Starting phenix.real_space_refine on Mon Jul 28 21:52:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dnj_30785/07_2025/7dnj_30785.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dnj_30785/07_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_30785/07_2025/7dnj_30785.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dnj_30785/07_2025/7dnj_30785.map" model { file = "/net/cci-nas-00/data/ceres_data/7dnj_30785/07_2025/7dnj_30785.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dnj_30785/07_2025/7dnj_30785.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP: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: 6.74, per 1000 atoms: 0.62 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: 2.71 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.09 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: 2.84 Time building geometry restraints manager: 3.22 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: 0.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 26.570 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.210 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (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 TRP 0.011 0.002 TRP D 177 HIS 0.007 0.002 HIS C 72 PHE 0.015 0.002 PHE C 178 TYR 0.031 0.002 TYR C 114 ARG 0.006 0.001 ARG G 72 Details of bonding type rmsd hydrogen bonds : bond 0.26285 ( 509) hydrogen bonds : angle 9.65571 ( 1470) covalent geometry : bond 0.00797 (11082) covalent geometry : angle 0.78189 (14991) *********************** 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 : 1.438 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: 0.8402 (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: 0.6869 (tp40) REVERT: F 50 LEU cc_start: 0.5041 (mt) cc_final: 0.4606 (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: 0.8281 (m-40) REVERT: J 52 ASP cc_start: 0.8145 (p0) cc_final: 0.7913 (t70) 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: 0.2396 time to fit residues: 106.0691 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 : 1.280 ------------------------------------------------------------------------------- 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 111 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 119 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.3548 r_free = 0.3548 target = 0.100948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.078113 restraints weight = 23446.145| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.95 r_work: 0.2999 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3006 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1830 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= 0.148 Angle : 0.677 8.025 14991 Z= 0.345 Chirality : 0.045 0.192 1765 Planarity : 0.005 0.046 1932 Dihedral : 5.504 51.432 1471 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.89 % Allowed : 12.55 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.23), residues: 1345 helix: -0.37 (0.20), residues: 668 sheet: -1.22 (0.37), residues: 197 loop : 0.10 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 71 HIS 0.006 0.002 HIS A 111 PHE 0.018 0.002 PHE H 4 TYR 0.017 0.002 TYR F 59 ARG 0.005 0.001 ARG K 42 Details of bonding type rmsd hydrogen bonds : bond 0.04264 ( 509) hydrogen bonds : angle 5.61821 ( 1470) covalent geometry : bond 0.00340 (11082) covalent geometry : angle 0.67683 (14991) *********************** 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 356 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 333 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.8573 (t70) cc_final: 0.8371 (t70) REVERT: A 128 LYS cc_start: 0.9043 (mmtm) cc_final: 0.8672 (mmtm) REVERT: A 146 ILE cc_start: 0.8691 (tp) cc_final: 0.8451 (tp) REVERT: B 127 ASP cc_start: 0.8349 (m-30) cc_final: 0.8137 (m-30) REVERT: C 13 TYR cc_start: 0.8592 (t80) cc_final: 0.8318 (t80) REVERT: D 166 GLU cc_start: 0.8843 (tp30) cc_final: 0.8531 (tp30) REVERT: E 6 LYS cc_start: 0.8786 (ptpp) cc_final: 0.8427 (ptpt) REVERT: F 1 MET cc_start: 0.7276 (ttp) cc_final: 0.6982 (ttp) REVERT: F 31 GLN cc_start: 0.7517 (tm-30) cc_final: 0.6791 (tp40) REVERT: F 50 LEU cc_start: 0.6283 (mt) cc_final: 0.5702 (mt) REVERT: F 54 ARG cc_start: 0.7871 (mmm160) cc_final: 0.7465 (mtm180) REVERT: F 59 TYR cc_start: 0.5834 (m-80) cc_final: 0.5368 (m-80) REVERT: F 62 GLN cc_start: 0.7019 (mp10) cc_final: 0.6730 (mp10) REVERT: F 65 SER cc_start: 0.7697 (m) cc_final: 0.7411 (m) REVERT: G 52 ASP cc_start: 0.9019 (t70) cc_final: 0.8818 (t0) REVERT: G 72 ARG cc_start: 0.8533 (ttp80) cc_final: 0.8073 (tmm-80) REVERT: H 2 GLN cc_start: 0.8600 (tp40) cc_final: 0.8210 (tp40) REVERT: H 49 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.8326 (tt0) REVERT: H 63 LYS cc_start: 0.7752 (ptmt) cc_final: 0.7358 (ptmt) REVERT: H 64 GLU cc_start: 0.7943 (mp0) cc_final: 0.7691 (mp0) REVERT: I 18 GLU cc_start: 0.8468 (tp30) cc_final: 0.8206 (mm-30) REVERT: I 21 ASP cc_start: 0.8606 (m-30) cc_final: 0.8363 (m-30) REVERT: I 60 ASN cc_start: 0.8556 (m110) cc_final: 0.8221 (m-40) REVERT: K 1 MET cc_start: 0.8236 (tpt) cc_final: 0.7841 (tpt) REVERT: K 56 LEU cc_start: 0.9063 (mm) cc_final: 0.8617 (tp) REVERT: L 6 LYS cc_start: 0.8961 (tptp) cc_final: 0.8573 (tppt) REVERT: L 18 GLU cc_start: 0.8870 (tm-30) cc_final: 0.8597 (tm-30) outliers start: 23 outliers final: 13 residues processed: 340 average time/residue: 0.2893 time to fit residues: 136.0700 Evaluate side-chains 293 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 279 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 SER 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 C residue 191 ASN 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 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 29 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 57 optimal weight: 10.0000 chunk 68 optimal weight: 4.9990 chunk 19 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 60 ASN ** H 25 ASN ** 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 = 0.3545 r_free = 0.3545 target = 0.100162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.076977 restraints weight = 23650.380| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.97 r_work: 0.2990 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2994 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2319 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= 0.140 Angle : 0.618 7.600 14991 Z= 0.311 Chirality : 0.044 0.172 1765 Planarity : 0.004 0.046 1932 Dihedral : 5.043 53.121 1468 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.95 % Allowed : 15.91 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.24), residues: 1345 helix: -0.11 (0.20), residues: 671 sheet: -1.36 (0.36), residues: 197 loop : 0.26 (0.30), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 177 HIS 0.007 0.002 HIS A 111 PHE 0.014 0.001 PHE A 107 TYR 0.022 0.001 TYR C 114 ARG 0.003 0.000 ARG I 54 Details of bonding type rmsd hydrogen bonds : bond 0.03662 ( 509) hydrogen bonds : angle 5.29939 ( 1470) covalent geometry : bond 0.00330 (11082) covalent geometry : angle 0.61795 (14991) *********************** 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 333 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 297 time to evaluate : 1.240 Fit side-chains revert: symmetry clash REVERT: A 47 GLN cc_start: 0.8070 (mm-40) cc_final: 0.7689 (tp-100) REVERT: A 127 ASP cc_start: 0.8577 (t70) cc_final: 0.8348 (t70) REVERT: A 128 LYS cc_start: 0.9110 (mmtm) cc_final: 0.8694 (mmtm) REVERT: C 13 TYR cc_start: 0.8627 (t80) cc_final: 0.8334 (t80) REVERT: D 166 GLU cc_start: 0.8723 (tp30) cc_final: 0.8358 (tp30) REVERT: E 6 LYS cc_start: 0.8831 (ptpp) cc_final: 0.8454 (ptpt) REVERT: F 1 MET cc_start: 0.7757 (ttp) cc_final: 0.7074 (ttp) REVERT: F 31 GLN cc_start: 0.7562 (tm-30) cc_final: 0.6841 (tp40) REVERT: F 50 LEU cc_start: 0.6023 (mt) cc_final: 0.5474 (mt) REVERT: F 54 ARG cc_start: 0.7895 (mmm160) cc_final: 0.7498 (mtm180) REVERT: F 59 TYR cc_start: 0.6391 (m-80) cc_final: 0.5889 (m-80) REVERT: F 62 GLN cc_start: 0.7013 (mp10) cc_final: 0.6706 (mp10) REVERT: F 65 SER cc_start: 0.7739 (m) cc_final: 0.7452 (m) REVERT: G 72 ARG cc_start: 0.8517 (ttp80) cc_final: 0.8227 (tmm-80) REVERT: H 49 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8226 (tt0) REVERT: H 63 LYS cc_start: 0.7735 (ptmt) cc_final: 0.7102 (ptmt) REVERT: H 64 GLU cc_start: 0.7924 (mp0) cc_final: 0.7611 (mp0) REVERT: I 18 GLU cc_start: 0.8401 (tp30) cc_final: 0.8144 (mm-30) REVERT: I 21 ASP cc_start: 0.8619 (m-30) cc_final: 0.8353 (m-30) REVERT: I 40 GLN cc_start: 0.8686 (pm20) cc_final: 0.8216 (pm20) REVERT: I 41 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.8140 (pm20) REVERT: I 60 ASN cc_start: 0.8534 (m110) cc_final: 0.8231 (m-40) REVERT: J 52 ASP cc_start: 0.7449 (t70) cc_final: 0.7115 (m-30) REVERT: K 1 MET cc_start: 0.8080 (tpt) cc_final: 0.7663 (tpt) REVERT: L 6 LYS cc_start: 0.8964 (tptp) cc_final: 0.8556 (tppt) outliers start: 36 outliers final: 18 residues processed: 315 average time/residue: 0.2485 time to fit residues: 110.8245 Evaluate side-chains 299 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 279 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 MET 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 193 LEU Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 14 THR 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 9 THR Chi-restraints excluded: chain J residue 71 LEU 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 71 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 121 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 173 GLN ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN F 41 GLN ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 60 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.101311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.078092 restraints weight = 23522.764| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 3.01 r_work: 0.3006 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3011 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3011 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11082 Z= 0.125 Angle : 0.608 8.061 14991 Z= 0.303 Chirality : 0.043 0.176 1765 Planarity : 0.004 0.052 1932 Dihedral : 4.904 56.474 1468 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.20 % Allowed : 17.39 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.23), residues: 1345 helix: 0.18 (0.21), residues: 653 sheet: -1.39 (0.36), residues: 197 loop : 0.27 (0.30), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 177 HIS 0.007 0.002 HIS A 111 PHE 0.016 0.001 PHE H 4 TYR 0.025 0.001 TYR C 114 ARG 0.003 0.000 ARG A 170 Details of bonding type rmsd hydrogen bonds : bond 0.03101 ( 509) hydrogen bonds : angle 5.04974 ( 1470) covalent geometry : bond 0.00296 (11082) covalent geometry : angle 0.60771 (14991) *********************** 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 344 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 305 time to evaluate : 1.347 Fit side-chains revert: symmetry clash REVERT: A 47 GLN cc_start: 0.7968 (mm-40) cc_final: 0.7599 (tp-100) REVERT: A 127 ASP cc_start: 0.8612 (t70) cc_final: 0.8315 (t70) REVERT: A 128 LYS cc_start: 0.9118 (mmtm) cc_final: 0.8636 (mmtm) REVERT: C 13 TYR cc_start: 0.8602 (t80) cc_final: 0.8320 (t80) REVERT: C 78 GLU cc_start: 0.8496 (tp30) cc_final: 0.8223 (tp30) REVERT: D 195 GLN cc_start: 0.8695 (tm-30) cc_final: 0.8117 (pp30) REVERT: E 6 LYS cc_start: 0.8893 (ptpp) cc_final: 0.8438 (ptpt) REVERT: F 1 MET cc_start: 0.7631 (ttp) cc_final: 0.7028 (ttp) REVERT: F 31 GLN cc_start: 0.7563 (tm-30) cc_final: 0.6898 (tp40) REVERT: F 50 LEU cc_start: 0.6168 (mt) cc_final: 0.5595 (mt) REVERT: F 54 ARG cc_start: 0.7823 (mmm160) cc_final: 0.7447 (mtp180) REVERT: F 59 TYR cc_start: 0.6436 (m-80) cc_final: 0.5880 (m-80) REVERT: F 62 GLN cc_start: 0.7062 (mp10) cc_final: 0.6702 (mp10) REVERT: F 65 SER cc_start: 0.7713 (m) cc_final: 0.7415 (m) REVERT: G 72 ARG cc_start: 0.8483 (ttp80) cc_final: 0.8190 (tmm-80) REVERT: H 43 LEU cc_start: 0.9030 (mt) cc_final: 0.8746 (mt) REVERT: H 49 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.8222 (tt0) REVERT: H 63 LYS cc_start: 0.7701 (ptmt) cc_final: 0.6826 (ptmt) REVERT: H 64 GLU cc_start: 0.7911 (mp0) cc_final: 0.7442 (mp0) REVERT: I 18 GLU cc_start: 0.8434 (tp30) cc_final: 0.8159 (mm-30) REVERT: I 21 ASP cc_start: 0.8618 (m-30) cc_final: 0.8347 (m-30) REVERT: I 40 GLN cc_start: 0.8599 (pm20) cc_final: 0.8106 (pm20) REVERT: I 60 ASN cc_start: 0.8479 (m110) cc_final: 0.8191 (m-40) REVERT: J 52 ASP cc_start: 0.7613 (t70) cc_final: 0.7341 (m-30) REVERT: K 1 MET cc_start: 0.8031 (tpt) cc_final: 0.7587 (tpt) REVERT: L 6 LYS cc_start: 0.8975 (tptp) cc_final: 0.8551 (tppt) REVERT: L 18 GLU cc_start: 0.8817 (tm-30) cc_final: 0.8398 (tm-30) REVERT: L 31 GLN cc_start: 0.8948 (pp30) cc_final: 0.8503 (pp30) outliers start: 39 outliers final: 20 residues processed: 323 average time/residue: 0.2418 time to fit residues: 109.7459 Evaluate side-chains 299 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 278 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain B residue 98 GLU 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 193 LEU Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 138 CYS Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 49 GLN Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 14 THR 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 14 THR Chi-restraints excluded: chain K residue 26 VAL 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 114 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 105 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 77 optimal weight: 9.9990 chunk 106 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 87 optimal weight: 0.4980 chunk 14 optimal weight: 0.2980 chunk 63 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 25 ASN ** 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 = 0.3546 r_free = 0.3546 target = 0.100597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.077439 restraints weight = 23488.379| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.99 r_work: 0.2985 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2989 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2989 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11082 Z= 0.169 Angle : 0.614 7.809 14991 Z= 0.308 Chirality : 0.044 0.173 1765 Planarity : 0.004 0.054 1932 Dihedral : 4.909 58.955 1468 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.61 % Allowed : 18.46 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.24), residues: 1345 helix: 0.22 (0.21), residues: 653 sheet: -1.33 (0.36), residues: 197 loop : 0.32 (0.30), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 177 HIS 0.007 0.002 HIS A 111 PHE 0.018 0.001 PHE H 4 TYR 0.027 0.001 TYR C 114 ARG 0.003 0.000 ARG I 54 Details of bonding type rmsd hydrogen bonds : bond 0.03186 ( 509) hydrogen bonds : angle 5.00857 ( 1470) covalent geometry : bond 0.00409 (11082) covalent geometry : angle 0.61396 (14991) *********************** 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 332 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 288 time to evaluate : 1.388 Fit side-chains revert: symmetry clash REVERT: A 128 LYS cc_start: 0.9179 (mmtm) cc_final: 0.8920 (mmtm) REVERT: A 195 GLN cc_start: 0.9052 (OUTLIER) cc_final: 0.8644 (tm-30) REVERT: C 13 TYR cc_start: 0.8661 (t80) cc_final: 0.8382 (t80) REVERT: C 78 GLU cc_start: 0.8469 (tp30) cc_final: 0.8172 (tp30) REVERT: D 195 GLN cc_start: 0.8712 (tm-30) cc_final: 0.8153 (pp30) REVERT: E 6 LYS cc_start: 0.8894 (ptpp) cc_final: 0.8429 (ptpt) REVERT: F 31 GLN cc_start: 0.7666 (tm-30) cc_final: 0.7039 (tp40) REVERT: F 50 LEU cc_start: 0.6215 (mt) cc_final: 0.5552 (mt) REVERT: F 54 ARG cc_start: 0.7815 (mmm160) cc_final: 0.7384 (mtm180) REVERT: F 59 TYR cc_start: 0.6481 (m-80) cc_final: 0.6039 (m-80) REVERT: F 62 GLN cc_start: 0.7106 (mp10) cc_final: 0.6852 (mp10) REVERT: F 65 SER cc_start: 0.7693 (m) cc_final: 0.7419 (m) REVERT: G 72 ARG cc_start: 0.8434 (ttp80) cc_final: 0.8136 (tmm-80) REVERT: H 43 LEU cc_start: 0.9067 (mt) cc_final: 0.8804 (mt) REVERT: H 63 LYS cc_start: 0.7787 (ptmt) cc_final: 0.6489 (pttt) REVERT: H 64 GLU cc_start: 0.7892 (mp0) cc_final: 0.6740 (mp0) REVERT: I 15 LEU cc_start: 0.7222 (mm) cc_final: 0.6892 (mm) REVERT: I 18 GLU cc_start: 0.8454 (tp30) cc_final: 0.8191 (mm-30) REVERT: I 21 ASP cc_start: 0.8610 (m-30) cc_final: 0.8355 (m-30) REVERT: I 54 ARG cc_start: 0.8866 (mtp85) cc_final: 0.8621 (mtp85) REVERT: I 60 ASN cc_start: 0.8408 (m110) cc_final: 0.8132 (m-40) REVERT: L 6 LYS cc_start: 0.8962 (tptp) cc_final: 0.8554 (tppt) REVERT: L 31 GLN cc_start: 0.8984 (pp30) cc_final: 0.8549 (pp30) outliers start: 44 outliers final: 35 residues processed: 310 average time/residue: 0.2725 time to fit residues: 118.3619 Evaluate side-chains 305 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 269 time to evaluate : 1.501 ------------------------------------------------------------------------------- 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 23 LYS 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 C residue 193 LEU Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 138 CYS Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain G residue 7 THR 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 58 ASP 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 43 LEU Chi-restraints excluded: chain K residue 57 SER Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 30 ILE 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 50 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 117 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 chunk 126 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 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 = 0.3539 r_free = 0.3539 target = 0.100240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.076884 restraints weight = 23705.676| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 3.01 r_work: 0.2980 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2986 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.95 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2986 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11082 Z= 0.169 Angle : 0.623 8.686 14991 Z= 0.310 Chirality : 0.044 0.189 1765 Planarity : 0.004 0.049 1932 Dihedral : 4.881 57.197 1468 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.36 % Allowed : 20.84 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.24), residues: 1345 helix: 0.28 (0.21), residues: 653 sheet: -1.32 (0.36), residues: 197 loop : 0.34 (0.30), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 177 HIS 0.007 0.002 HIS A 111 PHE 0.019 0.001 PHE H 4 TYR 0.029 0.001 TYR C 114 ARG 0.004 0.000 ARG A 170 Details of bonding type rmsd hydrogen bonds : bond 0.03091 ( 509) hydrogen bonds : angle 4.92785 ( 1470) covalent geometry : bond 0.00412 (11082) covalent geometry : angle 0.62298 (14991) *********************** 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 320 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 279 time to evaluate : 1.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.8605 (t70) cc_final: 0.8331 (t70) REVERT: A 128 LYS cc_start: 0.9136 (mmtm) cc_final: 0.8831 (mmtm) REVERT: A 195 GLN cc_start: 0.9062 (OUTLIER) cc_final: 0.8654 (tm-30) REVERT: C 13 TYR cc_start: 0.8616 (t80) cc_final: 0.8335 (t80) REVERT: C 78 GLU cc_start: 0.8484 (tp30) cc_final: 0.8169 (tp30) REVERT: D 195 GLN cc_start: 0.8741 (tm-30) cc_final: 0.8219 (pp30) REVERT: E 6 LYS cc_start: 0.8911 (ptpp) cc_final: 0.8454 (ptpt) REVERT: F 50 LEU cc_start: 0.6314 (mt) cc_final: 0.5692 (mt) REVERT: F 54 ARG cc_start: 0.7818 (mmm160) cc_final: 0.7330 (mtm180) REVERT: F 59 TYR cc_start: 0.6608 (m-80) cc_final: 0.6109 (m-80) REVERT: F 62 GLN cc_start: 0.7054 (mp10) cc_final: 0.6832 (mp10) REVERT: F 65 SER cc_start: 0.7796 (m) cc_final: 0.7543 (m) REVERT: G 72 ARG cc_start: 0.8455 (ttp80) cc_final: 0.8163 (tmm-80) REVERT: H 63 LYS cc_start: 0.7779 (ptmt) cc_final: 0.6457 (pttt) REVERT: H 64 GLU cc_start: 0.7911 (mp0) cc_final: 0.6753 (mp0) REVERT: I 18 GLU cc_start: 0.8485 (tp30) cc_final: 0.7990 (mm-30) REVERT: I 21 ASP cc_start: 0.8630 (m-30) cc_final: 0.8349 (m-30) REVERT: I 54 ARG cc_start: 0.8879 (mtp85) cc_final: 0.8615 (mtp85) REVERT: I 60 ASN cc_start: 0.8374 (m110) cc_final: 0.8145 (m-40) REVERT: K 1 MET cc_start: 0.7894 (tpt) cc_final: 0.7408 (tpt) REVERT: L 6 LYS cc_start: 0.8959 (tptp) cc_final: 0.8541 (tppt) REVERT: L 31 GLN cc_start: 0.8989 (pp30) cc_final: 0.8478 (pp30) outliers start: 41 outliers final: 32 residues processed: 300 average time/residue: 0.2714 time to fit residues: 113.0106 Evaluate side-chains 294 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 261 time to evaluate : 1.459 ------------------------------------------------------------------------------- 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 23 LYS Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 95 MET 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 24 MET Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 138 CYS Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain F residue 58 ASP 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 4 PHE Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 14 THR 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 14 THR 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 81 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 70 optimal weight: 0.0770 chunk 29 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 2 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 = 0.3545 r_free = 0.3545 target = 0.100603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.077091 restraints weight = 23988.040| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 3.09 r_work: 0.2970 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2975 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.95 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.95 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2975 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2916 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= 0.175 Angle : 0.634 8.757 14991 Z= 0.315 Chirality : 0.044 0.186 1765 Planarity : 0.004 0.050 1932 Dihedral : 4.845 52.691 1468 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.69 % Allowed : 20.67 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.24), residues: 1345 helix: 0.34 (0.21), residues: 653 sheet: -1.29 (0.36), residues: 197 loop : 0.33 (0.30), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 177 HIS 0.007 0.002 HIS A 111 PHE 0.023 0.002 PHE H 4 TYR 0.031 0.001 TYR C 114 ARG 0.008 0.000 ARG L 54 Details of bonding type rmsd hydrogen bonds : bond 0.03033 ( 509) hydrogen bonds : angle 4.91478 ( 1470) covalent geometry : bond 0.00426 (11082) covalent geometry : angle 0.63362 (14991) *********************** 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 318 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 273 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 GLU cc_start: 0.8713 (tp30) cc_final: 0.8399 (tp30) REVERT: A 195 GLN cc_start: 0.9068 (OUTLIER) cc_final: 0.8663 (tm-30) REVERT: C 13 TYR cc_start: 0.8614 (t80) cc_final: 0.8319 (t80) REVERT: C 78 GLU cc_start: 0.8475 (tp30) cc_final: 0.8104 (tp30) REVERT: D 195 GLN cc_start: 0.8765 (tm-30) cc_final: 0.8558 (tm-30) REVERT: E 6 LYS cc_start: 0.8904 (ptpp) cc_final: 0.8501 (ptpt) REVERT: F 50 LEU cc_start: 0.6311 (mt) cc_final: 0.5764 (mt) REVERT: F 54 ARG cc_start: 0.7866 (mmm160) cc_final: 0.7390 (mtp180) REVERT: F 59 TYR cc_start: 0.6652 (m-80) cc_final: 0.5781 (m-80) REVERT: F 62 GLN cc_start: 0.7054 (mp10) cc_final: 0.6832 (mp10) REVERT: F 65 SER cc_start: 0.7764 (m) cc_final: 0.7491 (m) REVERT: G 72 ARG cc_start: 0.8424 (ttp80) cc_final: 0.8093 (tmm-80) REVERT: H 63 LYS cc_start: 0.7719 (ptmt) cc_final: 0.6703 (ptmt) REVERT: H 64 GLU cc_start: 0.7937 (mp0) cc_final: 0.7443 (mp0) REVERT: I 15 LEU cc_start: 0.7093 (mm) cc_final: 0.6752 (mm) REVERT: I 18 GLU cc_start: 0.8498 (tp30) cc_final: 0.8022 (mm-30) REVERT: I 21 ASP cc_start: 0.8631 (m-30) cc_final: 0.8362 (m-30) REVERT: I 54 ARG cc_start: 0.8866 (mtp85) cc_final: 0.8599 (mtp85) REVERT: I 60 ASN cc_start: 0.8394 (m110) cc_final: 0.8157 (m-40) REVERT: K 1 MET cc_start: 0.7888 (tpt) cc_final: 0.7315 (tpt) REVERT: L 6 LYS cc_start: 0.8956 (tptp) cc_final: 0.8550 (tppt) REVERT: L 31 GLN cc_start: 0.9011 (pp30) cc_final: 0.8489 (pp30) outliers start: 45 outliers final: 35 residues processed: 299 average time/residue: 0.2436 time to fit residues: 101.9314 Evaluate side-chains 301 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 265 time to evaluate : 1.266 ------------------------------------------------------------------------------- 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 23 LYS Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 95 MET 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 24 MET Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 138 CYS Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 44 ILE 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 60 ASN 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 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 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 121 optimal weight: 0.8980 chunk 78 optimal weight: 7.9990 chunk 102 optimal weight: 0.0270 chunk 91 optimal weight: 7.9990 chunk 96 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 76 optimal weight: 9.9990 chunk 47 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 overall best weight: 1.1240 ------------------------------------------------------------------------------- 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** I 2 GLN I 68 HIS K 60 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.101254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.077820 restraints weight = 23339.976| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.99 r_work: 0.3000 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3000 ------------------------------------------------------------------------------- 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 = 0.95 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3005 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11082 Z= 0.134 Angle : 0.629 8.966 14991 Z= 0.313 Chirality : 0.043 0.220 1765 Planarity : 0.004 0.050 1932 Dihedral : 4.595 17.732 1467 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.71 % Allowed : 21.90 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.24), residues: 1345 helix: 0.46 (0.21), residues: 647 sheet: -1.07 (0.38), residues: 188 loop : 0.29 (0.29), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 177 HIS 0.006 0.002 HIS A 111 PHE 0.014 0.001 PHE A 107 TYR 0.031 0.001 TYR C 114 ARG 0.005 0.000 ARG L 54 Details of bonding type rmsd hydrogen bonds : bond 0.02873 ( 509) hydrogen bonds : angle 4.85790 ( 1470) covalent geometry : bond 0.00325 (11082) covalent geometry : angle 0.62944 (14991) *********************** 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 309 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 276 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 GLN cc_start: 0.9043 (OUTLIER) cc_final: 0.8643 (tm-30) REVERT: C 78 GLU cc_start: 0.8494 (tp30) cc_final: 0.8123 (tp30) REVERT: C 112 ASP cc_start: 0.8686 (m-30) cc_final: 0.8473 (m-30) REVERT: C 169 LYS cc_start: 0.8851 (mttm) cc_final: 0.8633 (mtmt) REVERT: D 195 GLN cc_start: 0.8750 (tm-30) cc_final: 0.8201 (pp30) REVERT: E 6 LYS cc_start: 0.8893 (ptpp) cc_final: 0.8499 (ptpt) REVERT: F 50 LEU cc_start: 0.6289 (mt) cc_final: 0.5745 (mt) REVERT: F 54 ARG cc_start: 0.7808 (mmm160) cc_final: 0.7341 (mtp180) REVERT: F 59 TYR cc_start: 0.6611 (m-80) cc_final: 0.5798 (m-80) REVERT: F 65 SER cc_start: 0.7718 (m) cc_final: 0.7425 (m) REVERT: G 72 ARG cc_start: 0.8395 (ttp80) cc_final: 0.8093 (tmm-80) REVERT: H 63 LYS cc_start: 0.7658 (ptmt) cc_final: 0.6327 (ptmt) REVERT: H 64 GLU cc_start: 0.7907 (mp0) cc_final: 0.6936 (mp0) REVERT: I 15 LEU cc_start: 0.7041 (mm) cc_final: 0.6648 (mm) REVERT: I 18 GLU cc_start: 0.8487 (tp30) cc_final: 0.7988 (mm-30) REVERT: I 21 ASP cc_start: 0.8617 (m-30) cc_final: 0.8300 (m-30) REVERT: I 54 ARG cc_start: 0.8783 (mtp85) cc_final: 0.8507 (mtp85) REVERT: I 60 ASN cc_start: 0.8344 (m110) cc_final: 0.8130 (m-40) REVERT: J 29 LYS cc_start: 0.8570 (ttmt) cc_final: 0.8361 (tptp) REVERT: K 1 MET cc_start: 0.7954 (tpt) cc_final: 0.7412 (tpt) REVERT: L 6 LYS cc_start: 0.8957 (tptp) cc_final: 0.8566 (tppt) REVERT: L 31 GLN cc_start: 0.8995 (pp30) cc_final: 0.8480 (pp30) outliers start: 33 outliers final: 27 residues processed: 298 average time/residue: 0.2744 time to fit residues: 115.6706 Evaluate side-chains 291 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 263 time to evaluate : 1.497 ------------------------------------------------------------------------------- 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 95 MET 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 24 MET 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 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 9 THR Chi-restraints excluded: chain K residue 14 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 101 optimal weight: 0.8980 chunk 88 optimal weight: 9.9990 chunk 121 optimal weight: 0.0060 chunk 115 optimal weight: 7.9990 chunk 116 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 overall best weight: 1.1802 ------------------------------------------------------------------------------- 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** ** 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 = 0.3561 r_free = 0.3561 target = 0.101587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.078099 restraints weight = 23793.412| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 3.05 r_work: 0.3004 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3008 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3008 r_free = 0.3008 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 = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.95 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3009 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3184 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= 0.137 Angle : 0.638 10.648 14991 Z= 0.317 Chirality : 0.044 0.175 1765 Planarity : 0.004 0.049 1932 Dihedral : 4.530 17.386 1467 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.38 % Allowed : 22.31 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.24), residues: 1345 helix: 0.51 (0.21), residues: 650 sheet: -1.22 (0.36), residues: 198 loop : 0.39 (0.30), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 177 HIS 0.006 0.002 HIS A 111 PHE 0.013 0.001 PHE A 107 TYR 0.031 0.002 TYR C 114 ARG 0.005 0.000 ARG L 54 Details of bonding type rmsd hydrogen bonds : bond 0.02851 ( 509) hydrogen bonds : angle 4.83892 ( 1470) covalent geometry : bond 0.00337 (11082) covalent geometry : angle 0.63816 (14991) *********************** 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 308 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 279 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 GLU cc_start: 0.8767 (tm-30) cc_final: 0.8057 (tm-30) REVERT: A 195 GLN cc_start: 0.9017 (OUTLIER) cc_final: 0.8624 (tm-30) REVERT: B 121 LEU cc_start: 0.9202 (mt) cc_final: 0.8953 (mt) REVERT: B 170 ARG cc_start: 0.8966 (mmt90) cc_final: 0.8714 (mmt90) REVERT: C 78 GLU cc_start: 0.8501 (tp30) cc_final: 0.8118 (tp30) REVERT: C 112 ASP cc_start: 0.8649 (m-30) cc_final: 0.8444 (m-30) REVERT: D 195 GLN cc_start: 0.8743 (tm-30) cc_final: 0.8195 (pp30) REVERT: E 6 LYS cc_start: 0.8851 (ptpp) cc_final: 0.8456 (ptpt) REVERT: E 54 ARG cc_start: 0.8037 (mmm160) cc_final: 0.7819 (mmm160) REVERT: F 31 GLN cc_start: 0.7677 (tm-30) cc_final: 0.7118 (tp40) REVERT: F 50 LEU cc_start: 0.6305 (mt) cc_final: 0.5700 (mt) REVERT: F 54 ARG cc_start: 0.7864 (mmm160) cc_final: 0.7381 (mtp180) REVERT: F 59 TYR cc_start: 0.6605 (m-80) cc_final: 0.5885 (m-80) REVERT: F 65 SER cc_start: 0.7649 (m) cc_final: 0.7423 (m) REVERT: G 72 ARG cc_start: 0.8405 (ttp80) cc_final: 0.8196 (tmm-80) REVERT: G 74 ARG cc_start: 0.6654 (mpt180) cc_final: 0.6373 (mpt180) REVERT: H 63 LYS cc_start: 0.7666 (ptmt) cc_final: 0.6317 (ptmt) REVERT: H 64 GLU cc_start: 0.7890 (mp0) cc_final: 0.6898 (mp0) REVERT: I 15 LEU cc_start: 0.7028 (mm) cc_final: 0.6614 (mm) REVERT: I 18 GLU cc_start: 0.8487 (tp30) cc_final: 0.7977 (mm-30) REVERT: I 21 ASP cc_start: 0.8598 (m-30) cc_final: 0.8278 (m-30) REVERT: I 54 ARG cc_start: 0.8798 (mtp85) cc_final: 0.8530 (mtp85) REVERT: K 1 MET cc_start: 0.7965 (tpt) cc_final: 0.7485 (tpt) REVERT: L 6 LYS cc_start: 0.8938 (tptp) cc_final: 0.8575 (tppt) REVERT: L 31 GLN cc_start: 0.8980 (pp30) cc_final: 0.8459 (pp30) outliers start: 29 outliers final: 27 residues processed: 299 average time/residue: 0.2386 time to fit residues: 99.2676 Evaluate side-chains 287 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 259 time to evaluate : 1.275 ------------------------------------------------------------------------------- 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 95 MET 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 24 MET 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 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 9 THR 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 65 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 92 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 96 optimal weight: 8.9990 chunk 124 optimal weight: 0.0070 chunk 77 optimal weight: 5.9990 chunk 72 optimal weight: 8.9990 chunk 46 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- 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 ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 68 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.102881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.079226 restraints weight = 23581.649| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 3.11 r_work: 0.3023 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3028 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3028 r_free = 0.3028 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 = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3028 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 11082 Z= 0.122 Angle : 0.649 9.359 14991 Z= 0.321 Chirality : 0.043 0.176 1765 Planarity : 0.004 0.049 1932 Dihedral : 4.486 18.344 1467 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.97 % Allowed : 23.30 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.24), residues: 1345 helix: 0.68 (0.21), residues: 647 sheet: -1.06 (0.37), residues: 192 loop : 0.37 (0.30), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 71 HIS 0.006 0.001 HIS B 111 PHE 0.024 0.001 PHE A 107 TYR 0.031 0.002 TYR C 13 ARG 0.005 0.000 ARG L 54 Details of bonding type rmsd hydrogen bonds : bond 0.02742 ( 509) hydrogen bonds : angle 4.78521 ( 1470) covalent geometry : bond 0.00293 (11082) covalent geometry : angle 0.64939 (14991) ********************** 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 307 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 283 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 LYS cc_start: 0.8856 (mmtp) cc_final: 0.8542 (mmtm) REVERT: A 195 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.8617 (tm-30) REVERT: B 170 ARG cc_start: 0.8946 (mmt90) cc_final: 0.8695 (mmt90) REVERT: C 78 GLU cc_start: 0.8447 (tp30) cc_final: 0.8092 (tp30) REVERT: C 112 ASP cc_start: 0.8648 (m-30) cc_final: 0.8437 (m-30) REVERT: C 169 LYS cc_start: 0.8836 (mttm) cc_final: 0.8610 (mtmt) REVERT: D 195 GLN cc_start: 0.8734 (tm-30) cc_final: 0.8179 (pp30) REVERT: E 6 LYS cc_start: 0.8849 (ptpp) cc_final: 0.8491 (ptpt) REVERT: E 54 ARG cc_start: 0.8017 (mmm160) cc_final: 0.7729 (mmm160) REVERT: F 31 GLN cc_start: 0.7659 (tm-30) cc_final: 0.7088 (tp40) REVERT: F 50 LEU cc_start: 0.6268 (mt) cc_final: 0.5572 (mt) REVERT: F 54 ARG cc_start: 0.7887 (mmm160) cc_final: 0.7432 (mtp180) REVERT: F 59 TYR cc_start: 0.6634 (m-80) cc_final: 0.6090 (m-80) REVERT: F 65 SER cc_start: 0.7629 (m) cc_final: 0.7425 (m) REVERT: G 72 ARG cc_start: 0.8357 (ttp80) cc_final: 0.8145 (tmm-80) REVERT: G 74 ARG cc_start: 0.6648 (mpt180) cc_final: 0.6347 (mpt180) REVERT: H 63 LYS cc_start: 0.7608 (ptmt) cc_final: 0.6239 (ptmt) REVERT: H 64 GLU cc_start: 0.7808 (mp0) cc_final: 0.6804 (mp0) REVERT: I 15 LEU cc_start: 0.7101 (mm) cc_final: 0.6727 (mm) REVERT: I 18 GLU cc_start: 0.8503 (tp30) cc_final: 0.7995 (mm-30) REVERT: I 21 ASP cc_start: 0.8592 (m-30) cc_final: 0.8293 (m-30) REVERT: I 54 ARG cc_start: 0.8725 (mtp85) cc_final: 0.8466 (mtp85) REVERT: L 6 LYS cc_start: 0.8920 (tptp) cc_final: 0.8551 (tppt) REVERT: L 31 GLN cc_start: 0.8972 (pp30) cc_final: 0.8467 (pp30) outliers start: 24 outliers final: 21 residues processed: 301 average time/residue: 0.2717 time to fit residues: 113.7729 Evaluate side-chains 292 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 270 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET 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 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 9 THR Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain L residue 17 VAL 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 69 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 99 optimal weight: 8.9990 chunk 2 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 76 optimal weight: 10.0000 chunk 10 optimal weight: 0.0870 chunk 71 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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** ** H 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.104091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.080430 restraints weight = 23545.843| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 3.14 r_work: 0.3033 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3037 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3037 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11082 Z= 0.122 Angle : 0.648 9.024 14991 Z= 0.321 Chirality : 0.043 0.169 1765 Planarity : 0.004 0.047 1932 Dihedral : 4.466 20.428 1467 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.13 % Allowed : 23.71 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.24), residues: 1345 helix: 0.73 (0.21), residues: 647 sheet: -0.93 (0.38), residues: 187 loop : 0.32 (0.29), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 177 HIS 0.006 0.001 HIS A 111 PHE 0.017 0.001 PHE B 107 TYR 0.029 0.002 TYR C 114 ARG 0.005 0.000 ARG L 54 Details of bonding type rmsd hydrogen bonds : bond 0.02703 ( 509) hydrogen bonds : angle 4.73446 ( 1470) covalent geometry : bond 0.00293 (11082) covalent geometry : angle 0.64832 (14991) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5612.56 seconds wall clock time: 101 minutes 10.52 seconds (6070.52 seconds total)