Starting phenix.real_space_refine on Sat Aug 23 08:03:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dnj_30785/08_2025/7dnj_30785.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dnj_30785/08_2025/7dnj_30785.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7dnj_30785/08_2025/7dnj_30785.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dnj_30785/08_2025/7dnj_30785.map" model { file = "/net/cci-nas-00/data/ceres_data/7dnj_30785/08_2025/7dnj_30785.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dnj_30785/08_2025/7dnj_30785.cif" } resolution = 3.3 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= 0.003 sd= 0.081 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: 4 Type Number sf(0) Gaussians S 32 5.16 5 C 6912 2.51 5 N 1877 2.21 5 O 2105 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 71 residue(s): 0.01s 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: 10926 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1580 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 189} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 1574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1574 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 189} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 1567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1567 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 189} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "D" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1570 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 7, 'TRANS': 189} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "E" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 574 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "F" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 574 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "G" Number of atoms: 593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 593 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "H" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 582 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "I" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 574 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "J" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 582 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "K" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 574 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "L" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 582 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N LEU G 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU G 73 " occ=0.45 residue: pdb=" N LEU H 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU H 73 " occ=0.45 residue: pdb=" N LEU J 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU J 73 " occ=0.45 residue: pdb=" N LEU L 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU L 73 " occ=0.45 Time building chain proxies: 2.52, per 1000 atoms: 0.23 Number of scatterers: 10926 At special positions: 0 Unit cell: (76.285, 113.905, 110.77, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 32 16.00 O 2105 8.00 N 1877 7.00 C 6912 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.99 Conformation dependent library (CDL) restraints added in 365.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2602 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 8 sheets defined 58.9% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 6 through 18 removed outlier: 3.768A pdb=" N SER A 16 " --> pdb=" O ARG A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 24 removed outlier: 4.047A pdb=" N MET A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 35 removed outlier: 3.558A pdb=" N VAL A 31 " --> pdb=" O GLN A 27 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ASP A 33 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N TYR A 34 " --> pdb=" O PRO A 30 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU A 35 " --> pdb=" O VAL A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 54 removed outlier: 3.796A pdb=" N THR A 49 " --> pdb=" O GLN A 45 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA A 51 " --> pdb=" O GLN A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 68 removed outlier: 3.525A pdb=" N LEU A 61 " --> pdb=" O GLN A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 86 Processing helix chain 'A' and resid 89 through 96 removed outlier: 3.961A pdb=" N TYR A 94 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 129 removed outlier: 3.737A pdb=" N LEU A 118 " --> pdb=" O TYR A 114 " (cutoff:3.500A) Proline residue: A 123 - end of helix Processing helix chain 'A' and resid 130 through 139 removed outlier: 5.210A pdb=" N ASP A 136 " --> pdb=" O ARG A 132 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LYS A 137 " --> pdb=" O ASP A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 156 removed outlier: 3.550A pdb=" N ARG A 149 " --> pdb=" O THR A 145 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 172 removed outlier: 3.529A pdb=" N GLY A 163 " --> pdb=" O GLY A 159 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS A 169 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N VAL A 172 " --> pdb=" O LEU A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 187 removed outlier: 4.046A pdb=" N ALA A 180 " --> pdb=" O ASN A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 199 removed outlier: 3.916A pdb=" N VAL A 194 " --> pdb=" O ASN A 190 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN A 195 " --> pdb=" O ASN A 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 18 removed outlier: 3.534A pdb=" N SER B 16 " --> pdb=" O ARG B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 24 removed outlier: 4.096A pdb=" N MET B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 32 removed outlier: 3.611A pdb=" N VAL B 31 " --> pdb=" O GLN B 27 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU B 32 " --> pdb=" O VAL B 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 27 through 32' Processing helix chain 'B' and resid 33 through 35 No H-bonds generated for 'chain 'B' and resid 33 through 35' Processing helix chain 'B' and resid 39 through 68 removed outlier: 7.858A pdb=" N ASN B 55 " --> pdb=" O ALA B 51 " (cutoff:3.500A) removed outlier: 9.649A pdb=" N MET B 56 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLN B 57 " --> pdb=" O SER B 53 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU B 61 " --> pdb=" O GLN B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 86 removed outlier: 3.731A pdb=" N GLU B 78 " --> pdb=" O GLY B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 94 removed outlier: 3.701A pdb=" N ALA B 92 " --> pdb=" O SER B 88 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N TYR B 94 " --> pdb=" O LEU B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 102 removed outlier: 3.974A pdb=" N ASP B 101 " --> pdb=" O GLU B 98 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU B 102 " --> pdb=" O LEU B 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 98 through 102' Processing helix chain 'B' and resid 104 through 121 Processing helix chain 'B' and resid 121 through 129 Processing helix chain 'B' and resid 134 through 141 Processing helix chain 'B' and resid 145 through 156 Processing helix chain 'B' and resid 159 through 171 removed outlier: 3.517A pdb=" N LYS B 169 " --> pdb=" O ARG B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 176 through 188 Processing helix chain 'B' and resid 190 through 199 removed outlier: 4.060A pdb=" N VAL B 194 " --> pdb=" O ASN B 190 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN B 195 " --> pdb=" O ASN B 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 18 removed outlier: 3.552A pdb=" N ASN C 10 " --> pdb=" O SER C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 26 removed outlier: 3.994A pdb=" N MET C 24 " --> pdb=" O ALA C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 32 removed outlier: 3.619A pdb=" N VAL C 31 " --> pdb=" O GLN C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 53 removed outlier: 3.728A pdb=" N GLN C 45 " --> pdb=" O GLU C 41 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA C 51 " --> pdb=" O GLN C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 68 removed outlier: 4.018A pdb=" N GLN C 57 " --> pdb=" O SER C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 86 removed outlier: 3.893A pdb=" N GLU C 78 " --> pdb=" O GLY C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 96 removed outlier: 3.542A pdb=" N ALA C 92 " --> pdb=" O SER C 88 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR C 94 " --> pdb=" O LEU C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 121 Processing helix chain 'C' and resid 121 through 129 Processing helix chain 'C' and resid 130 through 133 Processing helix chain 'C' and resid 134 through 141 Processing helix chain 'C' and resid 145 through 156 Processing helix chain 'C' and resid 159 through 172 removed outlier: 3.874A pdb=" N VAL C 172 " --> pdb=" O LEU C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 188 Processing helix chain 'C' and resid 190 through 198 removed outlier: 4.567A pdb=" N VAL C 194 " --> pdb=" O ASN C 190 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN C 195 " --> pdb=" O ASN C 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 24 removed outlier: 6.024A pdb=" N ALA D 20 " --> pdb=" O SER D 16 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ARG D 21 " --> pdb=" O CYS D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 35 removed outlier: 3.618A pdb=" N VAL D 31 " --> pdb=" O GLN D 27 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ASP D 33 " --> pdb=" O GLU D 29 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N TYR D 34 " --> pdb=" O PRO D 30 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU D 35 " --> pdb=" O VAL D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 68 removed outlier: 3.669A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA D 51 " --> pdb=" O GLN D 47 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY D 54 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ASN D 55 " --> pdb=" O ALA D 51 " (cutoff:3.500A) removed outlier: 9.210A pdb=" N MET D 56 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLN D 57 " --> pdb=" O SER D 53 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU D 61 " --> pdb=" O GLN D 57 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS D 68 " --> pdb=" O SER D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 86 removed outlier: 3.663A pdb=" N GLU D 78 " --> pdb=" O GLY D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 96 removed outlier: 3.646A pdb=" N ALA D 92 " --> pdb=" O SER D 88 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR D 94 " --> pdb=" O LEU D 90 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASN D 96 " --> pdb=" O ALA D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 129 removed outlier: 3.604A pdb=" N GLN D 116 " --> pdb=" O ASP D 112 " (cutoff:3.500A) Proline residue: D 123 - end of helix Processing helix chain 'D' and resid 130 through 133 Processing helix chain 'D' and resid 134 through 141 removed outlier: 4.009A pdb=" N GLU D 140 " --> pdb=" O ASP D 136 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU D 141 " --> pdb=" O LYS D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 156 removed outlier: 3.778A pdb=" N ARG D 151 " --> pdb=" O GLU D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 172 removed outlier: 3.512A pdb=" N GLY D 163 " --> pdb=" O GLY D 159 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL D 172 " --> pdb=" O LEU D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 188 Processing helix chain 'D' and resid 190 through 199 removed outlier: 3.806A pdb=" N VAL D 194 " --> pdb=" O ASN D 190 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN D 195 " --> pdb=" O ASN D 191 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR D 198 " --> pdb=" O VAL D 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 35 removed outlier: 3.544A pdb=" N ILE E 30 " --> pdb=" O VAL E 26 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP E 32 " --> pdb=" O ALA E 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 34 removed outlier: 3.910A pdb=" N ALA F 28 " --> pdb=" O GLU F 24 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN F 31 " --> pdb=" O LYS F 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 34 Processing helix chain 'G' and resid 37 through 39 No H-bonds generated for 'chain 'G' and resid 37 through 39' Processing helix chain 'G' and resid 55 through 60 Processing helix chain 'H' and resid 22 through 34 removed outlier: 3.503A pdb=" N GLU H 34 " --> pdb=" O ILE H 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 39 No H-bonds generated for 'chain 'H' and resid 37 through 39' Processing helix chain 'H' and resid 55 through 60 removed outlier: 3.917A pdb=" N TYR H 59 " --> pdb=" O THR H 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 22 through 34 removed outlier: 3.687A pdb=" N VAL I 26 " --> pdb=" O THR I 22 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS I 33 " --> pdb=" O LYS I 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 22 through 35 removed outlier: 3.513A pdb=" N LYS J 33 " --> pdb=" O LYS J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 60 Processing helix chain 'K' and resid 22 through 34 removed outlier: 3.607A pdb=" N VAL K 26 " --> pdb=" O THR K 22 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLN K 31 " --> pdb=" O LYS K 27 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 41 Processing helix chain 'K' and resid 55 through 60 Processing helix chain 'L' and resid 22 through 34 removed outlier: 3.629A pdb=" N VAL L 26 " --> pdb=" O THR L 22 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN L 31 " --> pdb=" O LYS L 27 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 12 through 16 removed outlier: 8.547A pdb=" N LEU E 67 " --> pdb=" O GLN E 2 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N PHE E 4 " --> pdb=" O LEU E 67 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LEU E 69 " --> pdb=" O PHE E 4 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LYS E 6 " --> pdb=" O LEU E 69 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 12 through 16 removed outlier: 8.392A pdb=" N LEU F 67 " --> pdb=" O GLN F 2 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N PHE F 4 " --> pdb=" O LEU F 67 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N LEU F 69 " --> pdb=" O PHE F 4 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LYS F 6 " --> pdb=" O LEU F 69 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N LEU F 71 " --> pdb=" O LYS F 6 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 12 through 15 Processing sheet with id=AA4, first strand: chain 'H' and resid 12 through 16 removed outlier: 3.882A pdb=" N ILE H 3 " --> pdb=" O LEU H 15 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N GLN H 2 " --> pdb=" O SER H 65 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N LEU H 67 " --> pdb=" O GLN H 2 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N PHE H 4 " --> pdb=" O LEU H 67 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N LEU H 69 " --> pdb=" O PHE H 4 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LYS H 6 " --> pdb=" O LEU H 69 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N LEU H 71 " --> pdb=" O LYS H 6 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 14 through 16 removed outlier: 6.821A pdb=" N GLN I 2 " --> pdb=" O SER I 65 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N LEU I 67 " --> pdb=" O GLN I 2 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N PHE I 4 " --> pdb=" O LEU I 67 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N LEU I 69 " --> pdb=" O PHE I 4 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N LYS I 6 " --> pdb=" O LEU I 69 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL I 70 " --> pdb=" O ARG I 42 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'J' and resid 12 through 16 removed outlier: 7.741A pdb=" N GLN J 2 " --> pdb=" O SER J 65 " (cutoff:3.500A) removed outlier: 8.865A pdb=" N LEU J 67 " --> pdb=" O GLN J 2 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N PHE J 4 " --> pdb=" O LEU J 67 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N LEU J 69 " --> pdb=" O PHE J 4 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LYS J 6 " --> pdb=" O LEU J 69 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N LEU J 71 " --> pdb=" O LYS J 6 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 13 through 16 removed outlier: 3.900A pdb=" N SER K 65 " --> pdb=" O GLN K 2 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 13 through 14 509 hydrogen bonds defined for protein. 1470 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: 1.57 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2553 1.33 - 1.45: 1982 1.45 - 1.57: 6491 1.57 - 1.69: 0 1.69 - 1.81: 56 Bond restraints: 11082 Sorted by residual: bond pdb=" CA PRO L 37 " pdb=" C PRO L 37 " ideal model delta sigma weight residual 1.517 1.547 -0.030 9.30e-03 1.16e+04 1.05e+01 bond pdb=" CA GLU A 141 " pdb=" C GLU A 141 " ideal model delta sigma weight residual 1.523 1.483 0.040 1.41e-02 5.03e+03 8.09e+00 bond pdb=" N ILE L 36 " pdb=" CA ILE L 36 " ideal model delta sigma weight residual 1.461 1.495 -0.033 1.23e-02 6.61e+03 7.38e+00 bond pdb=" N GLY L 35 " pdb=" CA GLY L 35 " ideal model delta sigma weight residual 1.443 1.480 -0.037 1.38e-02 5.25e+03 7.32e+00 bond pdb=" C PRO L 38 " pdb=" O PRO L 38 " ideal model delta sigma weight residual 1.235 1.207 0.028 1.30e-02 5.92e+03 4.53e+00 ... (remaining 11077 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 14581 2.04 - 4.08: 359 4.08 - 6.11: 44 6.11 - 8.15: 5 8.15 - 10.19: 2 Bond angle restraints: 14991 Sorted by residual: angle pdb=" N PRO L 37 " pdb=" CA PRO L 37 " pdb=" C PRO L 37 " ideal model delta sigma weight residual 110.70 116.83 -6.13 1.22e+00 6.72e-01 2.52e+01 angle pdb=" CA PRO L 37 " pdb=" C PRO L 37 " pdb=" N PRO L 38 " ideal model delta sigma weight residual 117.93 122.69 -4.76 1.20e+00 6.94e-01 1.58e+01 angle pdb=" CA PRO L 37 " pdb=" C PRO L 37 " pdb=" O PRO L 37 " ideal model delta sigma weight residual 120.56 115.93 4.63 1.45e+00 4.76e-01 1.02e+01 angle pdb=" N GLU D 166 " pdb=" CA GLU D 166 " pdb=" C GLU D 166 " ideal model delta sigma weight residual 112.45 108.05 4.40 1.39e+00 5.18e-01 1.00e+01 angle pdb=" CA GLN L 41 " pdb=" C GLN L 41 " pdb=" O GLN L 41 " ideal model delta sigma weight residual 120.92 117.43 3.49 1.14e+00 7.69e-01 9.39e+00 ... (remaining 14986 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 6073 17.70 - 35.40: 605 35.40 - 53.10: 118 53.10 - 70.80: 26 70.80 - 88.50: 19 Dihedral angle restraints: 6841 sinusoidal: 2850 harmonic: 3991 Sorted by residual: dihedral pdb=" CA GLN H 41 " pdb=" C GLN H 41 " pdb=" N ARG H 42 " pdb=" CA ARG H 42 " ideal model delta harmonic sigma weight residual 180.00 159.14 20.86 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA PRO B 97 " pdb=" C PRO B 97 " pdb=" N GLU B 98 " pdb=" CA GLU B 98 " ideal model delta harmonic sigma weight residual 180.00 160.61 19.39 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" C ASP L 39 " pdb=" N ASP L 39 " pdb=" CA ASP L 39 " pdb=" CB ASP L 39 " ideal model delta harmonic sigma weight residual -122.60 -113.67 -8.93 0 2.50e+00 1.60e-01 1.28e+01 ... (remaining 6838 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1402 0.060 - 0.120: 339 0.120 - 0.181: 21 0.181 - 0.241: 2 0.241 - 0.301: 1 Chirality restraints: 1765 Sorted by residual: chirality pdb=" CA ASP L 39 " pdb=" N ASP L 39 " pdb=" C ASP L 39 " pdb=" CB ASP L 39 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CB ILE F 36 " pdb=" CA ILE F 36 " pdb=" CG1 ILE F 36 " pdb=" CG2 ILE F 36 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA PRO L 37 " pdb=" N PRO L 37 " pdb=" C PRO L 37 " pdb=" CB PRO L 37 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.36e-01 ... (remaining 1762 not shown) Planarity restraints: 1932 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU F 18 " -0.042 5.00e-02 4.00e+02 6.33e-02 6.40e+00 pdb=" N PRO F 19 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO F 19 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO F 19 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 114 " 0.012 2.00e-02 2.50e+03 1.26e-02 3.18e+00 pdb=" CG TYR C 114 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR C 114 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR C 114 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR C 114 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR C 114 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR C 114 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 114 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU K 18 " -0.029 5.00e-02 4.00e+02 4.40e-02 3.09e+00 pdb=" N PRO K 19 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO K 19 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO K 19 " -0.024 5.00e-02 4.00e+02 ... (remaining 1929 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1531 2.74 - 3.28: 11854 3.28 - 3.82: 18135 3.82 - 4.36: 22858 4.36 - 4.90: 37590 Nonbonded interactions: 91968 Sorted by model distance: nonbonded pdb=" O GLN E 62 " pdb=" OG SER E 65 " model vdw 2.199 3.040 nonbonded pdb=" OG SER A 6 " pdb=" OE1 GLU A 9 " model vdw 2.209 3.040 nonbonded pdb=" OG1 THR J 22 " pdb=" OD1 ASN J 25 " model vdw 2.221 3.040 nonbonded pdb=" O ASP E 21 " pdb=" OG1 THR E 55 " model vdw 2.221 3.040 nonbonded pdb=" N MET H 1 " pdb=" O VAL H 17 " model vdw 2.230 3.120 ... (remaining 91963 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 4 through 100 or (resid 101 and (name N or name CA or name \ C or name O or name CB )) or resid 102 through 131 or (resid 132 and (name N or \ name CA or name C or name O or name CB )) or resid 133 through 186 or (resid 18 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 188 through \ 200)) selection = (chain 'B' and (resid 4 through 100 or (resid 101 and (name N or name CA or name \ C or name O or name CB )) or resid 102 through 186 or (resid 187 and (name N or \ name CA or name C or name O or name CB )) or resid 188 through 200)) selection = chain 'C' selection = (chain 'D' and (resid 4 through 100 or (resid 101 and (name N or name CA or name \ C or name O or name CB )) or resid 102 through 200)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = (chain 'G' and resid 1 through 72) selection = (chain 'H' and resid 1 through 72) selection = chain 'I' selection = (chain 'J' and resid 1 through 72) selection = chain 'K' selection = (chain 'L' and resid 1 through 72) } 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=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.600 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.700 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 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 : 0.008 0.052 11082 Z= 0.348 Angle : 0.782 10.189 14991 Z= 0.430 Chirality : 0.049 0.301 1765 Planarity : 0.005 0.063 1932 Dihedral : 15.345 88.498 4239 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.94 % Favored : 95.99 % Rotamer: Outliers : 0.33 % Allowed : 0.41 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.61 (0.23), residues: 1345 helix: -1.51 (0.20), residues: 647 sheet: -0.96 (0.39), residues: 188 loop : -0.13 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 72 TYR 0.031 0.002 TYR C 114 PHE 0.015 0.002 PHE C 178 TRP 0.011 0.002 TRP D 177 HIS 0.007 0.002 HIS C 72 Details of bonding type rmsd covalent geometry : bond 0.00797 (11082) covalent geometry : angle 0.78189 (14991) hydrogen bonds : bond 0.26285 ( 509) hydrogen bonds : angle 9.65571 ( 1470) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 320 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 146 ILE cc_start: 0.8898 (tp) cc_final: 0.8648 (tp) REVERT: C 112 ASP cc_start: 0.8235 (m-30) cc_final: 0.7997 (m-30) REVERT: D 128 LYS cc_start: 0.8752 (ttmm) cc_final: 0.8403 (mtpp) REVERT: D 146 ILE cc_start: 0.9226 (mm) cc_final: 0.8943 (tp) REVERT: D 166 GLU cc_start: 0.8922 (tp30) cc_final: 0.8458 (tp30) REVERT: E 6 LYS cc_start: 0.8700 (ptpp) cc_final: 0.8443 (ptpt) REVERT: F 31 GLN cc_start: 0.7546 (tm-30) cc_final: 0.6868 (tp40) REVERT: F 50 LEU cc_start: 0.5041 (mt) cc_final: 0.4607 (mt) REVERT: F 65 SER cc_start: 0.7654 (m) cc_final: 0.7442 (m) REVERT: G 52 ASP cc_start: 0.8874 (t70) cc_final: 0.8645 (t0) REVERT: G 72 ARG cc_start: 0.7895 (ttp80) cc_final: 0.7549 (tmm-80) REVERT: H 13 ILE cc_start: 0.8417 (mp) cc_final: 0.8004 (mp) REVERT: I 16 GLU cc_start: 0.6736 (tp30) cc_final: 0.6296 (tp30) REVERT: I 21 ASP cc_start: 0.8552 (m-30) cc_final: 0.8250 (m-30) REVERT: I 40 GLN cc_start: 0.8487 (pm20) cc_final: 0.8091 (pm20) REVERT: I 60 ASN cc_start: 0.8497 (m110) cc_final: 0.8280 (m-40) REVERT: K 56 LEU cc_start: 0.8933 (mm) cc_final: 0.8470 (tp) outliers start: 4 outliers final: 2 residues processed: 321 average time/residue: 0.1022 time to fit residues: 45.6026 Evaluate side-chains 277 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 275 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain L residue 40 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.1980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 ASN C 191 ASN ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 25 ASN ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 60 ASN L 2 GLN L 40 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.099692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.076785 restraints weight = 23821.018| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.97 r_work: 0.2961 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2978 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2971 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11082 Z= 0.179 Angle : 0.682 8.435 14991 Z= 0.349 Chirality : 0.046 0.200 1765 Planarity : 0.005 0.048 1932 Dihedral : 5.565 51.059 1471 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.97 % Allowed : 13.13 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.85 (0.23), residues: 1345 helix: -0.51 (0.20), residues: 689 sheet: -1.22 (0.37), residues: 197 loop : 0.06 (0.31), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 170 TYR 0.017 0.002 TYR A 25 PHE 0.018 0.002 PHE H 4 TRP 0.008 0.001 TRP C 71 HIS 0.006 0.001 HIS A 111 Details of bonding type rmsd covalent geometry : bond 0.00418 (11082) covalent geometry : angle 0.68193 (14991) hydrogen bonds : bond 0.04468 ( 509) hydrogen bonds : angle 5.74270 ( 1470) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 325 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: A 128 LYS cc_start: 0.9074 (mmtm) cc_final: 0.8701 (mmtm) REVERT: A 146 ILE cc_start: 0.8727 (tp) cc_final: 0.8486 (tp) REVERT: C 13 TYR cc_start: 0.8592 (t80) cc_final: 0.8320 (t80) REVERT: D 166 GLU cc_start: 0.8863 (tp30) cc_final: 0.8525 (tp30) REVERT: E 6 LYS cc_start: 0.8765 (ptpp) cc_final: 0.8406 (ptpt) REVERT: F 31 GLN cc_start: 0.7522 (tm-30) cc_final: 0.6840 (tp40) REVERT: F 50 LEU cc_start: 0.6304 (mt) cc_final: 0.5860 (mt) REVERT: F 54 ARG cc_start: 0.8020 (mmm160) cc_final: 0.7503 (mtm180) REVERT: F 59 TYR cc_start: 0.5932 (m-80) cc_final: 0.5481 (m-80) REVERT: F 65 SER cc_start: 0.7698 (m) cc_final: 0.7409 (m) REVERT: G 52 ASP cc_start: 0.9071 (t70) cc_final: 0.8866 (t0) REVERT: G 72 ARG cc_start: 0.8549 (ttp80) cc_final: 0.8063 (tmm-80) REVERT: H 49 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.8271 (tt0) REVERT: H 63 LYS cc_start: 0.7608 (ptmt) cc_final: 0.7127 (ptmt) REVERT: H 64 GLU cc_start: 0.7945 (mp0) cc_final: 0.7562 (mp0) REVERT: I 18 GLU cc_start: 0.8473 (tp30) cc_final: 0.8189 (mm-30) REVERT: I 21 ASP cc_start: 0.8646 (m-30) cc_final: 0.8389 (m-30) REVERT: I 60 ASN cc_start: 0.8543 (m110) cc_final: 0.8226 (m-40) REVERT: J 33 LYS cc_start: 0.7203 (mtmm) cc_final: 0.6803 (tttt) REVERT: K 1 MET cc_start: 0.8234 (tpt) cc_final: 0.7807 (tpt) REVERT: K 56 LEU cc_start: 0.9075 (mm) cc_final: 0.8625 (tp) REVERT: L 6 LYS cc_start: 0.8963 (tptp) cc_final: 0.8571 (tppt) REVERT: L 31 GLN cc_start: 0.8770 (pp30) cc_final: 0.8381 (pp30) outliers start: 24 outliers final: 13 residues processed: 332 average time/residue: 0.0887 time to fit residues: 41.4283 Evaluate side-chains 284 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 270 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 49 GLN Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain K residue 14 THR Chi-restraints excluded: chain L residue 65 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 110 optimal weight: 8.9990 chunk 75 optimal weight: 5.9990 chunk 111 optimal weight: 10.0000 chunk 64 optimal weight: 0.9990 chunk 72 optimal weight: 10.0000 chunk 125 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 99 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 191 ASN ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN K 25 ASN ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 60 ASN L 49 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.099739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.076380 restraints weight = 23824.778| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 3.01 r_work: 0.2973 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2977 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2977 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11082 Z= 0.148 Angle : 0.627 7.861 14991 Z= 0.315 Chirality : 0.044 0.174 1765 Planarity : 0.004 0.048 1932 Dihedral : 5.109 52.290 1468 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.53 % Allowed : 15.09 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.44 (0.23), residues: 1345 helix: -0.02 (0.21), residues: 650 sheet: -1.43 (0.36), residues: 200 loop : 0.17 (0.30), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 54 TYR 0.023 0.001 TYR C 114 PHE 0.018 0.001 PHE H 4 TRP 0.006 0.001 TRP D 177 HIS 0.006 0.002 HIS A 111 Details of bonding type rmsd covalent geometry : bond 0.00356 (11082) covalent geometry : angle 0.62655 (14991) hydrogen bonds : bond 0.03687 ( 509) hydrogen bonds : angle 5.34350 ( 1470) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 300 time to evaluate : 0.453 Fit side-chains revert: symmetry clash REVERT: A 47 GLN cc_start: 0.8045 (mm-40) cc_final: 0.7684 (tp-100) REVERT: C 13 TYR cc_start: 0.8626 (t80) cc_final: 0.8339 (t80) REVERT: D 166 GLU cc_start: 0.8742 (tp30) cc_final: 0.8396 (tp30) REVERT: E 6 LYS cc_start: 0.8870 (ptpp) cc_final: 0.8435 (ptpt) REVERT: E 16 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7804 (pm20) REVERT: F 31 GLN cc_start: 0.7572 (tm-30) cc_final: 0.6857 (tp40) REVERT: F 50 LEU cc_start: 0.6087 (mt) cc_final: 0.5533 (mt) REVERT: F 54 ARG cc_start: 0.7934 (mmm160) cc_final: 0.7517 (mtm180) REVERT: F 59 TYR cc_start: 0.6347 (m-80) cc_final: 0.5876 (m-80) REVERT: F 65 SER cc_start: 0.7647 (m) cc_final: 0.7387 (m) REVERT: H 49 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.8222 (tt0) REVERT: H 63 LYS cc_start: 0.7790 (ptmt) cc_final: 0.7148 (ptmt) REVERT: H 64 GLU cc_start: 0.7935 (mp0) cc_final: 0.7605 (mp0) REVERT: I 18 GLU cc_start: 0.8436 (tp30) cc_final: 0.8139 (mm-30) REVERT: I 21 ASP cc_start: 0.8633 (m-30) cc_final: 0.8360 (m-30) REVERT: I 40 GLN cc_start: 0.8648 (pm20) cc_final: 0.8192 (pm20) REVERT: I 41 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.8112 (pm20) REVERT: I 60 ASN cc_start: 0.8530 (m110) cc_final: 0.8219 (m-40) REVERT: J 33 LYS cc_start: 0.7180 (mtmm) cc_final: 0.6877 (tttt) REVERT: K 1 MET cc_start: 0.8196 (tpt) cc_final: 0.7782 (tpt) REVERT: L 6 LYS cc_start: 0.8949 (tptp) cc_final: 0.8530 (tppt) outliers start: 43 outliers final: 23 residues processed: 324 average time/residue: 0.1023 time to fit residues: 46.8754 Evaluate side-chains 302 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 277 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 191 ASN Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 122 GLN Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 49 GLN Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 41 GLN Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain J residue 6 LYS Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 24 GLU Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain K residue 14 THR Chi-restraints excluded: chain K residue 57 SER Chi-restraints excluded: chain L residue 48 LYS Chi-restraints excluded: chain L residue 65 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 19 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 108 optimal weight: 4.9990 chunk 97 optimal weight: 9.9990 chunk 40 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 126 optimal weight: 6.9990 chunk 57 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 41 GLN ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 60 ASN ** L 49 GLN ** 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 = 0.3527 r_free = 0.3527 target = 0.099427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.076148 restraints weight = 23952.173| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 3.04 r_work: 0.2956 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2965 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2965 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 11082 Z= 0.189 Angle : 0.643 8.387 14991 Z= 0.320 Chirality : 0.044 0.165 1765 Planarity : 0.004 0.050 1932 Dihedral : 5.043 52.795 1468 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.61 % Allowed : 18.05 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.37 (0.24), residues: 1345 helix: 0.04 (0.21), residues: 653 sheet: -1.47 (0.36), residues: 200 loop : 0.23 (0.30), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 72 TYR 0.018 0.001 TYR C 114 PHE 0.018 0.001 PHE H 4 TRP 0.010 0.001 TRP A 177 HIS 0.006 0.002 HIS A 111 Details of bonding type rmsd covalent geometry : bond 0.00456 (11082) covalent geometry : angle 0.64315 (14991) hydrogen bonds : bond 0.03457 ( 509) hydrogen bonds : angle 5.22289 ( 1470) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 281 time to evaluate : 0.475 Fit side-chains revert: symmetry clash REVERT: A 47 GLN cc_start: 0.8072 (mm-40) cc_final: 0.7707 (tp-100) REVERT: C 13 TYR cc_start: 0.8664 (t80) cc_final: 0.8391 (t80) REVERT: C 169 LYS cc_start: 0.8843 (mttm) cc_final: 0.8597 (mtmt) REVERT: D 166 GLU cc_start: 0.8690 (tp30) cc_final: 0.8298 (tp30) REVERT: E 6 LYS cc_start: 0.8879 (ptpp) cc_final: 0.8414 (ptpt) REVERT: F 31 GLN cc_start: 0.7577 (tm-30) cc_final: 0.6870 (tp40) REVERT: F 50 LEU cc_start: 0.6178 (mt) cc_final: 0.5575 (mt) REVERT: F 54 ARG cc_start: 0.7933 (mmm160) cc_final: 0.7515 (mtm180) REVERT: F 59 TYR cc_start: 0.6544 (m-80) cc_final: 0.6073 (m-80) REVERT: F 65 SER cc_start: 0.7643 (m) cc_final: 0.7390 (m) REVERT: H 63 LYS cc_start: 0.7797 (ptmt) cc_final: 0.6968 (ptmt) REVERT: H 64 GLU cc_start: 0.7963 (mp0) cc_final: 0.7588 (mp0) REVERT: I 18 GLU cc_start: 0.8432 (tp30) cc_final: 0.8154 (mm-30) REVERT: I 21 ASP cc_start: 0.8627 (m-30) cc_final: 0.8355 (m-30) REVERT: I 40 GLN cc_start: 0.8628 (pm20) cc_final: 0.8191 (pm20) REVERT: I 41 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.8121 (pm20) REVERT: I 60 ASN cc_start: 0.8435 (m110) cc_final: 0.8154 (m-40) REVERT: J 52 ASP cc_start: 0.8392 (p0) cc_final: 0.8027 (t70) REVERT: K 1 MET cc_start: 0.8087 (tpt) cc_final: 0.7591 (tpt) REVERT: K 24 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8415 (mm-30) REVERT: L 6 LYS cc_start: 0.8967 (tptp) cc_final: 0.8546 (tppt) REVERT: L 31 GLN cc_start: 0.8976 (pp30) cc_final: 0.8538 (pp30) outliers start: 44 outliers final: 31 residues processed: 307 average time/residue: 0.1030 time to fit residues: 44.7941 Evaluate side-chains 301 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 269 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 41 GLN Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain J residue 6 LYS Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain K residue 14 THR Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain K residue 57 SER Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 48 LYS Chi-restraints excluded: chain L residue 65 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 99 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 83 optimal weight: 9.9990 chunk 119 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 34 optimal weight: 7.9990 chunk 117 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.100073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.076999 restraints weight = 23632.262| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.98 r_work: 0.2975 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2980 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.95 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2980 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11082 Z= 0.161 Angle : 0.619 9.140 14991 Z= 0.310 Chirality : 0.044 0.175 1765 Planarity : 0.004 0.052 1932 Dihedral : 4.945 53.811 1468 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.36 % Allowed : 19.36 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.22 (0.24), residues: 1345 helix: 0.17 (0.21), residues: 653 sheet: -1.37 (0.36), residues: 197 loop : 0.28 (0.30), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 72 TYR 0.023 0.001 TYR C 114 PHE 0.018 0.001 PHE H 4 TRP 0.007 0.001 TRP D 177 HIS 0.007 0.002 HIS A 111 Details of bonding type rmsd covalent geometry : bond 0.00391 (11082) covalent geometry : angle 0.61895 (14991) hydrogen bonds : bond 0.03217 ( 509) hydrogen bonds : angle 5.07567 ( 1470) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 290 time to evaluate : 0.451 Fit side-chains revert: symmetry clash REVERT: A 195 GLN cc_start: 0.9071 (OUTLIER) cc_final: 0.8649 (tm-30) REVERT: C 13 TYR cc_start: 0.8647 (t80) cc_final: 0.8369 (t80) REVERT: C 78 GLU cc_start: 0.8467 (tp30) cc_final: 0.8187 (tp30) REVERT: C 169 LYS cc_start: 0.8843 (mttm) cc_final: 0.8583 (mtmt) REVERT: D 166 GLU cc_start: 0.8690 (tp30) cc_final: 0.8474 (tp30) REVERT: D 195 GLN cc_start: 0.8699 (tm-30) cc_final: 0.8070 (pp30) REVERT: E 6 LYS cc_start: 0.8903 (ptpp) cc_final: 0.8434 (ptpt) REVERT: E 15 LEU cc_start: 0.9220 (mt) cc_final: 0.8972 (mt) REVERT: F 31 GLN cc_start: 0.7676 (tm-30) cc_final: 0.6998 (tp-100) REVERT: F 50 LEU cc_start: 0.6220 (mt) cc_final: 0.5702 (mt) REVERT: F 54 ARG cc_start: 0.7903 (mmm160) cc_final: 0.7509 (mtp180) REVERT: F 59 TYR cc_start: 0.6571 (m-80) cc_final: 0.5884 (m-80) REVERT: F 65 SER cc_start: 0.7661 (m) cc_final: 0.7410 (m) REVERT: H 63 LYS cc_start: 0.7796 (ptmt) cc_final: 0.7430 (pttt) REVERT: I 18 GLU cc_start: 0.8468 (tp30) cc_final: 0.8193 (mm-30) REVERT: I 21 ASP cc_start: 0.8620 (m-30) cc_final: 0.8362 (m-30) REVERT: I 40 GLN cc_start: 0.8605 (pm20) cc_final: 0.8135 (pm20) REVERT: I 41 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.8106 (pm20) REVERT: I 60 ASN cc_start: 0.8424 (m110) cc_final: 0.8143 (m-40) REVERT: J 52 ASP cc_start: 0.8155 (p0) cc_final: 0.7887 (t70) REVERT: K 1 MET cc_start: 0.8009 (tpt) cc_final: 0.7470 (tpt) REVERT: L 6 LYS cc_start: 0.8958 (tptp) cc_final: 0.8553 (tppt) REVERT: L 31 GLN cc_start: 0.9007 (pp30) cc_final: 0.8577 (pp30) outliers start: 41 outliers final: 29 residues processed: 314 average time/residue: 0.0998 time to fit residues: 44.0351 Evaluate side-chains 300 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 269 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 195 GLN Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 41 GLN Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain J residue 6 LYS Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain K residue 14 THR Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 48 LYS Chi-restraints excluded: chain L residue 65 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 57 optimal weight: 10.0000 chunk 53 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 88 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 3 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN K 60 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.101231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.078084 restraints weight = 23405.637| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 3.01 r_work: 0.3008 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3016 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.95 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.95 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3016 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11082 Z= 0.122 Angle : 0.607 10.085 14991 Z= 0.304 Chirality : 0.043 0.174 1765 Planarity : 0.004 0.048 1932 Dihedral : 4.833 56.361 1468 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.12 % Allowed : 21.33 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.07 (0.24), residues: 1345 helix: 0.31 (0.21), residues: 653 sheet: -1.24 (0.37), residues: 191 loop : 0.26 (0.29), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 54 TYR 0.023 0.001 TYR C 114 PHE 0.019 0.001 PHE H 4 TRP 0.007 0.001 TRP D 177 HIS 0.006 0.001 HIS A 111 Details of bonding type rmsd covalent geometry : bond 0.00295 (11082) covalent geometry : angle 0.60698 (14991) hydrogen bonds : bond 0.02898 ( 509) hydrogen bonds : angle 4.86462 ( 1470) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 295 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 195 GLN cc_start: 0.9019 (OUTLIER) cc_final: 0.8622 (tm-30) REVERT: B 121 LEU cc_start: 0.9168 (mt) cc_final: 0.8933 (mt) REVERT: C 13 TYR cc_start: 0.8567 (t80) cc_final: 0.8268 (t80) REVERT: C 78 GLU cc_start: 0.8477 (tp30) cc_final: 0.8102 (tp30) REVERT: D 166 GLU cc_start: 0.8493 (tp30) cc_final: 0.7964 (tp30) REVERT: D 195 GLN cc_start: 0.8704 (tm-30) cc_final: 0.8123 (pp30) REVERT: E 4 PHE cc_start: 0.8609 (m-80) cc_final: 0.8354 (m-80) REVERT: E 6 LYS cc_start: 0.8922 (ptpp) cc_final: 0.8454 (ptpt) REVERT: F 50 LEU cc_start: 0.6406 (mt) cc_final: 0.5736 (mt) REVERT: F 54 ARG cc_start: 0.7796 (mmm160) cc_final: 0.7402 (mtp180) REVERT: F 59 TYR cc_start: 0.6531 (m-80) cc_final: 0.5935 (m-80) REVERT: F 64 GLU cc_start: 0.7543 (tp30) cc_final: 0.7231 (tp30) REVERT: F 65 SER cc_start: 0.7662 (m) cc_final: 0.7415 (m) REVERT: H 63 LYS cc_start: 0.7751 (ptmt) cc_final: 0.6719 (ptmt) REVERT: H 64 GLU cc_start: 0.7925 (mp0) cc_final: 0.7417 (mp0) REVERT: I 15 LEU cc_start: 0.7238 (mm) cc_final: 0.6920 (mm) REVERT: I 18 GLU cc_start: 0.8471 (tp30) cc_final: 0.8196 (mm-30) REVERT: I 21 ASP cc_start: 0.8608 (m-30) cc_final: 0.8350 (m-30) REVERT: I 40 GLN cc_start: 0.8583 (pm20) cc_final: 0.8083 (pm20) REVERT: I 54 ARG cc_start: 0.8839 (mtp85) cc_final: 0.8596 (mtp85) REVERT: I 60 ASN cc_start: 0.8374 (m110) cc_final: 0.8152 (m-40) REVERT: J 52 ASP cc_start: 0.8013 (p0) cc_final: 0.7543 (m-30) REVERT: L 6 LYS cc_start: 0.8970 (tptp) cc_final: 0.8558 (tppt) REVERT: L 18 GLU cc_start: 0.8809 (tm-30) cc_final: 0.8287 (tm-30) REVERT: L 31 GLN cc_start: 0.8985 (pp30) cc_final: 0.8497 (pp30) outliers start: 38 outliers final: 27 residues processed: 319 average time/residue: 0.1026 time to fit residues: 45.9577 Evaluate side-chains 297 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 269 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 195 GLN Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 138 CYS Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 57 SER Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 65 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 16 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 117 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 2 GLN K 60 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.101411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.078219 restraints weight = 23549.130| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 3.01 r_work: 0.2996 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3005 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.95 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3005 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11082 Z= 0.142 Angle : 0.616 8.936 14991 Z= 0.309 Chirality : 0.043 0.158 1765 Planarity : 0.004 0.048 1932 Dihedral : 4.826 59.047 1468 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.20 % Allowed : 21.90 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.03 (0.24), residues: 1345 helix: 0.40 (0.21), residues: 653 sheet: -1.23 (0.37), residues: 191 loop : 0.32 (0.30), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 54 TYR 0.024 0.001 TYR C 114 PHE 0.022 0.001 PHE H 4 TRP 0.007 0.001 TRP D 177 HIS 0.007 0.002 HIS A 111 Details of bonding type rmsd covalent geometry : bond 0.00348 (11082) covalent geometry : angle 0.61592 (14991) hydrogen bonds : bond 0.02906 ( 509) hydrogen bonds : angle 4.85657 ( 1470) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 282 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.8472 (t70) cc_final: 0.8224 (t70) REVERT: C 78 GLU cc_start: 0.8469 (tp30) cc_final: 0.8100 (tp30) REVERT: D 166 GLU cc_start: 0.8465 (tp30) cc_final: 0.7970 (tp30) REVERT: D 195 GLN cc_start: 0.8726 (tm-30) cc_final: 0.8134 (pp30) REVERT: E 6 LYS cc_start: 0.8934 (ptpp) cc_final: 0.8534 (ptpt) REVERT: F 50 LEU cc_start: 0.6303 (mt) cc_final: 0.5533 (mt) REVERT: F 54 ARG cc_start: 0.7815 (mmm160) cc_final: 0.7413 (mtp180) REVERT: F 59 TYR cc_start: 0.6522 (m-80) cc_final: 0.5951 (m-80) REVERT: F 64 GLU cc_start: 0.7533 (tp30) cc_final: 0.7180 (tp30) REVERT: F 65 SER cc_start: 0.7664 (m) cc_final: 0.7412 (m) REVERT: H 63 LYS cc_start: 0.7674 (ptmt) cc_final: 0.6347 (ptmt) REVERT: H 64 GLU cc_start: 0.7914 (mp0) cc_final: 0.6944 (mp0) REVERT: I 15 LEU cc_start: 0.7169 (mm) cc_final: 0.6839 (mm) REVERT: I 18 GLU cc_start: 0.8492 (tp30) cc_final: 0.8011 (mm-30) REVERT: I 21 ASP cc_start: 0.8613 (m-30) cc_final: 0.8334 (m-30) REVERT: I 54 ARG cc_start: 0.8852 (mtp85) cc_final: 0.8600 (mtp85) REVERT: I 60 ASN cc_start: 0.8396 (m110) cc_final: 0.8179 (m-40) REVERT: J 52 ASP cc_start: 0.7952 (p0) cc_final: 0.7536 (m-30) REVERT: K 1 MET cc_start: 0.7928 (tpt) cc_final: 0.7424 (tpt) REVERT: L 6 LYS cc_start: 0.8948 (tptp) cc_final: 0.8547 (tppt) REVERT: L 16 GLU cc_start: 0.7480 (tp30) cc_final: 0.7248 (tp30) REVERT: L 31 GLN cc_start: 0.8998 (pp30) cc_final: 0.8484 (pp30) outliers start: 39 outliers final: 32 residues processed: 309 average time/residue: 0.1023 time to fit residues: 44.5795 Evaluate side-chains 301 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 269 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 138 CYS Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 4 PHE Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain J residue 6 LYS Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 57 SER Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 65 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 103 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 113 optimal weight: 0.5980 chunk 0 optimal weight: 8.9990 chunk 76 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 96 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 104 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 25 ASN K 60 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.101075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.077844 restraints weight = 23520.024| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 3.01 r_work: 0.2997 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3004 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3004 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11082 Z= 0.142 Angle : 0.634 8.950 14991 Z= 0.316 Chirality : 0.044 0.213 1765 Planarity : 0.004 0.044 1932 Dihedral : 4.807 57.249 1468 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.79 % Allowed : 22.15 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.10 (0.24), residues: 1345 helix: 0.47 (0.21), residues: 647 sheet: -1.17 (0.38), residues: 188 loop : 0.30 (0.29), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 54 TYR 0.025 0.001 TYR C 114 PHE 0.021 0.001 PHE H 4 TRP 0.007 0.001 TRP D 177 HIS 0.006 0.002 HIS A 111 Details of bonding type rmsd covalent geometry : bond 0.00347 (11082) covalent geometry : angle 0.63377 (14991) hydrogen bonds : bond 0.02859 ( 509) hydrogen bonds : angle 4.82447 ( 1470) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 281 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 GLN cc_start: 0.9009 (OUTLIER) cc_final: 0.8611 (tm-30) REVERT: C 78 GLU cc_start: 0.8519 (tp30) cc_final: 0.8149 (tp30) REVERT: C 112 ASP cc_start: 0.8669 (m-30) cc_final: 0.8455 (m-30) REVERT: C 169 LYS cc_start: 0.8854 (mttm) cc_final: 0.8612 (mtmt) REVERT: D 166 GLU cc_start: 0.8476 (tp30) cc_final: 0.7964 (tp30) REVERT: D 195 GLN cc_start: 0.8722 (tm-30) cc_final: 0.8145 (pp30) REVERT: E 6 LYS cc_start: 0.8913 (ptpp) cc_final: 0.8513 (ptpt) REVERT: E 54 ARG cc_start: 0.8040 (mmm160) cc_final: 0.7825 (mmm160) REVERT: F 50 LEU cc_start: 0.6316 (mt) cc_final: 0.5338 (mp) REVERT: F 54 ARG cc_start: 0.7915 (mmm160) cc_final: 0.7447 (mtp180) REVERT: F 59 TYR cc_start: 0.6487 (m-80) cc_final: 0.5885 (m-80) REVERT: F 64 GLU cc_start: 0.7545 (tp30) cc_final: 0.7224 (tp30) REVERT: F 65 SER cc_start: 0.7638 (m) cc_final: 0.7393 (m) REVERT: H 63 LYS cc_start: 0.7675 (ptmt) cc_final: 0.6324 (ptmt) REVERT: H 64 GLU cc_start: 0.7884 (mp0) cc_final: 0.6911 (mp0) REVERT: I 15 LEU cc_start: 0.7076 (mm) cc_final: 0.6733 (mm) REVERT: I 18 GLU cc_start: 0.8499 (tp30) cc_final: 0.8002 (mm-30) REVERT: I 21 ASP cc_start: 0.8597 (m-30) cc_final: 0.8280 (m-30) REVERT: I 54 ARG cc_start: 0.8845 (mtp85) cc_final: 0.8583 (mtp85) REVERT: J 52 ASP cc_start: 0.7934 (p0) cc_final: 0.7619 (m-30) REVERT: K 1 MET cc_start: 0.7896 (tpt) cc_final: 0.7336 (tpt) REVERT: L 6 LYS cc_start: 0.8949 (tptp) cc_final: 0.8551 (tppt) REVERT: L 31 GLN cc_start: 0.8984 (pp30) cc_final: 0.8431 (pp30) outliers start: 34 outliers final: 27 residues processed: 305 average time/residue: 0.1017 time to fit residues: 43.8695 Evaluate side-chains 292 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 264 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 195 GLN Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 138 CYS Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain I residue 4 PHE Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain J residue 6 LYS Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 57 SER Chi-restraints excluded: chain L residue 65 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 72 optimal weight: 8.9990 chunk 24 optimal weight: 0.9980 chunk 61 optimal weight: 0.0670 chunk 5 optimal weight: 3.9990 chunk 128 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 129 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.101661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.078244 restraints weight = 23268.140| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 3.02 r_work: 0.3006 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3014 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.95 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3014 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11082 Z= 0.135 Angle : 0.632 8.878 14991 Z= 0.313 Chirality : 0.043 0.171 1765 Planarity : 0.004 0.046 1932 Dihedral : 4.529 19.802 1467 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.71 % Allowed : 22.64 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.18 (0.24), residues: 1345 helix: 0.55 (0.21), residues: 647 sheet: -1.10 (0.38), residues: 188 loop : 0.31 (0.29), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 54 TYR 0.032 0.001 TYR A 13 PHE 0.014 0.001 PHE A 107 TRP 0.007 0.001 TRP D 177 HIS 0.006 0.002 HIS A 111 Details of bonding type rmsd covalent geometry : bond 0.00331 (11082) covalent geometry : angle 0.63165 (14991) hydrogen bonds : bond 0.02838 ( 509) hydrogen bonds : angle 4.78384 ( 1470) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 285 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 GLU cc_start: 0.8688 (tp30) cc_final: 0.8160 (tp30) REVERT: A 195 GLN cc_start: 0.9004 (OUTLIER) cc_final: 0.8611 (tm-30) REVERT: B 121 LEU cc_start: 0.9193 (mt) cc_final: 0.8961 (mt) REVERT: B 170 ARG cc_start: 0.8945 (mmt90) cc_final: 0.8663 (mmt90) REVERT: C 78 GLU cc_start: 0.8474 (tp30) cc_final: 0.8064 (tp30) REVERT: C 112 ASP cc_start: 0.8640 (m-30) cc_final: 0.8425 (m-30) REVERT: C 169 LYS cc_start: 0.8855 (mttm) cc_final: 0.8617 (mtmt) REVERT: D 166 GLU cc_start: 0.8438 (tp30) cc_final: 0.7932 (tp30) REVERT: D 195 GLN cc_start: 0.8644 (tm-30) cc_final: 0.8102 (pp30) REVERT: E 6 LYS cc_start: 0.8874 (ptpp) cc_final: 0.8492 (ptpt) REVERT: E 54 ARG cc_start: 0.8043 (mmm160) cc_final: 0.7758 (mmm160) REVERT: F 50 LEU cc_start: 0.6267 (mt) cc_final: 0.5252 (mp) REVERT: F 54 ARG cc_start: 0.7902 (mmm160) cc_final: 0.7455 (mtp180) REVERT: F 59 TYR cc_start: 0.6474 (m-80) cc_final: 0.5925 (m-80) REVERT: F 64 GLU cc_start: 0.7522 (tp30) cc_final: 0.7160 (tp30) REVERT: F 65 SER cc_start: 0.7607 (m) cc_final: 0.7371 (m) REVERT: H 63 LYS cc_start: 0.7643 (ptmt) cc_final: 0.6285 (ptmt) REVERT: H 64 GLU cc_start: 0.7870 (mp0) cc_final: 0.6884 (mp0) REVERT: I 15 LEU cc_start: 0.7083 (mm) cc_final: 0.6717 (mm) REVERT: I 18 GLU cc_start: 0.8458 (tp30) cc_final: 0.7925 (mm-30) REVERT: I 21 ASP cc_start: 0.8597 (m-30) cc_final: 0.8279 (m-30) REVERT: I 54 ARG cc_start: 0.8804 (mtp85) cc_final: 0.8539 (mtp85) REVERT: J 29 LYS cc_start: 0.8685 (ttmt) cc_final: 0.8459 (ttmt) REVERT: J 52 ASP cc_start: 0.7927 (p0) cc_final: 0.7594 (m-30) REVERT: K 1 MET cc_start: 0.7910 (tpt) cc_final: 0.7401 (tpt) REVERT: L 6 LYS cc_start: 0.8936 (tptp) cc_final: 0.8564 (tppt) REVERT: L 31 GLN cc_start: 0.8953 (pp30) cc_final: 0.8398 (pp30) outliers start: 33 outliers final: 25 residues processed: 308 average time/residue: 0.0983 time to fit residues: 42.5531 Evaluate side-chains 296 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 270 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 195 GLN Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 138 CYS Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain I residue 4 PHE Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain J residue 6 LYS Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain L residue 65 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 95 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 97 optimal weight: 8.9990 chunk 53 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 46 optimal weight: 0.1980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN A 111 HIS I 31 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.102603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.079245 restraints weight = 23381.874| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 3.04 r_work: 0.3024 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3033 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.95 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3033 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11082 Z= 0.122 Angle : 0.640 8.941 14991 Z= 0.318 Chirality : 0.043 0.164 1765 Planarity : 0.004 0.049 1932 Dihedral : 4.509 23.416 1467 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.21 % Allowed : 23.54 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.26 (0.24), residues: 1345 helix: 0.64 (0.21), residues: 647 sheet: -1.10 (0.37), residues: 192 loop : 0.35 (0.30), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 72 TYR 0.032 0.001 TYR C 114 PHE 0.024 0.001 PHE A 107 TRP 0.007 0.001 TRP C 71 HIS 0.006 0.001 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00293 (11082) covalent geometry : angle 0.64002 (14991) hydrogen bonds : bond 0.02759 ( 509) hydrogen bonds : angle 4.75526 ( 1470) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 277 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 GLU cc_start: 0.8587 (tp30) cc_final: 0.8171 (tp30) REVERT: A 195 GLN cc_start: 0.8977 (OUTLIER) cc_final: 0.8588 (tm-30) REVERT: B 170 ARG cc_start: 0.8940 (mmt90) cc_final: 0.8674 (mmt90) REVERT: C 78 GLU cc_start: 0.8448 (tp30) cc_final: 0.8094 (tp30) REVERT: D 166 GLU cc_start: 0.8372 (tp30) cc_final: 0.7914 (tp30) REVERT: D 195 GLN cc_start: 0.8618 (tm-30) cc_final: 0.8070 (pp30) REVERT: E 6 LYS cc_start: 0.8868 (ptpp) cc_final: 0.8483 (ptpt) REVERT: E 54 ARG cc_start: 0.8041 (mmm160) cc_final: 0.7799 (mmm160) REVERT: F 31 GLN cc_start: 0.7709 (tm-30) cc_final: 0.7118 (tp40) REVERT: F 50 LEU cc_start: 0.6222 (mt) cc_final: 0.5430 (mt) REVERT: F 54 ARG cc_start: 0.7831 (mmm160) cc_final: 0.7436 (mtp180) REVERT: F 59 TYR cc_start: 0.6427 (m-80) cc_final: 0.5999 (m-80) REVERT: F 64 GLU cc_start: 0.7502 (tp30) cc_final: 0.7103 (tp30) REVERT: F 65 SER cc_start: 0.7563 (m) cc_final: 0.7326 (m) REVERT: H 43 LEU cc_start: 0.9001 (mt) cc_final: 0.8658 (mt) REVERT: H 63 LYS cc_start: 0.7635 (ptmt) cc_final: 0.6244 (ptmt) REVERT: H 64 GLU cc_start: 0.7811 (mp0) cc_final: 0.6823 (mp0) REVERT: I 15 LEU cc_start: 0.7145 (mm) cc_final: 0.6783 (mm) REVERT: I 18 GLU cc_start: 0.8505 (tp30) cc_final: 0.7995 (mm-30) REVERT: I 21 ASP cc_start: 0.8594 (m-30) cc_final: 0.8329 (m-30) REVERT: I 54 ARG cc_start: 0.8814 (mtp85) cc_final: 0.8557 (mtp85) REVERT: J 29 LYS cc_start: 0.8702 (ttmt) cc_final: 0.8456 (ttmt) REVERT: J 52 ASP cc_start: 0.7921 (p0) cc_final: 0.7641 (m-30) REVERT: L 6 LYS cc_start: 0.8933 (tptp) cc_final: 0.8555 (tppt) REVERT: L 31 GLN cc_start: 0.8977 (pp30) cc_final: 0.8468 (pp30) outliers start: 27 outliers final: 24 residues processed: 297 average time/residue: 0.0955 time to fit residues: 39.8732 Evaluate side-chains 295 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 270 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 195 GLN Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 138 CYS Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain I residue 4 PHE Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain J residue 6 LYS Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain L residue 65 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 31 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 130 optimal weight: 10.0000 chunk 52 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 chunk 65 optimal weight: 0.4980 chunk 22 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 41 GLN ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.102665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.079206 restraints weight = 23513.305| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 3.04 r_work: 0.3025 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3033 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.95 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3032 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11082 Z= 0.124 Angle : 0.638 8.905 14991 Z= 0.316 Chirality : 0.043 0.161 1765 Planarity : 0.004 0.047 1932 Dihedral : 4.459 22.629 1467 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.30 % Allowed : 23.71 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.31 (0.24), residues: 1345 helix: 0.68 (0.21), residues: 641 sheet: -1.05 (0.37), residues: 191 loop : 0.37 (0.29), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 72 TYR 0.032 0.001 TYR C 114 PHE 0.017 0.001 PHE B 107 TRP 0.007 0.001 TRP D 177 HIS 0.006 0.001 HIS C 111 Details of bonding type rmsd covalent geometry : bond 0.00301 (11082) covalent geometry : angle 0.63774 (14991) hydrogen bonds : bond 0.02731 ( 509) hydrogen bonds : angle 4.72578 ( 1470) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2229.30 seconds wall clock time: 39 minutes 7.10 seconds (2347.10 seconds total)