: 0.8037 (tpt) REVERT: E 80 ILE cc_start: 0.9009 (OUTLIER) cc_final: 0.8441 (mp) REVERT: E 95 GLU cc_start: 0.8586 (mp0) cc_final: 0.8302 (mp0) REVERT: E 128 TYR cc_start: 0.7257 (t80) cc_final: 0.6940 (t80) REVERT: E 207 GLN cc_start: 0.8998 (tm-30) cc_final: 0.8783 (tm-30) REVERT: F 24 MET cc_start: 0.9035 (tpt) cc_final: 0.8824 (tpt) REVERT: F 61 SER cc_start: 0.8996 (t) cc_final: 0.8507 (p) REVERT: F 65 ARG cc_start: 0.8541 (mtm-85) cc_final: 0.7823 (mtm110) REVERT: F 67 CYS cc_start: 0.7626 (m) cc_final: 0.6798 (m) REVERT: F 81 ASP cc_start: 0.8405 (t0) cc_final: 0.8058 (t70) REVERT: G 81 ASP cc_start: 0.8814 (p0) cc_final: 0.8524 (t0) REVERT: G 140 ILE cc_start: 0.9096 (mm) cc_final: 0.8867 (mm) REVERT: H 35 TYR cc_start: 0.8827 (m-80) cc_final: 0.8387 (m-80) REVERT: H 61 SER cc_start: 0.9381 (t) cc_final: 0.8553 (p) REVERT: H 74 LYS cc_start: 0.9104 (ttpp) cc_final: 0.8893 (ttmt) outliers start: 56 outliers final: 18 residues processed: 225 average time/residue: 0.5494 time to fit residues: 139.2892 Evaluate side-chains 201 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 179 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 544 SER Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 106 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 22 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 chunk 36 optimal weight: 6.9990 chunk 145 optimal weight: 8.9990 chunk 88 optimal weight: 30.0000 chunk 181 optimal weight: 4.9990 chunk 89 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 chunk 165 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 205 HIS F 205 HIS ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 149 ASN ** G 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.150398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.086478 restraints weight = 91696.019| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 6.36 r_work: 0.2911 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2922 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2922 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 18592 Z= 0.238 Angle : 0.658 11.857 25062 Z= 0.336 Chirality : 0.044 0.283 2793 Planarity : 0.004 0.043 3050 Dihedral : 10.570 89.632 2828 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.97 % Favored : 96.85 % Rotamer: Outliers : 3.99 % Allowed : 16.71 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.18), residues: 2268 helix: 2.30 (0.14), residues: 1352 sheet: -1.18 (0.39), residues: 142 loop : -1.04 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 586 TYR 0.023 0.002 TYR A 768 PHE 0.024 0.002 PHE H 127 TRP 0.010 0.001 TRP D 671 HIS 0.005 0.001 HIS G 60 Details of bonding type rmsd covalent geometry : bond 0.00556 (18580) covalent geometry : angle 0.65539 (25038) SS BOND : bond 0.00972 ( 12) SS BOND : angle 2.08418 ( 24) hydrogen bonds : bond 0.04668 ( 1131) hydrogen bonds : angle 4.21453 ( 3272) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 181 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.7888 (mpt) cc_final: 0.6506 (mmt) REVERT: A 463 MET cc_start: 0.5452 (mtm) cc_final: 0.4909 (mmm) REVERT: A 486 GLU cc_start: 0.8357 (mt-10) cc_final: 0.7717 (tp30) REVERT: A 496 MET cc_start: 0.6834 (tmm) cc_final: 0.5762 (tmm) REVERT: A 707 THR cc_start: 0.9038 (OUTLIER) cc_final: 0.8767 (p) REVERT: A 721 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.8127 (pmt) REVERT: B 407 MET cc_start: 0.7431 (OUTLIER) cc_final: 0.7112 (mpp) REVERT: B 486 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6845 (mm-30) REVERT: B 493 LYS cc_start: 0.6515 (OUTLIER) cc_final: 0.6047 (tptp) REVERT: B 496 MET cc_start: 0.7911 (mtp) cc_final: 0.7564 (mtp) REVERT: B 659 PHE cc_start: 0.8133 (OUTLIER) cc_final: 0.7839 (t80) REVERT: B 674 MET cc_start: 0.8556 (ptp) cc_final: 0.8088 (ptp) REVERT: B 714 GLN cc_start: 0.8865 (mm-40) cc_final: 0.8543 (mm-40) REVERT: C 414 MET cc_start: 0.2415 (mtm) cc_final: 0.2191 (mtp) REVERT: C 674 MET cc_start: -0.4264 (ptm) cc_final: -0.4630 (ptp) REVERT: C 695 LYS cc_start: 0.6900 (mmtt) cc_final: 0.6478 (pptt) REVERT: C 708 MET cc_start: 0.0385 (OUTLIER) cc_final: 0.0036 (mmm) REVERT: D 401 LEU cc_start: 0.6817 (OUTLIER) cc_final: 0.6339 (mp) REVERT: D 408 MET cc_start: 0.6384 (mpm) cc_final: 0.5899 (mpm) REVERT: D 463 MET cc_start: 0.5743 (mmt) cc_final: 0.5534 (mmm) REVERT: D 496 MET cc_start: 0.6480 (mmm) cc_final: 0.6214 (mtp) REVERT: D 508 GLN cc_start: 0.8623 (pt0) cc_final: 0.7756 (pm20) REVERT: D 629 MET cc_start: 0.6925 (ppp) cc_final: 0.6498 (ppp) REVERT: E 11 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.9020 (pp) REVERT: E 58 MET cc_start: 0.8302 (mmp) cc_final: 0.8022 (tpt) REVERT: E 80 ILE cc_start: 0.9007 (OUTLIER) cc_final: 0.8422 (mp) REVERT: E 95 GLU cc_start: 0.8660 (mp0) cc_final: 0.8365 (mp0) REVERT: E 128 TYR cc_start: 0.7338 (t80) cc_final: 0.7095 (t80) REVERT: F 24 MET cc_start: 0.9100 (tpt) cc_final: 0.8878 (tpt) REVERT: F 61 SER cc_start: 0.9128 (t) cc_final: 0.8650 (p) REVERT: F 65 ARG cc_start: 0.8537 (mtm-85) cc_final: 0.7850 (mtm180) REVERT: F 81 ASP cc_start: 0.8481 (t0) cc_final: 0.8142 (t70) REVERT: G 81 ASP cc_start: 0.8820 (p0) cc_final: 0.8575 (t0) REVERT: G 99 ARG cc_start: 0.9230 (tpp80) cc_final: 0.8826 (tpp80) REVERT: G 126 GLU cc_start: 0.8907 (tt0) cc_final: 0.8437 (tp30) REVERT: G 140 ILE cc_start: 0.9120 (mm) cc_final: 0.8872 (mm) REVERT: H 35 TYR cc_start: 0.8899 (m-80) cc_final: 0.8481 (m-80) REVERT: H 61 SER cc_start: 0.9497 (t) cc_final: 0.8928 (p) REVERT: H 74 LYS cc_start: 0.9138 (ttpp) cc_final: 0.8791 (ttmm) REVERT: H 81 ASP cc_start: 0.9117 (t0) cc_final: 0.8869 (t0) outliers start: 73 outliers final: 28 residues processed: 230 average time/residue: 0.5053 time to fit residues: 130.8256 Evaluate side-chains 209 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 171 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 TYR Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 486 GLU Chi-restraints excluded: chain B residue 493 LYS Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 659 PHE Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 708 MET Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 544 SER Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 713 GLU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 150 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 224 optimal weight: 0.6980 chunk 173 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 4 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 210 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 11 optimal weight: 8.9990 chunk 36 optimal weight: 6.9990 chunk 199 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 HIS F 205 HIS ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 149 ASN ** G 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 160 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.151834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.082832 restraints weight = 65292.317| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 4.08 r_work: 0.3009 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2994 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.4353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 18592 Z= 0.172 Angle : 0.630 13.011 25062 Z= 0.319 Chirality : 0.043 0.204 2793 Planarity : 0.004 0.042 3050 Dihedral : 10.088 86.675 2828 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.08 % Favored : 97.74 % Rotamer: Outliers : 3.55 % Allowed : 16.99 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.70 (0.18), residues: 2268 helix: 2.50 (0.14), residues: 1347 sheet: -0.96 (0.41), residues: 134 loop : -0.99 (0.22), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 586 TYR 0.019 0.001 TYR C 647 PHE 0.031 0.001 PHE A 658 TRP 0.011 0.001 TRP B 766 HIS 0.005 0.001 HIS D 412 Details of bonding type rmsd covalent geometry : bond 0.00401 (18580) covalent geometry : angle 0.62645 (25038) SS BOND : bond 0.00978 ( 12) SS BOND : angle 2.14866 ( 24) hydrogen bonds : bond 0.04194 ( 1131) hydrogen bonds : angle 4.06426 ( 3272) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 190 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.7878 (mpt) cc_final: 0.6567 (mmt) REVERT: A 463 MET cc_start: 0.5467 (mtm) cc_final: 0.5239 (mpp) REVERT: A 479 LEU cc_start: 0.8388 (tp) cc_final: 0.7807 (mm) REVERT: A 486 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7830 (tp30) REVERT: A 493 LYS cc_start: 0.7622 (mmmt) cc_final: 0.7418 (ptpt) REVERT: A 586 ARG cc_start: 0.8965 (mmm-85) cc_final: 0.8330 (tmm160) REVERT: B 407 MET cc_start: 0.7221 (OUTLIER) cc_final: 0.6968 (mpp) REVERT: B 486 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6803 (mm-30) REVERT: B 493 LYS cc_start: 0.6571 (OUTLIER) cc_final: 0.6213 (tmtt) REVERT: B 496 MET cc_start: 0.7551 (mtp) cc_final: 0.7301 (mtp) REVERT: B 659 PHE cc_start: 0.8071 (OUTLIER) cc_final: 0.7757 (t80) REVERT: B 670 MET cc_start: 0.9184 (mpp) cc_final: 0.8876 (mpp) REVERT: B 674 MET cc_start: 0.8497 (ptp) cc_final: 0.8004 (ptp) REVERT: B 714 GLN cc_start: 0.8875 (mm-40) cc_final: 0.8552 (mm-40) REVERT: B 768 TYR cc_start: 0.8352 (OUTLIER) cc_final: 0.8041 (p90) REVERT: C 414 MET cc_start: 0.2584 (mtm) cc_final: 0.2331 (mtp) REVERT: C 586 ARG cc_start: 0.9183 (mmm-85) cc_final: 0.8983 (mmm-85) REVERT: C 674 MET cc_start: -0.4243 (ptm) cc_final: -0.4590 (ptp) REVERT: C 695 LYS cc_start: 0.7010 (mmtt) cc_final: 0.6569 (pptt) REVERT: D 401 LEU cc_start: 0.6705 (OUTLIER) cc_final: 0.6294 (mp) REVERT: D 408 MET cc_start: 0.6135 (mpm) cc_final: 0.5729 (mpm) REVERT: D 463 MET cc_start: 0.5629 (mmt) cc_final: 0.5426 (mmm) REVERT: D 503 MET cc_start: 0.5851 (OUTLIER) cc_final: 0.5540 (tpt) REVERT: D 508 GLN cc_start: 0.8657 (pt0) cc_final: 0.7815 (pm20) REVERT: D 629 MET cc_start: 0.7512 (ppp) cc_final: 0.7254 (ppp) REVERT: D 755 GLU cc_start: 0.6377 (mt-10) cc_final: 0.6079 (pp20) REVERT: E 11 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8991 (pp) REVERT: E 80 ILE cc_start: 0.8978 (OUTLIER) cc_final: 0.8415 (mp) REVERT: E 95 GLU cc_start: 0.8621 (mp0) cc_final: 0.8312 (mp0) REVERT: E 128 TYR cc_start: 0.7369 (t80) cc_final: 0.7067 (t80) REVERT: F 65 ARG cc_start: 0.8480 (mtm-85) cc_final: 0.7815 (mtm180) REVERT: F 81 ASP cc_start: 0.8368 (t0) cc_final: 0.8024 (t70) REVERT: G 58 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.8094 (tpt) REVERT: G 81 ASP cc_start: 0.8725 (p0) cc_final: 0.8490 (t0) REVERT: G 99 ARG cc_start: 0.9198 (tpp80) cc_final: 0.8776 (tpp80) REVERT: G 126 GLU cc_start: 0.8916 (tt0) cc_final: 0.8491 (tp30) REVERT: G 140 ILE cc_start: 0.9111 (mm) cc_final: 0.8873 (mm) REVERT: H 35 TYR cc_start: 0.8816 (m-80) cc_final: 0.8492 (m-80) REVERT: H 61 SER cc_start: 0.9241 (t) cc_final: 0.8382 (p) REVERT: H 74 LYS cc_start: 0.9132 (ttpp) cc_final: 0.8787 (ttmm) REVERT: H 81 ASP cc_start: 0.9047 (t0) cc_final: 0.8825 (t0) REVERT: H 205 HIS cc_start: 0.8581 (OUTLIER) cc_final: 0.7455 (m-70) outliers start: 65 outliers final: 23 residues processed: 232 average time/residue: 0.5993 time to fit residues: 155.1836 Evaluate side-chains 210 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 176 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 TYR Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 486 GLU Chi-restraints excluded: chain B residue 493 LYS Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 659 PHE Chi-restraints excluded: chain B residue 768 TYR Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 544 SER Chi-restraints excluded: chain D residue 670 MET Chi-restraints excluded: chain D residue 713 GLU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain G residue 58 MET Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 205 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 74 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 89 optimal weight: 8.9990 chunk 81 optimal weight: 20.0000 chunk 117 optimal weight: 1.9990 chunk 203 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 49 optimal weight: 8.9990 chunk 98 optimal weight: 0.7980 chunk 134 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 412 HIS ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 HIS F 205 HIS G 149 ASN H 160 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.149531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.085902 restraints weight = 95236.987| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 6.16 r_work: 0.2899 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2904 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2904 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.4589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 18592 Z= 0.255 Angle : 0.683 12.446 25062 Z= 0.348 Chirality : 0.045 0.249 2793 Planarity : 0.004 0.045 3050 Dihedral : 10.300 89.217 2828 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.01 % Favored : 96.81 % Rotamer: Outliers : 3.17 % Allowed : 18.35 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.51 (0.18), residues: 2268 helix: 2.32 (0.14), residues: 1351 sheet: -0.77 (0.44), residues: 129 loop : -1.09 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 586 TYR 0.017 0.002 TYR C 647 PHE 0.026 0.002 PHE A 658 TRP 0.011 0.002 TRP B 460 HIS 0.005 0.001 HIS G 60 Details of bonding type rmsd covalent geometry : bond 0.00598 (18580) covalent geometry : angle 0.68033 (25038) SS BOND : bond 0.00753 ( 12) SS BOND : angle 2.19357 ( 24) hydrogen bonds : bond 0.04728 ( 1131) hydrogen bonds : angle 4.25772 ( 3272) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 165 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.7833 (mpt) cc_final: 0.6532 (mmt) REVERT: A 463 MET cc_start: 0.5819 (mtm) cc_final: 0.5107 (mpp) REVERT: A 486 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7879 (tp30) REVERT: A 496 MET cc_start: 0.7089 (tmm) cc_final: 0.5961 (tmm) REVERT: A 586 ARG cc_start: 0.8998 (mmm-85) cc_final: 0.8363 (tmm160) REVERT: B 407 MET cc_start: 0.7213 (OUTLIER) cc_final: 0.6960 (mpp) REVERT: B 460 TRP cc_start: 0.7043 (OUTLIER) cc_final: 0.6296 (t-100) REVERT: B 486 GLU cc_start: 0.6862 (OUTLIER) cc_final: 0.6565 (mm-30) REVERT: B 493 LYS cc_start: 0.6661 (OUTLIER) cc_final: 0.6004 (ttpp) REVERT: B 496 MET cc_start: 0.7708 (mtp) cc_final: 0.7464 (mtp) REVERT: B 659 PHE cc_start: 0.8169 (t80) cc_final: 0.7878 (t80) REVERT: B 674 MET cc_start: 0.8541 (ptp) cc_final: 0.8048 (ptp) REVERT: B 714 GLN cc_start: 0.8758 (mm-40) cc_final: 0.8335 (mm-40) REVERT: B 768 TYR cc_start: 0.8178 (p90) cc_final: 0.7868 (p90) REVERT: C 414 MET cc_start: 0.2170 (mtm) cc_final: 0.1936 (mtp) REVERT: C 641 LYS cc_start: 0.6225 (mttt) cc_final: 0.5864 (pptt) REVERT: C 674 MET cc_start: -0.4034 (ptm) cc_final: -0.4403 (ptp) REVERT: C 695 LYS cc_start: 0.6942 (mmtt) cc_final: 0.6543 (pptt) REVERT: D 401 LEU cc_start: 0.6900 (OUTLIER) cc_final: 0.6347 (mp) REVERT: D 408 MET cc_start: 0.6393 (mpm) cc_final: 0.6095 (mpm) REVERT: D 508 GLN cc_start: 0.8634 (pt0) cc_final: 0.7857 (pm20) REVERT: D 629 MET cc_start: 0.7573 (ppp) cc_final: 0.7268 (ppp) REVERT: D 721 MET cc_start: 0.7697 (tpt) cc_final: 0.7489 (tpt) REVERT: E 11 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.9016 (pp) REVERT: E 80 ILE cc_start: 0.8980 (OUTLIER) cc_final: 0.8497 (mp) REVERT: E 95 GLU cc_start: 0.8627 (mp0) cc_final: 0.8359 (mp0) REVERT: E 128 TYR cc_start: 0.7577 (t80) cc_final: 0.7336 (t80) REVERT: F 81 ASP cc_start: 0.8604 (t0) cc_final: 0.8253 (t70) REVERT: G 58 MET cc_start: 0.8490 (OUTLIER) cc_final: 0.8041 (tpt) REVERT: G 81 ASP cc_start: 0.8811 (p0) cc_final: 0.8588 (t0) REVERT: G 99 ARG cc_start: 0.9226 (tpp80) cc_final: 0.8820 (tpp80) REVERT: G 126 GLU cc_start: 0.8934 (tt0) cc_final: 0.8488 (tp30) REVERT: H 58 MET cc_start: 0.9283 (mmm) cc_final: 0.8812 (mmm) REVERT: H 69 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7836 (pp) REVERT: H 74 LYS cc_start: 0.9152 (ttpp) cc_final: 0.8928 (ttmt) REVERT: H 81 ASP cc_start: 0.9125 (t0) cc_final: 0.8830 (t0) REVERT: H 205 HIS cc_start: 0.8586 (OUTLIER) cc_final: 0.7683 (m-70) outliers start: 58 outliers final: 29 residues processed: 211 average time/residue: 0.5719 time to fit residues: 135.9339 Evaluate side-chains 200 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 161 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 460 TRP Chi-restraints excluded: chain B residue 486 GLU Chi-restraints excluded: chain B residue 493 LYS Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 544 SER Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain G residue 58 MET Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 205 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 104 optimal weight: 30.0000 chunk 85 optimal weight: 30.0000 chunk 69 optimal weight: 3.9990 chunk 183 optimal weight: 5.9990 chunk 151 optimal weight: 10.0000 chunk 213 optimal weight: 0.6980 chunk 124 optimal weight: 30.0000 chunk 51 optimal weight: 0.0030 chunk 136 optimal weight: 0.5980 chunk 187 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 overall best weight: 0.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 GLN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 HIS F 205 HIS G 149 ASN ** G 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 160 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.152983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.082567 restraints weight = 75860.111| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 4.28 r_work: 0.3036 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3031 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3031 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.4729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 18592 Z= 0.137 Angle : 0.657 13.704 25062 Z= 0.326 Chirality : 0.042 0.239 2793 Planarity : 0.004 0.046 3050 Dihedral : 9.551 89.385 2828 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.13 % Favored : 97.70 % Rotamer: Outliers : 2.95 % Allowed : 18.62 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.79 (0.18), residues: 2268 helix: 2.59 (0.14), residues: 1349 sheet: -0.93 (0.47), residues: 109 loop : -1.01 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 586 TYR 0.019 0.001 TYR A 768 PHE 0.027 0.001 PHE A 658 TRP 0.011 0.001 TRP B 460 HIS 0.006 0.001 HIS G 60 Details of bonding type rmsd covalent geometry : bond 0.00315 (18580) covalent geometry : angle 0.65379 (25038) SS BOND : bond 0.00754 ( 12) SS BOND : angle 2.27759 ( 24) hydrogen bonds : bond 0.03988 ( 1131) hydrogen bonds : angle 3.99773 ( 3272) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 182 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.7850 (mpt) cc_final: 0.6521 (mmt) REVERT: A 463 MET cc_start: 0.5802 (mtm) cc_final: 0.5250 (mpp) REVERT: A 486 GLU cc_start: 0.8419 (mt-10) cc_final: 0.7852 (tp30) REVERT: A 493 LYS cc_start: 0.7479 (mmmt) cc_final: 0.6990 (mttm) REVERT: A 496 MET cc_start: 0.7259 (tmm) cc_final: 0.6563 (tmm) REVERT: A 587 GLN cc_start: 0.9001 (OUTLIER) cc_final: 0.8722 (tp40) REVERT: A 721 MET cc_start: 0.7916 (pmt) cc_final: 0.7714 (pmm) REVERT: B 460 TRP cc_start: 0.6628 (OUTLIER) cc_final: 0.6063 (t-100) REVERT: B 463 MET cc_start: 0.4734 (mmm) cc_final: 0.3744 (mmm) REVERT: B 486 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.6760 (mm-30) REVERT: B 659 PHE cc_start: 0.7974 (OUTLIER) cc_final: 0.7738 (t80) REVERT: B 674 MET cc_start: 0.8430 (ptp) cc_final: 0.7932 (ptp) REVERT: B 768 TYR cc_start: 0.8155 (OUTLIER) cc_final: 0.7850 (p90) REVERT: C 414 MET cc_start: 0.2231 (mtm) cc_final: 0.1986 (mtp) REVERT: C 641 LYS cc_start: 0.6033 (mttt) cc_final: 0.5781 (pptt) REVERT: C 674 MET cc_start: -0.4059 (ptm) cc_final: -0.4366 (ptp) REVERT: C 695 LYS cc_start: 0.7218 (mmtt) cc_final: 0.6833 (pptt) REVERT: D 401 LEU cc_start: 0.6965 (OUTLIER) cc_final: 0.6323 (mp) REVERT: D 408 MET cc_start: 0.6114 (mpm) cc_final: 0.5768 (mpm) REVERT: D 503 MET cc_start: 0.5492 (tpp) cc_final: 0.5230 (tpt) REVERT: D 508 GLN cc_start: 0.8701 (pt0) cc_final: 0.7919 (pm20) REVERT: D 629 MET cc_start: 0.7614 (ppp) cc_final: 0.7311 (ppp) REVERT: D 755 GLU cc_start: 0.6588 (mt-10) cc_final: 0.6337 (pp20) REVERT: E 11 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.9037 (pp) REVERT: E 37 ARG cc_start: 0.9405 (ttm-80) cc_final: 0.9128 (ttm-80) REVERT: E 80 ILE cc_start: 0.9044 (OUTLIER) cc_final: 0.8605 (mp) REVERT: E 95 GLU cc_start: 0.8648 (mp0) cc_final: 0.8387 (mp0) REVERT: E 128 TYR cc_start: 0.7367 (t80) cc_final: 0.7087 (t80) REVERT: F 78 LYS cc_start: 0.9090 (OUTLIER) cc_final: 0.8593 (pmtt) REVERT: F 81 ASP cc_start: 0.8436 (t0) cc_final: 0.8107 (t70) REVERT: G 99 ARG cc_start: 0.9245 (tpp80) cc_final: 0.8830 (tpp80) REVERT: G 126 GLU cc_start: 0.8890 (tt0) cc_final: 0.8482 (tp30) REVERT: H 35 TYR cc_start: 0.8920 (m-80) cc_final: 0.8631 (m-80) REVERT: H 61 SER cc_start: 0.9201 (t) cc_final: 0.8220 (p) REVERT: H 69 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7960 (pp) REVERT: H 74 LYS cc_start: 0.9036 (ttpp) cc_final: 0.8813 (ttmt) REVERT: H 81 ASP cc_start: 0.9082 (t0) cc_final: 0.8792 (t0) REVERT: H 205 HIS cc_start: 0.8561 (OUTLIER) cc_final: 0.7482 (m-70) outliers start: 54 outliers final: 20 residues processed: 220 average time/residue: 0.5716 time to fit residues: 140.4317 Evaluate side-chains 201 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 170 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain B residue 460 TRP Chi-restraints excluded: chain B residue 486 GLU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 659 PHE Chi-restraints excluded: chain B residue 768 TYR Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 544 SER Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 77 CYS Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 205 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 183 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 177 optimal weight: 5.9990 chunk 143 optimal weight: 8.9990 chunk 17 optimal weight: 0.9980 chunk 204 optimal weight: 0.9990 chunk 104 optimal weight: 30.0000 chunk 27 optimal weight: 9.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 GLN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 HIS ** G 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 160 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.151890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.087100 restraints weight = 85448.123| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 5.87 r_work: 0.2959 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2972 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2972 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.4804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 18592 Z= 0.170 Angle : 0.681 14.065 25062 Z= 0.338 Chirality : 0.043 0.253 2793 Planarity : 0.004 0.053 3050 Dihedral : 9.543 89.587 2828 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.75 % Favored : 97.07 % Rotamer: Outliers : 2.51 % Allowed : 19.39 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.74 (0.18), residues: 2268 helix: 2.54 (0.14), residues: 1350 sheet: -0.92 (0.45), residues: 122 loop : -1.01 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 586 TYR 0.017 0.001 TYR C 647 PHE 0.029 0.001 PHE H 127 TRP 0.043 0.001 TRP D 460 HIS 0.004 0.001 HIS E 132 Details of bonding type rmsd covalent geometry : bond 0.00399 (18580) covalent geometry : angle 0.67841 (25038) SS BOND : bond 0.00715 ( 12) SS BOND : angle 2.11142 ( 24) hydrogen bonds : bond 0.04185 ( 1131) hydrogen bonds : angle 4.07602 ( 3272) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 176 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.7960 (mpt) cc_final: 0.6614 (mmt) REVERT: A 463 MET cc_start: 0.5666 (mtm) cc_final: 0.5254 (mmm) REVERT: A 486 GLU cc_start: 0.8334 (mt-10) cc_final: 0.7956 (tp30) REVERT: A 493 LYS cc_start: 0.7582 (mmmt) cc_final: 0.7173 (mttm) REVERT: A 496 MET cc_start: 0.7278 (tmm) cc_final: 0.6572 (tmm) REVERT: A 585 MET cc_start: 0.8869 (mpt) cc_final: 0.8344 (mpt) REVERT: A 586 ARG cc_start: 0.9010 (mmm-85) cc_final: 0.8289 (tmm160) REVERT: A 587 GLN cc_start: 0.9080 (OUTLIER) cc_final: 0.8867 (tp40) REVERT: A 721 MET cc_start: 0.7935 (pmt) cc_final: 0.7718 (pmm) REVERT: B 408 MET cc_start: 0.7284 (mmm) cc_final: 0.6484 (tpp) REVERT: B 460 TRP cc_start: 0.6747 (OUTLIER) cc_final: 0.6391 (t-100) REVERT: B 463 MET cc_start: 0.4324 (mmm) cc_final: 0.3884 (mmm) REVERT: B 486 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6785 (mm-30) REVERT: B 493 LYS cc_start: 0.6899 (OUTLIER) cc_final: 0.6561 (tmtt) REVERT: B 659 PHE cc_start: 0.8102 (OUTLIER) cc_final: 0.7836 (t80) REVERT: B 707 THR cc_start: 0.9049 (OUTLIER) cc_final: 0.8795 (p) REVERT: B 768 TYR cc_start: 0.8186 (p90) cc_final: 0.7885 (p90) REVERT: C 414 MET cc_start: 0.2354 (mtm) cc_final: 0.2092 (mtp) REVERT: C 496 MET cc_start: 0.0119 (ptt) cc_final: -0.1100 (pmm) REVERT: C 641 LYS cc_start: 0.6217 (mttt) cc_final: 0.5882 (pptt) REVERT: C 674 MET cc_start: -0.3871 (ptm) cc_final: -0.4116 (ptp) REVERT: C 695 LYS cc_start: 0.7180 (mmtt) cc_final: 0.6839 (pptt) REVERT: D 401 LEU cc_start: 0.6837 (OUTLIER) cc_final: 0.6097 (mp) REVERT: D 408 MET cc_start: 0.6244 (mpm) cc_final: 0.5857 (mpm) REVERT: D 508 GLN cc_start: 0.8763 (pt0) cc_final: 0.7896 (pm20) REVERT: D 629 MET cc_start: 0.7710 (ppp) cc_final: 0.7413 (ppp) REVERT: E 11 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.9042 (pp) REVERT: E 37 ARG cc_start: 0.9450 (ttm-80) cc_final: 0.9042 (ttm-80) REVERT: E 80 ILE cc_start: 0.9056 (OUTLIER) cc_final: 0.8597 (mp) REVERT: E 95 GLU cc_start: 0.8670 (mp0) cc_final: 0.8381 (mp0) REVERT: E 128 TYR cc_start: 0.7481 (t80) cc_final: 0.7190 (t80) REVERT: F 78 LYS cc_start: 0.9096 (OUTLIER) cc_final: 0.8623 (pmtt) REVERT: F 81 ASP cc_start: 0.8494 (t0) cc_final: 0.8181 (t70) REVERT: G 58 MET cc_start: 0.8812 (tpt) cc_final: 0.8599 (tpt) REVERT: G 99 ARG cc_start: 0.9287 (tpp80) cc_final: 0.8806 (tpp80) REVERT: G 126 GLU cc_start: 0.8871 (tt0) cc_final: 0.8459 (tp30) REVERT: H 61 SER cc_start: 0.9332 (t) cc_final: 0.8563 (p) REVERT: H 74 LYS cc_start: 0.9072 (ttpp) cc_final: 0.8840 (ttmt) REVERT: H 81 ASP cc_start: 0.9155 (t0) cc_final: 0.8923 (t0) REVERT: H 205 HIS cc_start: 0.8602 (OUTLIER) cc_final: 0.7582 (m-70) outliers start: 46 outliers final: 26 residues processed: 211 average time/residue: 0.6435 time to fit residues: 151.2451 Evaluate side-chains 203 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 166 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain B residue 460 TRP Chi-restraints excluded: chain B residue 486 GLU Chi-restraints excluded: chain B residue 493 LYS Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 659 PHE Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 647 TYR Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 544 SER Chi-restraints excluded: chain D residue 807 MET Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 77 CYS Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 160 ASN Chi-restraints excluded: chain H residue 205 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 87 optimal weight: 9.9990 chunk 85 optimal weight: 20.0000 chunk 50 optimal weight: 6.9990 chunk 190 optimal weight: 0.9980 chunk 186 optimal weight: 9.9990 chunk 18 optimal weight: 0.6980 chunk 219 optimal weight: 1.9990 chunk 199 optimal weight: 0.0020 chunk 212 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 111 optimal weight: 8.9990 overall best weight: 0.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 HIS ** G 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 160 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.153187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.089299 restraints weight = 91961.574| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 6.20 r_work: 0.2983 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2983 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2983 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.4894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 18592 Z= 0.138 Angle : 0.703 15.169 25062 Z= 0.345 Chirality : 0.042 0.237 2793 Planarity : 0.004 0.046 3050 Dihedral : 9.322 89.577 2828 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.08 % Favored : 97.74 % Rotamer: Outliers : 2.24 % Allowed : 19.77 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.18), residues: 2268 helix: 2.60 (0.14), residues: 1350 sheet: -0.94 (0.44), residues: 121 loop : -0.99 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 586 TYR 0.031 0.001 TYR A 768 PHE 0.024 0.001 PHE G 73 TRP 0.011 0.001 TRP C 460 HIS 0.005 0.001 HIS E 132 Details of bonding type rmsd covalent geometry : bond 0.00317 (18580) covalent geometry : angle 0.70101 (25038) SS BOND : bond 0.00694 ( 12) SS BOND : angle 1.95566 ( 24) hydrogen bonds : bond 0.04000 ( 1131) hydrogen bonds : angle 4.01727 ( 3272) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 175 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.7962 (mpt) cc_final: 0.6627 (mmt) REVERT: A 463 MET cc_start: 0.5627 (mtm) cc_final: 0.5000 (mpp) REVERT: A 486 GLU cc_start: 0.8334 (mt-10) cc_final: 0.7949 (tp30) REVERT: A 493 LYS cc_start: 0.7593 (mmmt) cc_final: 0.7133 (mttm) REVERT: A 496 MET cc_start: 0.7295 (OUTLIER) cc_final: 0.6595 (tmm) REVERT: A 721 MET cc_start: 0.7975 (pmt) cc_final: 0.7743 (pmm) REVERT: B 408 MET cc_start: 0.7422 (mmm) cc_final: 0.6837 (tpp) REVERT: B 460 TRP cc_start: 0.6672 (OUTLIER) cc_final: 0.6136 (t-100) REVERT: B 463 MET cc_start: 0.4257 (mmm) cc_final: 0.3928 (mmm) REVERT: B 486 GLU cc_start: 0.7080 (OUTLIER) cc_final: 0.6810 (mm-30) REVERT: B 659 PHE cc_start: 0.8349 (OUTLIER) cc_final: 0.8040 (t80) REVERT: B 707 THR cc_start: 0.9053 (OUTLIER) cc_final: 0.8832 (p) REVERT: B 768 TYR cc_start: 0.8151 (p90) cc_final: 0.7847 (p90) REVERT: C 414 MET cc_start: 0.2377 (mtm) cc_final: 0.2112 (mtp) REVERT: C 496 MET cc_start: 0.0287 (ptt) cc_final: -0.0885 (pmm) REVERT: C 641 LYS cc_start: 0.6219 (mttt) cc_final: 0.5854 (pptt) REVERT: C 695 LYS cc_start: 0.7350 (mmtt) cc_final: 0.6964 (pptt) REVERT: D 401 LEU cc_start: 0.6817 (OUTLIER) cc_final: 0.6058 (mp) REVERT: D 408 MET cc_start: 0.6176 (mpm) cc_final: 0.5814 (mpm) REVERT: D 463 MET cc_start: 0.5232 (mmm) cc_final: 0.4497 (mmm) REVERT: D 508 GLN cc_start: 0.8702 (pt0) cc_final: 0.7944 (pm20) REVERT: D 629 MET cc_start: 0.7649 (ppp) cc_final: 0.7345 (ppp) REVERT: E 11 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.9001 (pp) REVERT: E 37 ARG cc_start: 0.9439 (ttm-80) cc_final: 0.9198 (ttm-80) REVERT: E 95 GLU cc_start: 0.8671 (mp0) cc_final: 0.8368 (mp0) REVERT: E 128 TYR cc_start: 0.7422 (t80) cc_final: 0.7119 (t80) REVERT: F 78 LYS cc_start: 0.9066 (OUTLIER) cc_final: 0.8587 (pmtt) REVERT: F 81 ASP cc_start: 0.8448 (t0) cc_final: 0.8142 (t70) REVERT: G 58 MET cc_start: 0.8815 (tpt) cc_final: 0.8515 (tpt) REVERT: G 99 ARG cc_start: 0.9286 (tpp80) cc_final: 0.8802 (tpp80) REVERT: G 126 GLU cc_start: 0.8875 (tt0) cc_final: 0.8467 (tp30) REVERT: H 61 SER cc_start: 0.9258 (t) cc_final: 0.8486 (p) REVERT: H 74 LYS cc_start: 0.8989 (ttpp) cc_final: 0.8725 (ttmt) REVERT: H 81 ASP cc_start: 0.9133 (t0) cc_final: 0.8893 (t0) REVERT: H 205 HIS cc_start: 0.8561 (OUTLIER) cc_final: 0.7499 (m-70) outliers start: 41 outliers final: 25 residues processed: 202 average time/residue: 0.6737 time to fit residues: 151.7375 Evaluate side-chains 203 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 169 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain B residue 460 TRP Chi-restraints excluded: chain B residue 486 GLU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 659 PHE Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 544 SER Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 77 CYS Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 203 ASP Chi-restraints excluded: chain H residue 205 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 10 optimal weight: 7.9990 chunk 164 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 160 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 84 optimal weight: 0.0980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 GLN ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 HIS F 205 HIS ** G 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.153499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.089169 restraints weight = 92382.690| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 6.16 r_work: 0.3005 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3014 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3014 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.4966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 18592 Z= 0.131 Angle : 0.701 15.452 25062 Z= 0.343 Chirality : 0.042 0.225 2793 Planarity : 0.004 0.045 3050 Dihedral : 9.131 89.337 2828 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.08 % Favored : 97.74 % Rotamer: Outliers : 2.13 % Allowed : 19.88 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.85 (0.18), residues: 2268 helix: 2.64 (0.14), residues: 1351 sheet: -0.90 (0.44), residues: 120 loop : -0.99 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 586 TYR 0.017 0.001 TYR C 647 PHE 0.029 0.001 PHE H 127 TRP 0.012 0.001 TRP D 460 HIS 0.005 0.001 HIS E 132 Details of bonding type rmsd covalent geometry : bond 0.00296 (18580) covalent geometry : angle 0.69900 (25038) SS BOND : bond 0.00673 ( 12) SS BOND : angle 1.87988 ( 24) hydrogen bonds : bond 0.03875 ( 1131) hydrogen bonds : angle 3.98428 ( 3272) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7933.62 seconds wall clock time: 135 minutes 34.26 seconds (8134.26 seconds total)