Starting phenix.real_space_refine on Thu Aug 6 07:14:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wo4_37678/08_2026/8wo4_37678.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wo4_37678/08_2026/8wo4_37678.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wo4_37678/08_2026/8wo4_37678.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wo4_37678/08_2026/8wo4_37678.map" model { file = "/net/cci-nas-00/data/ceres_data/8wo4_37678/08_2026/8wo4_37678.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wo4_37678/08_2026/8wo4_37678.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.050 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 74 5.16 5 C 8888 2.51 5 N 2456 2.21 5 O 2770 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14188 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1652 Classifications: {'peptide': 215} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 203} Chain: "B" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1689 Classifications: {'peptide': 228} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 216} Chain: "C" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1652 Classifications: {'peptide': 215} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 203} Chain breaks: 1 Chain: "D" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1689 Classifications: {'peptide': 228} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 216} Chain: "E" Number of atoms: 2817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2817 Classifications: {'peptide': 352} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 332} Chain: "F" Number of atoms: 2817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2817 Classifications: {'peptide': 352} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 332} Chain: "G" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 922 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "H" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 922 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.17, per 1000 atoms: 0.15 Number of scatterers: 14188 At special positions: 0 Unit cell: (89.08, 150.28, 132.6, 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 74 16.00 O 2770 8.00 N 2456 7.00 C 8888 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=22, symmetry=0 Simple disulfide: pdb=" SG CYS A 24 " - pdb=" SG CYS A 89 " distance=2.03 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 195 " distance=2.03 Simple disulfide: pdb=" SG CYS A 215 " - pdb=" SG CYS B 223 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 147 " - pdb=" SG CYS B 203 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 89 " distance=2.04 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 195 " distance=2.03 Simple disulfide: pdb=" SG CYS C 215 " - pdb=" SG CYS D 223 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 203 " distance=2.03 Simple disulfide: pdb=" SG CYS E 4 " - pdb=" SG CYS F 4 " distance=2.05 Simple disulfide: pdb=" SG CYS E 55 " - pdb=" SG CYS E 143 " distance=2.03 Simple disulfide: pdb=" SG CYS E 179 " - pdb=" SG CYS E 223 " distance=2.03 Simple disulfide: pdb=" SG CYS E 280 " - pdb=" SG CYS E 329 " distance=2.03 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 312 " distance=2.03 Simple disulfide: pdb=" SG CYS E 313 " - pdb=" SG CYS E 316 " distance=2.04 Simple disulfide: pdb=" SG CYS F 4 " - pdb=" SG CYS F 15 " distance=2.04 Simple disulfide: pdb=" SG CYS F 55 " - pdb=" SG CYS F 143 " distance=2.03 Simple disulfide: pdb=" SG CYS F 179 " - pdb=" SG CYS F 223 " distance=2.03 Simple disulfide: pdb=" SG CYS F 280 " - pdb=" SG CYS F 329 " distance=2.03 Simple disulfide: pdb=" SG CYS F 291 " - pdb=" SG CYS F 312 " distance=2.03 Simple disulfide: pdb=" SG CYS F 313 " - pdb=" SG CYS F 316 " distance=2.03 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 Links applied NAG-ASN " NAG E 401 " - " ASN E 207 " " NAG F 401 " - " ASN F 207 " Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 397.5 milliseconds 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3352 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 35 sheets defined 12.8% alpha, 36.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 80 through 84 removed outlier: 4.190A pdb=" N PHE A 84 " --> pdb=" O PRO A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 128 removed outlier: 3.714A pdb=" N SER A 128 " --> pdb=" O GLU A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 189 Processing helix chain 'B' and resid 62 through 65 Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'B' and resid 134 through 136 No H-bonds generated for 'chain 'B' and resid 134 through 136' Processing helix chain 'B' and resid 163 through 165 No H-bonds generated for 'chain 'B' and resid 163 through 165' Processing helix chain 'B' and resid 194 through 196 No H-bonds generated for 'chain 'B' and resid 194 through 196' Processing helix chain 'B' and resid 224 through 228 removed outlier: 3.882A pdb=" N HIS B 227 " --> pdb=" O ASP B 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 84 removed outlier: 4.033A pdb=" N PHE C 84 " --> pdb=" O PRO C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 128 removed outlier: 3.623A pdb=" N SER C 128 " --> pdb=" O GLU C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 190 removed outlier: 3.587A pdb=" N LYS C 189 " --> pdb=" O ALA C 185 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N HIS C 190 " --> pdb=" O ASP C 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 65 Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.569A pdb=" N ASP D 90 " --> pdb=" O ARG D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 136 No H-bonds generated for 'chain 'D' and resid 134 through 136' Processing helix chain 'D' and resid 163 through 165 No H-bonds generated for 'chain 'D' and resid 163 through 165' Processing helix chain 'D' and resid 194 through 196 No H-bonds generated for 'chain 'D' and resid 194 through 196' Processing helix chain 'D' and resid 224 through 228 removed outlier: 4.029A pdb=" N HIS D 227 " --> pdb=" O ASP D 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 28 Processing helix chain 'E' and resid 38 through 53 removed outlier: 3.775A pdb=" N ALA E 44 " --> pdb=" O ARG E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 80 removed outlier: 5.995A pdb=" N GLY E 73 " --> pdb=" O LYS E 69 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N GLU E 74 " --> pdb=" O SER E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 118 Processing helix chain 'E' and resid 139 through 143 Processing helix chain 'E' and resid 144 through 146 No H-bonds generated for 'chain 'E' and resid 144 through 146' Processing helix chain 'E' and resid 180 through 183 removed outlier: 4.056A pdb=" N VAL E 183 " --> pdb=" O ASP E 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 180 through 183' Processing helix chain 'E' and resid 244 through 248 Processing helix chain 'E' and resid 341 through 345 Processing helix chain 'F' and resid 38 through 52 removed outlier: 3.635A pdb=" N GLU F 52 " --> pdb=" O GLN F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 82 removed outlier: 3.575A pdb=" N ASN F 65 " --> pdb=" O SER F 61 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N GLY F 73 " --> pdb=" O LYS F 69 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N GLU F 74 " --> pdb=" O SER F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 146 No H-bonds generated for 'chain 'F' and resid 144 through 146' Processing helix chain 'F' and resid 180 through 183 removed outlier: 3.972A pdb=" N VAL F 183 " --> pdb=" O ASP F 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 180 through 183' Processing helix chain 'F' and resid 237 through 241 removed outlier: 3.517A pdb=" N LEU F 241 " --> pdb=" O GLU F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 248 removed outlier: 3.504A pdb=" N ALA F 248 " --> pdb=" O LYS F 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 256 Processing helix chain 'F' and resid 341 through 345 removed outlier: 3.549A pdb=" N ASN F 344 " --> pdb=" O PRO F 341 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.575A pdb=" N ARG G 31 " --> pdb=" O THR G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 8 removed outlier: 3.694A pdb=" N VAL A 20 " --> pdb=" O ILE A 76 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASP A 71 " --> pdb=" O SER A 68 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER A 68 " --> pdb=" O ASP A 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 14 removed outlier: 6.181A pdb=" N LEU A 12 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU A 34 " --> pdb=" O TYR A 50 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N TYR A 50 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TRP A 36 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 115 through 119 removed outlier: 5.715A pdb=" N TYR A 174 " --> pdb=" O ASN A 139 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 154 through 155 Processing sheet with id=AA5, first strand: chain 'B' and resid 4 through 8 removed outlier: 3.572A pdb=" N GLN B 4 " --> pdb=" O SER B 26 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER B 26 " --> pdb=" O GLN B 4 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR B 78 " --> pdb=" O ASP B 73 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 12 through 13 removed outlier: 3.522A pdb=" N ALA B 92 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N MET B 35 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL B 51 " --> pdb=" O MET B 35 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N TRP B 37 " --> pdb=" O VAL B 49 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 12 through 13 removed outlier: 3.522A pdb=" N ALA B 92 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE B 109 " --> pdb=" O ARG B 98 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 127 through 131 removed outlier: 6.312A pdb=" N TYR B 183 " --> pdb=" O ASP B 151 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 138 through 139 removed outlier: 6.312A pdb=" N TYR B 183 " --> pdb=" O ASP B 151 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 158 through 161 removed outlier: 4.265A pdb=" N TYR B 201 " --> pdb=" O VAL B 218 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 5 through 8 Processing sheet with id=AB3, first strand: chain 'C' and resid 11 through 13 removed outlier: 6.545A pdb=" N LEU C 34 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N TYR C 50 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 115 through 119 removed outlier: 5.935A pdb=" N TYR C 174 " --> pdb=" O ASN C 139 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 154 through 155 Processing sheet with id=AB6, first strand: chain 'D' and resid 5 through 8 Processing sheet with id=AB7, first strand: chain 'D' and resid 11 through 13 removed outlier: 6.222A pdb=" N GLY D 11 " --> pdb=" O THR D 117 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER D 36 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N MET D 35 " --> pdb=" O VAL D 51 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL D 51 " --> pdb=" O MET D 35 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TRP D 37 " --> pdb=" O VAL D 49 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 11 through 13 removed outlier: 6.222A pdb=" N GLY D 11 " --> pdb=" O THR D 117 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 127 through 131 removed outlier: 6.232A pdb=" N TYR D 183 " --> pdb=" O ASP D 151 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 138 through 139 removed outlier: 6.232A pdb=" N TYR D 183 " --> pdb=" O ASP D 151 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 158 through 161 removed outlier: 4.531A pdb=" N TYR D 201 " --> pdb=" O VAL D 218 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 3 through 6 removed outlier: 3.973A pdb=" N VAL F 2 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG F 14 " --> pdb=" O SER F 5 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 87 through 90 removed outlier: 6.467A pdb=" N THR E 87 " --> pdb=" O PHE E 133 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL E 135 " --> pdb=" O THR E 87 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N VAL E 89 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N GLY E 56 " --> pdb=" O ALA E 149 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 153 through 157 removed outlier: 6.982A pdb=" N TRP E 168 " --> pdb=" O GLU E 156 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 329 through 331 removed outlier: 6.559A pdb=" N GLU E 203 " --> pdb=" O LYS E 213 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ALA E 215 " --> pdb=" O TRP E 201 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TRP E 201 " --> pdb=" O ALA E 215 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU F 192 " --> pdb=" O LYS F 189 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N GLU F 205 " --> pdb=" O LEU F 212 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N LEU F 212 " --> pdb=" O GLU F 205 " (cutoff:3.500A) removed outlier: 9.411A pdb=" N LYS F 213 " --> pdb=" O PHE F 277 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N PHE F 277 " --> pdb=" O LYS F 213 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 284 through 285 removed outlier: 6.275A pdb=" N LYS E 284 " --> pdb=" O TRP E 311 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 56 through 57 removed outlier: 7.176A pdb=" N GLY F 56 " --> pdb=" O ALA F 149 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'F' and resid 87 through 91 removed outlier: 6.500A pdb=" N THR F 87 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N VAL F 135 " --> pdb=" O THR F 87 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N VAL F 89 " --> pdb=" O VAL F 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'F' and resid 284 through 287 Processing sheet with id=AD2, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.522A pdb=" N CYS G 22 " --> pdb=" O VAL G 78 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL G 78 " --> pdb=" O CYS G 22 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU G 18 " --> pdb=" O MET G 82 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.522A pdb=" N CYS G 22 " --> pdb=" O VAL G 78 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL G 78 " --> pdb=" O CYS G 22 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR G 77 " --> pdb=" O ASP G 72 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 57 through 59 removed outlier: 5.547A pdb=" N PHE G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ARG G 38 " --> pdb=" O PHE G 47 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA G 33 " --> pdb=" O ASP G 95 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N CYS G 92 " --> pdb=" O TRP G 103 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N TRP G 103 " --> pdb=" O CYS G 92 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ILE G 94 " --> pdb=" O ASP G 101 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP G 101 " --> pdb=" O ILE G 94 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 57 through 59 removed outlier: 5.547A pdb=" N PHE G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ARG G 38 " --> pdb=" O PHE G 47 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA G 33 " --> pdb=" O ASP G 95 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR G 107 " --> pdb=" O TYR G 90 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.669A pdb=" N GLN H 5 " --> pdb=" O ALA H 23 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 57 through 59 removed outlier: 3.534A pdb=" N PHE H 58 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N PHE H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ARG H 38 " --> pdb=" O PHE H 47 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ALA H 33 " --> pdb=" O ASP H 95 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N TYR H 102 " --> pdb=" O ILE H 94 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 57 through 59 removed outlier: 3.534A pdb=" N PHE H 58 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N PHE H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ARG H 38 " --> pdb=" O PHE H 47 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ALA H 33 " --> pdb=" O ASP H 95 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR H 107 " --> pdb=" O TYR H 90 " (cutoff:3.500A) 525 hydrogen bonds defined for protein. 1323 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.96 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.57: 14430 1.57 - 1.93: 100 1.93 - 2.28: 0 2.28 - 2.63: 0 2.63 - 2.98: 1 Bond restraints: 14531 Sorted by residual: bond pdb=" C ARG A 109 " pdb=" N THR A 110 " ideal model delta sigma weight residual 1.329 2.983 -1.655 1.44e-02 4.82e+03 1.32e+04 bond pdb=" N THR A 110 " pdb=" CA THR A 110 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.22e-02 6.72e+03 8.17e+00 bond pdb=" N THR C 110 " pdb=" CA THR C 110 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.21e+00 bond pdb=" N ASP E 1 " pdb=" CA ASP E 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.19e+00 bond pdb=" N SER B 1 " pdb=" CA SER B 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.96e+00 ... (remaining 14526 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.40: 19708 6.40 - 12.81: 3 12.81 - 19.21: 0 19.21 - 25.62: 1 25.62 - 32.02: 1 Bond angle restraints: 19713 Sorted by residual: angle pdb=" O ARG A 109 " pdb=" C ARG A 109 " pdb=" N THR A 110 " ideal model delta sigma weight residual 123.33 101.03 22.30 1.13e+00 7.83e-01 3.89e+02 angle pdb=" C ARG A 109 " pdb=" N THR A 110 " pdb=" CA THR A 110 " ideal model delta sigma weight residual 122.03 90.01 32.02 2.01e+00 2.48e-01 2.54e+02 angle pdb=" C ASP F 136 " pdb=" CA ASP F 136 " pdb=" CB ASP F 136 " ideal model delta sigma weight residual 117.23 111.52 5.71 1.36e+00 5.41e-01 1.76e+01 angle pdb=" C1 NAG F 401 " pdb=" O5 NAG F 401 " pdb=" C5 NAG F 401 " ideal model delta sigma weight residual 113.21 124.37 -11.16 3.00e+00 1.11e-01 1.38e+01 angle pdb=" CA CYS E 4 " pdb=" CB CYS E 4 " pdb=" SG CYS E 4 " ideal model delta sigma weight residual 114.40 120.84 -6.44 2.30e+00 1.89e-01 7.84e+00 ... (remaining 19708 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 8073 17.81 - 35.62: 465 35.62 - 53.44: 120 53.44 - 71.25: 35 71.25 - 89.06: 8 Dihedral angle restraints: 8701 sinusoidal: 3454 harmonic: 5247 Sorted by residual: dihedral pdb=" CB CYS E 4 " pdb=" SG CYS E 4 " pdb=" SG CYS F 4 " pdb=" CB CYS F 4 " ideal model delta sinusoidal sigma weight residual -86.00 -15.55 -70.45 1 1.00e+01 1.00e-02 6.39e+01 dihedral pdb=" CA LYS E 33 " pdb=" C LYS E 33 " pdb=" N TYR E 34 " pdb=" CA TYR E 34 " ideal model delta harmonic sigma weight residual -180.00 -154.02 -25.98 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA TRP E 28 " pdb=" C TRP E 28 " pdb=" N ARG E 29 " pdb=" CA ARG E 29 " ideal model delta harmonic sigma weight residual -180.00 -154.52 -25.48 0 5.00e+00 4.00e-02 2.60e+01 ... (remaining 8698 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1596 0.040 - 0.080: 356 0.080 - 0.121: 160 0.121 - 0.161: 23 0.161 - 0.201: 1 Chirality restraints: 2136 Sorted by residual: chirality pdb=" C1 NAG F 401 " pdb=" ND2 ASN F 207 " pdb=" C2 NAG F 401 " pdb=" O5 NAG F 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA VAL H 2 " pdb=" N VAL H 2 " pdb=" C VAL H 2 " pdb=" CB VAL H 2 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.81e-01 chirality pdb=" CA ILE C 22 " pdb=" N ILE C 22 " pdb=" C ILE C 22 " pdb=" CB ILE C 22 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.75e-01 ... (remaining 2133 not shown) Planarity restraints: 2537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 109 " -0.133 2.00e-02 2.50e+03 1.99e-01 3.95e+02 pdb=" C ARG A 109 " 0.337 2.00e-02 2.50e+03 pdb=" O ARG A 109 " -0.157 2.00e-02 2.50e+03 pdb=" N THR A 110 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU D 155 " 0.032 5.00e-02 4.00e+02 4.80e-02 3.69e+00 pdb=" N PRO D 156 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO D 156 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 156 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 155 " 0.031 5.00e-02 4.00e+02 4.66e-02 3.47e+00 pdb=" N PRO B 156 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 156 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 156 " 0.023 5.00e-02 4.00e+02 ... (remaining 2534 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.54: 96 2.54 - 3.13: 10829 3.13 - 3.72: 20068 3.72 - 4.31: 28770 4.31 - 4.90: 49852 Nonbonded interactions: 109615 Sorted by model distance: nonbonded pdb=" O GLY F 159 " pdb=" OG SER F 166 " model vdw 1.955 3.040 nonbonded pdb=" OD1 ASP E 234 " pdb=" OG1 THR F 233 " model vdw 1.974 3.040 nonbonded pdb=" NE2 GLN A 101 " pdb=" O GLY A 102 " model vdw 2.003 3.120 nonbonded pdb=" OD1 ASP B 224 " pdb=" OG1 THR B 226 " model vdw 2.228 3.040 nonbonded pdb=" OD1 ASP C 18 " pdb=" N ARG C 19 " model vdw 2.228 3.120 ... (remaining 109610 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } 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=1.00 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: 17.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.190 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6348 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 : 0.014 1.655 14555 Z= 0.961 Angle : 0.604 32.023 19763 Z= 0.342 Chirality : 0.042 0.201 2136 Planarity : 0.005 0.199 2535 Dihedral : 12.778 89.062 5283 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.96 % Allowed : 8.39 % Favored : 90.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.20), residues: 1810 helix: 0.49 (0.51), residues: 105 sheet: 0.58 (0.22), residues: 589 loop : -0.32 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 212 TYR 0.022 0.001 TYR H 91 PHE 0.009 0.001 PHE G 99 TRP 0.015 0.001 TRP D 99 HIS 0.003 0.001 HIS E 195 Details of bonding type rmsd/Z covalent geometry : bond 0.01397 / 0.96 (14531) covalent geometry : angle 0.59732 / 0.34 (19713) SS BOND : bond 0.00623 / 0.40 ( 22) SS BOND : angle 1.47973 / 1.02 ( 44) hydrogen bonds : bond 0.24879 / 16.39 ( 469) hydrogen bonds : angle 9.62659 / 6.69 ( 1323) link_NAG-ASN : bond 0.00311 / 0.16 ( 2) link_NAG-ASN : angle 3.55065 / 2.01 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 0.427 Fit side-chains REVERT: D 65 LYS cc_start: 0.6649 (ttpt) cc_final: 0.6342 (tptt) REVERT: F 138 ASP cc_start: 0.7366 (t0) cc_final: 0.6812 (t0) outliers start: 15 outliers final: 2 residues processed: 143 average time/residue: 0.5092 time to fit residues: 79.8988 Evaluate side-chains 103 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 101 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain F residue 4 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 0.0370 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.0370 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.0020 chunk 122 optimal weight: 0.0670 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.2282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 35 ASN A 56 GLN A 156 GLN A 159 ASN C 91 GLN C 211 ASN ** F 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4784 r_free = 0.4784 target = 0.243972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.200010 restraints weight = 17387.159| |-----------------------------------------------------------------------------| r_work (start): 0.4365 rms_B_bonded: 3.38 r_work: 0.4047 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.4047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6794 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14555 Z= 0.114 Angle : 0.592 9.207 19763 Z= 0.307 Chirality : 0.042 0.158 2136 Planarity : 0.004 0.051 2535 Dihedral : 4.850 57.499 2033 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.92 % Allowed : 9.48 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.20), residues: 1812 helix: 0.68 (0.52), residues: 110 sheet: 0.85 (0.22), residues: 606 loop : -0.15 (0.20), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 109 TYR 0.022 0.001 TYR H 91 PHE 0.023 0.001 PHE D 68 TRP 0.016 0.001 TRP H 36 HIS 0.005 0.001 HIS E 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (14531) covalent geometry : angle 0.58389 / 0.30 (19713) SS BOND : bond 0.00542 / 0.35 ( 22) SS BOND : angle 1.45893 / 0.94 ( 44) hydrogen bonds : bond 0.04032 / 2.64 ( 469) hydrogen bonds : angle 6.52251 / 4.50 ( 1323) link_NAG-ASN : bond 0.00323 / 0.16 ( 2) link_NAG-ASN : angle 4.51863 / 2.61 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 125 time to evaluate : 0.405 Fit side-chains REVERT: C 76 ILE cc_start: 0.6087 (OUTLIER) cc_final: 0.5372 (tp) REVERT: C 148 GLN cc_start: 0.6058 (OUTLIER) cc_final: 0.5855 (mm-40) REVERT: D 65 LYS cc_start: 0.6596 (ttpt) cc_final: 0.6079 (tptt) REVERT: F 314 ARG cc_start: 0.6600 (ttm-80) cc_final: 0.6042 (ttm-80) outliers start: 30 outliers final: 13 residues processed: 148 average time/residue: 0.4686 time to fit residues: 76.4640 Evaluate side-chains 125 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 148 GLN Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain F residue 1 ASP Chi-restraints excluded: chain F residue 4 CYS Chi-restraints excluded: chain F residue 67 MET Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 313 CYS Chi-restraints excluded: chain F residue 316 CYS Chi-restraints excluded: chain F residue 329 CYS Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain H residue 36 TRP Chi-restraints excluded: chain H residue 89 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 7 optimal weight: 4.9990 chunk 165 optimal weight: 20.0000 chunk 24 optimal weight: 3.9990 chunk 160 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 81 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 26 optimal weight: 0.0870 chunk 149 optimal weight: 0.8980 chunk 42 optimal weight: 10.0000 overall best weight: 1.3962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4747 r_free = 0.4747 target = 0.238744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.191794 restraints weight = 17355.034| |-----------------------------------------------------------------------------| r_work (start): 0.4271 rms_B_bonded: 4.03 r_work: 0.3971 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 14555 Z= 0.153 Angle : 0.636 10.353 19763 Z= 0.329 Chirality : 0.044 0.181 2136 Planarity : 0.005 0.049 2535 Dihedral : 5.087 58.302 2032 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.33 % Allowed : 10.50 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.20), residues: 1812 helix: 0.04 (0.49), residues: 116 sheet: 0.71 (0.22), residues: 596 loop : -0.32 (0.19), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 67 TYR 0.019 0.002 TYR H 91 PHE 0.024 0.002 PHE D 68 TRP 0.031 0.002 TRP D 99 HIS 0.006 0.001 HIS E 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (14531) covalent geometry : angle 0.62618 / 0.33 (19713) SS BOND : bond 0.00930 / 0.61 ( 22) SS BOND : angle 1.85626 / 1.22 ( 44) hydrogen bonds : bond 0.04313 / 2.77 ( 469) hydrogen bonds : angle 6.01489 / 4.14 ( 1323) link_NAG-ASN : bond 0.00351 / 0.17 ( 2) link_NAG-ASN : angle 4.37658 / 2.54 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 118 time to evaluate : 0.376 Fit side-chains REVERT: C 76 ILE cc_start: 0.6132 (OUTLIER) cc_final: 0.5301 (tp) REVERT: C 78 SER cc_start: 0.6706 (p) cc_final: 0.6322 (t) REVERT: D 58 THR cc_start: 0.7997 (p) cc_final: 0.7692 (p) REVERT: D 65 LYS cc_start: 0.6893 (ttpt) cc_final: 0.6282 (tptt) REVERT: E 11 LYS cc_start: 0.6117 (tppt) cc_final: 0.4818 (mppt) REVERT: E 85 GLN cc_start: 0.7972 (OUTLIER) cc_final: 0.7664 (mm-40) REVERT: F 85 GLN cc_start: 0.6738 (tm-30) cc_final: 0.6020 (tp40) REVERT: F 133 PHE cc_start: 0.7586 (t80) cc_final: 0.7310 (t80) REVERT: F 138 ASP cc_start: 0.7552 (t0) cc_final: 0.6992 (t0) outliers start: 52 outliers final: 25 residues processed: 154 average time/residue: 0.4870 time to fit residues: 82.7626 Evaluate side-chains 140 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 80 GLN Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain E residue 85 GLN Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain F residue 1 ASP Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 313 CYS Chi-restraints excluded: chain F residue 329 CYS Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain H residue 36 TRP Chi-restraints excluded: chain H residue 89 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 89 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 20 optimal weight: 7.9990 chunk 176 optimal weight: 10.0000 chunk 163 optimal weight: 20.0000 chunk 3 optimal weight: 3.9990 chunk 151 optimal weight: 8.9990 chunk 133 optimal weight: 6.9990 chunk 81 optimal weight: 10.0000 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 138 ASN B 204 ASN C 167 GLN D 204 ASN ** F 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.234089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.171136 restraints weight = 17551.097| |-----------------------------------------------------------------------------| r_work (start): 0.4082 rms_B_bonded: 2.21 r_work: 0.3983 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3868 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 14555 Z= 0.223 Angle : 0.733 10.227 19763 Z= 0.382 Chirality : 0.047 0.185 2136 Planarity : 0.006 0.056 2535 Dihedral : 5.570 58.318 2031 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.71 % Allowed : 12.87 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.20), residues: 1812 helix: -0.35 (0.49), residues: 105 sheet: 0.53 (0.21), residues: 623 loop : -0.69 (0.19), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 212 TYR 0.026 0.002 TYR F 32 PHE 0.045 0.003 PHE D 68 TRP 0.051 0.003 TRP D 99 HIS 0.008 0.002 HIS E 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.22 (14531) covalent geometry : angle 0.72060 / 0.38 (19713) SS BOND : bond 0.01223 / 0.81 ( 22) SS BOND : angle 2.22805 / 1.55 ( 44) hydrogen bonds : bond 0.04875 / 3.11 ( 469) hydrogen bonds : angle 6.11274 / 4.21 ( 1323) link_NAG-ASN : bond 0.00525 / 0.25 ( 2) link_NAG-ASN : angle 5.00156 / 2.90 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 124 time to evaluate : 0.516 Fit side-chains REVERT: A 111 VAL cc_start: 0.5651 (m) cc_final: 0.5334 (t) REVERT: A 124 GLU cc_start: 0.4903 (tm-30) cc_final: 0.4472 (tm-30) REVERT: A 127 LYS cc_start: 0.6327 (OUTLIER) cc_final: 0.5804 (tttm) REVERT: C 76 ILE cc_start: 0.6384 (OUTLIER) cc_final: 0.5571 (tp) REVERT: C 78 SER cc_start: 0.6753 (p) cc_final: 0.6465 (t) REVERT: C 101 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7575 (mt0) REVERT: E 11 LYS cc_start: 0.6180 (tppt) cc_final: 0.5184 (mppt) REVERT: E 85 GLN cc_start: 0.8061 (OUTLIER) cc_final: 0.7815 (mm-40) REVERT: F 47 LYS cc_start: 0.6311 (OUTLIER) cc_final: 0.5834 (ttmm) outliers start: 58 outliers final: 30 residues processed: 167 average time/residue: 0.4905 time to fit residues: 90.5443 Evaluate side-chains 143 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 108 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 127 LYS Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 80 GLN Chi-restraints excluded: chain C residue 101 GLN Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain E residue 85 GLN Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain F residue 47 LYS Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 313 CYS Chi-restraints excluded: chain F residue 329 CYS Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain H residue 36 TRP Chi-restraints excluded: chain H residue 89 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 104 optimal weight: 2.9990 chunk 134 optimal weight: 5.9990 chunk 93 optimal weight: 0.6980 chunk 76 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 chunk 87 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 172 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 138 ASN ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 HIS ** F 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4715 r_free = 0.4715 target = 0.235566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.178833 restraints weight = 17564.216| |-----------------------------------------------------------------------------| r_work (start): 0.4141 rms_B_bonded: 3.03 r_work: 0.3966 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3850 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 14555 Z= 0.156 Angle : 0.632 8.897 19763 Z= 0.329 Chirality : 0.043 0.166 2136 Planarity : 0.005 0.056 2535 Dihedral : 5.251 58.037 2031 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.71 % Allowed : 14.21 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.20), residues: 1812 helix: 0.15 (0.52), residues: 103 sheet: 0.53 (0.21), residues: 630 loop : -0.69 (0.19), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 314 TYR 0.020 0.002 TYR F 32 PHE 0.035 0.002 PHE D 68 TRP 0.039 0.002 TRP D 99 HIS 0.007 0.001 HIS E 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 (14531) covalent geometry : angle 0.62254 / 0.33 (19713) SS BOND : bond 0.00861 / 0.57 ( 22) SS BOND : angle 1.81354 / 1.23 ( 44) hydrogen bonds : bond 0.04053 / 2.60 ( 469) hydrogen bonds : angle 5.79648 / 4.00 ( 1323) link_NAG-ASN : bond 0.00443 / 0.21 ( 2) link_NAG-ASN : angle 4.33153 / 2.52 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 119 time to evaluate : 0.551 Fit side-chains REVERT: A 19 ARG cc_start: 0.6563 (mmm-85) cc_final: 0.6316 (tpt-90) REVERT: A 111 VAL cc_start: 0.5675 (m) cc_final: 0.5352 (t) REVERT: C 76 ILE cc_start: 0.6378 (OUTLIER) cc_final: 0.5575 (tp) REVERT: C 78 SER cc_start: 0.6732 (p) cc_final: 0.6386 (t) REVERT: C 101 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7523 (mt0) REVERT: E 11 LYS cc_start: 0.6221 (tppt) cc_final: 0.5229 (mppt) REVERT: F 21 ILE cc_start: 0.7889 (OUTLIER) cc_final: 0.6964 (mp) REVERT: F 314 ARG cc_start: 0.6735 (ttm-80) cc_final: 0.6405 (ttm-80) REVERT: H 82 MET cc_start: 0.0702 (OUTLIER) cc_final: 0.0410 (mtt) outliers start: 58 outliers final: 34 residues processed: 160 average time/residue: 0.4946 time to fit residues: 87.4284 Evaluate side-chains 150 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 112 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 80 GLN Chi-restraints excluded: chain C residue 101 GLN Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain F residue 1 ASP Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 58 SER Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 313 CYS Chi-restraints excluded: chain F residue 329 CYS Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 44 GLU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain H residue 36 TRP Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 89 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 25 optimal weight: 0.7980 chunk 40 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 68.9924 > 50:) chunk 13 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 164 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 125 optimal weight: 4.9990 chunk 111 optimal weight: 0.5980 chunk 43 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 HIS ** 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 = 0.4679 r_free = 0.4679 target = 0.231863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.169772 restraints weight = 17474.277| |-----------------------------------------------------------------------------| r_work (start): 0.4064 rms_B_bonded: 2.18 r_work: 0.3966 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3851 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 14555 Z= 0.217 Angle : 0.742 10.151 19763 Z= 0.387 Chirality : 0.046 0.181 2136 Planarity : 0.006 0.061 2535 Dihedral : 5.699 58.287 2031 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 4.48 % Allowed : 14.66 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.20), residues: 1812 helix: -0.44 (0.50), residues: 105 sheet: 0.51 (0.21), residues: 607 loop : -1.06 (0.19), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 19 TYR 0.017 0.002 TYR B 95 PHE 0.049 0.003 PHE D 68 TRP 0.055 0.003 TRP D 99 HIS 0.008 0.002 HIS E 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.22 (14531) covalent geometry : angle 0.73014 / 0.38 (19713) SS BOND : bond 0.01164 / 0.80 ( 22) SS BOND : angle 2.23221 / 1.50 ( 44) hydrogen bonds : bond 0.04850 / 3.11 ( 469) hydrogen bonds : angle 6.05938 / 4.17 ( 1323) link_NAG-ASN : bond 0.00675 / 0.32 ( 2) link_NAG-ASN : angle 5.02474 / 2.91 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 116 time to evaluate : 0.480 Fit side-chains revert: symmetry clash REVERT: A 19 ARG cc_start: 0.6673 (mmm-85) cc_final: 0.6354 (tpt-90) REVERT: A 111 VAL cc_start: 0.6073 (m) cc_final: 0.5806 (t) REVERT: A 127 LYS cc_start: 0.6378 (OUTLIER) cc_final: 0.5957 (tttm) REVERT: C 76 ILE cc_start: 0.6398 (OUTLIER) cc_final: 0.5674 (tp) REVERT: C 78 SER cc_start: 0.6783 (p) cc_final: 0.6458 (t) REVERT: D 99 TRP cc_start: 0.7196 (t-100) cc_final: 0.6914 (t-100) REVERT: E 11 LYS cc_start: 0.6358 (tppt) cc_final: 0.5485 (mppt) REVERT: F 21 ILE cc_start: 0.7980 (OUTLIER) cc_final: 0.7047 (mp) REVERT: F 47 LYS cc_start: 0.6279 (OUTLIER) cc_final: 0.5728 (ttmm) outliers start: 70 outliers final: 42 residues processed: 169 average time/residue: 0.4712 time to fit residues: 88.5881 Evaluate side-chains 154 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 108 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 127 LYS Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 80 GLN Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain F residue 1 ASP Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 4 CYS Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 47 LYS Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 58 SER Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 120 LYS Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain F residue 313 CYS Chi-restraints excluded: chain F residue 329 CYS Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 44 GLU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain H residue 36 TRP Chi-restraints excluded: chain H residue 89 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 153 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 132 optimal weight: 7.9990 chunk 50 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 172 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4694 r_free = 0.4694 target = 0.233519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.171251 restraints weight = 17540.414| |-----------------------------------------------------------------------------| r_work (start): 0.4090 rms_B_bonded: 2.21 r_work: 0.3993 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3879 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 14555 Z= 0.166 Angle : 0.650 8.328 19763 Z= 0.339 Chirality : 0.044 0.157 2136 Planarity : 0.005 0.058 2535 Dihedral : 5.353 57.735 2031 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.52 % Allowed : 16.13 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.20), residues: 1812 helix: -0.01 (0.52), residues: 105 sheet: 0.42 (0.21), residues: 622 loop : -0.95 (0.19), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 314 TYR 0.024 0.002 TYR B 152 PHE 0.045 0.002 PHE D 68 TRP 0.043 0.002 TRP D 99 HIS 0.007 0.001 HIS E 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (14531) covalent geometry : angle 0.64029 / 0.34 (19713) SS BOND : bond 0.00932 / 0.60 ( 22) SS BOND : angle 1.85860 / 1.23 ( 44) hydrogen bonds : bond 0.04054 / 2.61 ( 469) hydrogen bonds : angle 5.79646 / 3.99 ( 1323) link_NAG-ASN : bond 0.00507 / 0.24 ( 2) link_NAG-ASN : angle 4.18387 / 2.42 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 115 time to evaluate : 0.416 Fit side-chains REVERT: A 19 ARG cc_start: 0.6525 (mmm-85) cc_final: 0.5906 (mpt-90) REVERT: A 111 VAL cc_start: 0.6113 (m) cc_final: 0.5872 (t) REVERT: C 76 ILE cc_start: 0.6409 (OUTLIER) cc_final: 0.5660 (tp) REVERT: E 11 LYS cc_start: 0.6515 (tppt) cc_final: 0.5673 (mppt) REVERT: F 21 ILE cc_start: 0.7976 (OUTLIER) cc_final: 0.7079 (mp) REVERT: F 47 LYS cc_start: 0.6171 (OUTLIER) cc_final: 0.5615 (ttmm) outliers start: 55 outliers final: 38 residues processed: 157 average time/residue: 0.4609 time to fit residues: 80.3862 Evaluate side-chains 154 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 113 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 80 GLN Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain F residue 1 ASP Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 47 LYS Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 58 SER Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain F residue 313 CYS Chi-restraints excluded: chain F residue 329 CYS Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 44 GLU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain H residue 36 TRP Chi-restraints excluded: chain H residue 89 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 25 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 34 optimal weight: 0.0670 chunk 106 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 165 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 138 ASN ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4709 r_free = 0.4709 target = 0.234837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.173174 restraints weight = 17306.582| |-----------------------------------------------------------------------------| r_work (start): 0.4081 rms_B_bonded: 2.18 r_work: 0.3986 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3874 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 14555 Z= 0.149 Angle : 0.622 7.804 19763 Z= 0.326 Chirality : 0.043 0.154 2136 Planarity : 0.005 0.056 2535 Dihedral : 5.173 57.731 2031 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.59 % Allowed : 16.45 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.20), residues: 1812 helix: 0.30 (0.53), residues: 103 sheet: 0.45 (0.21), residues: 632 loop : -0.84 (0.19), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 314 TYR 0.022 0.002 TYR B 152 PHE 0.040 0.002 PHE D 68 TRP 0.040 0.002 TRP D 99 HIS 0.006 0.001 HIS E 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (14531) covalent geometry : angle 0.61489 / 0.32 (19713) SS BOND : bond 0.00838 / 0.55 ( 22) SS BOND : angle 1.69475 / 1.12 ( 44) hydrogen bonds : bond 0.03834 / 2.47 ( 469) hydrogen bonds : angle 5.63821 / 3.88 ( 1323) link_NAG-ASN : bond 0.00363 / 0.17 ( 2) link_NAG-ASN : angle 3.53558 / 2.03 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 117 time to evaluate : 0.421 Fit side-chains REVERT: A 19 ARG cc_start: 0.6518 (mmm-85) cc_final: 0.5904 (mpt-90) REVERT: A 124 GLU cc_start: 0.5126 (tm-30) cc_final: 0.4892 (tm-30) REVERT: A 127 LYS cc_start: 0.6422 (OUTLIER) cc_final: 0.6086 (tttm) REVERT: B 34 TYR cc_start: 0.7729 (OUTLIER) cc_final: 0.7046 (m-10) REVERT: B 83 MET cc_start: 0.7550 (mtm) cc_final: 0.7275 (mmm) REVERT: C 5 MET cc_start: 0.5159 (mtp) cc_final: 0.4712 (mmm) REVERT: C 76 ILE cc_start: 0.6492 (OUTLIER) cc_final: 0.5739 (tp) REVERT: C 101 GLN cc_start: 0.8038 (OUTLIER) cc_final: 0.7529 (mt0) REVERT: E 11 LYS cc_start: 0.6617 (tppt) cc_final: 0.5743 (mppt) REVERT: E 81 GLU cc_start: 0.6227 (tm-30) cc_final: 0.5961 (tm-30) REVERT: F 8 PHE cc_start: 0.6192 (OUTLIER) cc_final: 0.5834 (m-80) REVERT: F 21 ILE cc_start: 0.7928 (OUTLIER) cc_final: 0.7020 (mp) REVERT: F 47 LYS cc_start: 0.6131 (OUTLIER) cc_final: 0.5571 (ttmm) REVERT: G 44 GLU cc_start: 0.3032 (OUTLIER) cc_final: 0.2821 (mp0) outliers start: 56 outliers final: 38 residues processed: 159 average time/residue: 0.4898 time to fit residues: 86.3735 Evaluate side-chains 156 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 110 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 127 LYS Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 34 TYR Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 80 GLN Chi-restraints excluded: chain C residue 101 GLN Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain F residue 1 ASP Chi-restraints excluded: chain F residue 8 PHE Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 47 LYS Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 58 SER Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain F residue 329 CYS Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 44 GLU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain H residue 36 TRP Chi-restraints excluded: chain H residue 89 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 112 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 171 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 61 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 82 optimal weight: 7.9990 chunk 122 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 138 ASN ** F 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.230846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.168529 restraints weight = 17362.334| |-----------------------------------------------------------------------------| r_work (start): 0.4041 rms_B_bonded: 2.20 r_work: 0.3948 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3836 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 14555 Z= 0.225 Angle : 0.752 10.246 19763 Z= 0.393 Chirality : 0.047 0.197 2136 Planarity : 0.006 0.062 2535 Dihedral : 5.697 58.456 2031 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 3.97 % Allowed : 16.39 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.20), residues: 1812 helix: -0.40 (0.50), residues: 103 sheet: 0.29 (0.21), residues: 634 loop : -1.08 (0.19), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 314 TYR 0.025 0.002 TYR B 152 PHE 0.064 0.003 PHE D 68 TRP 0.056 0.003 TRP D 99 HIS 0.008 0.002 HIS F 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.22 (14531) covalent geometry : angle 0.74193 / 0.39 (19713) SS BOND : bond 0.01136 / 0.76 ( 22) SS BOND : angle 2.18605 / 1.49 ( 44) hydrogen bonds : bond 0.04837 / 3.10 ( 469) hydrogen bonds : angle 6.03433 / 4.15 ( 1323) link_NAG-ASN : bond 0.00518 / 0.25 ( 2) link_NAG-ASN : angle 4.57349 / 2.56 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 115 time to evaluate : 0.517 Fit side-chains REVERT: A 19 ARG cc_start: 0.6608 (mmm-85) cc_final: 0.6004 (mpt-90) REVERT: A 124 GLU cc_start: 0.5157 (tm-30) cc_final: 0.4929 (tm-30) REVERT: A 127 LYS cc_start: 0.6383 (OUTLIER) cc_final: 0.5985 (tttm) REVERT: B 34 TYR cc_start: 0.7867 (OUTLIER) cc_final: 0.7219 (m-10) REVERT: B 83 MET cc_start: 0.7567 (mtm) cc_final: 0.7227 (mmm) REVERT: C 76 ILE cc_start: 0.6508 (OUTLIER) cc_final: 0.5731 (tp) REVERT: C 78 SER cc_start: 0.6853 (p) cc_final: 0.6527 (t) REVERT: C 101 GLN cc_start: 0.8144 (OUTLIER) cc_final: 0.7662 (mt0) REVERT: D 99 TRP cc_start: 0.7241 (t-100) cc_final: 0.6918 (t-100) REVERT: E 11 LYS cc_start: 0.6789 (tppt) cc_final: 0.5939 (mppt) REVERT: E 138 ASP cc_start: 0.6009 (OUTLIER) cc_final: 0.5562 (m-30) REVERT: E 168 TRP cc_start: 0.6482 (m100) cc_final: 0.6243 (m100) REVERT: F 8 PHE cc_start: 0.6319 (OUTLIER) cc_final: 0.5898 (m-80) REVERT: F 21 ILE cc_start: 0.7993 (OUTLIER) cc_final: 0.7069 (mp) REVERT: F 47 LYS cc_start: 0.6326 (OUTLIER) cc_final: 0.5767 (ttmm) REVERT: F 67 MET cc_start: 0.6753 (OUTLIER) cc_final: 0.6537 (ppp) REVERT: F 261 ARG cc_start: 0.6975 (mmm-85) cc_final: 0.6731 (mmm-85) REVERT: G 44 GLU cc_start: 0.3041 (OUTLIER) cc_final: 0.2829 (mp0) outliers start: 62 outliers final: 43 residues processed: 162 average time/residue: 0.4742 time to fit residues: 85.5918 Evaluate side-chains 162 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 109 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 127 LYS Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 34 TYR Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 80 GLN Chi-restraints excluded: chain C residue 101 GLN Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain F residue 1 ASP Chi-restraints excluded: chain F residue 8 PHE Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 47 LYS Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 58 SER Chi-restraints excluded: chain F residue 67 MET Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain F residue 329 CYS Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 44 GLU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain H residue 36 TRP Chi-restraints excluded: chain H residue 89 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 38 optimal weight: 10.0000 chunk 149 optimal weight: 0.0060 chunk 124 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 39 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 166 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 69 optimal weight: 0.9990 overall best weight: 1.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 GLN F 164 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.233507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.171747 restraints weight = 17365.262| |-----------------------------------------------------------------------------| r_work (start): 0.4075 rms_B_bonded: 2.20 r_work: 0.3982 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3870 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 14555 Z= 0.151 Angle : 0.635 8.970 19763 Z= 0.332 Chirality : 0.043 0.170 2136 Planarity : 0.005 0.059 2535 Dihedral : 5.301 57.524 2031 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.27 % Allowed : 17.61 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.20), residues: 1812 helix: 0.17 (0.52), residues: 103 sheet: 0.43 (0.21), residues: 636 loop : -0.95 (0.20), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 314 TYR 0.024 0.002 TYR B 152 PHE 0.039 0.002 PHE D 68 TRP 0.038 0.002 TRP D 99 HIS 0.007 0.001 HIS E 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (14531) covalent geometry : angle 0.62702 / 0.33 (19713) SS BOND : bond 0.00868 / 0.56 ( 22) SS BOND : angle 1.74853 / 1.13 ( 44) hydrogen bonds : bond 0.03870 / 2.51 ( 469) hydrogen bonds : angle 5.74554 / 3.95 ( 1323) link_NAG-ASN : bond 0.00303 / 0.15 ( 2) link_NAG-ASN : angle 3.47388 / 1.95 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 116 time to evaluate : 0.469 Fit side-chains revert: symmetry clash REVERT: A 13 SER cc_start: 0.7762 (OUTLIER) cc_final: 0.7350 (m) REVERT: A 19 ARG cc_start: 0.6463 (mmm-85) cc_final: 0.5856 (mpt-90) REVERT: A 124 GLU cc_start: 0.5232 (tm-30) cc_final: 0.4970 (tm-30) REVERT: A 127 LYS cc_start: 0.6411 (OUTLIER) cc_final: 0.6056 (tttm) REVERT: C 5 MET cc_start: 0.5232 (mtp) cc_final: 0.4737 (mmm) REVERT: C 76 ILE cc_start: 0.6515 (OUTLIER) cc_final: 0.5776 (tp) REVERT: C 101 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7534 (mt0) REVERT: E 11 LYS cc_start: 0.6809 (tppt) cc_final: 0.6010 (mppt) REVERT: E 81 GLU cc_start: 0.6314 (tm-30) cc_final: 0.6017 (tm-30) REVERT: E 168 TRP cc_start: 0.6366 (m100) cc_final: 0.6129 (m100) REVERT: F 21 ILE cc_start: 0.7978 (OUTLIER) cc_final: 0.7000 (mp) REVERT: F 47 LYS cc_start: 0.6119 (OUTLIER) cc_final: 0.5572 (ttmm) REVERT: G 44 GLU cc_start: 0.3116 (OUTLIER) cc_final: 0.2732 (mt-10) outliers start: 51 outliers final: 35 residues processed: 154 average time/residue: 0.4822 time to fit residues: 82.0912 Evaluate side-chains 150 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 108 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 127 LYS Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 80 GLN Chi-restraints excluded: chain C residue 101 GLN Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain F residue 1 ASP Chi-restraints excluded: chain F residue 8 PHE Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 47 LYS Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 58 SER Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain F residue 329 CYS Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 44 GLU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain H residue 36 TRP Chi-restraints excluded: chain H residue 89 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 62 optimal weight: 6.9990 chunk 67 optimal weight: 0.8980 chunk 106 optimal weight: 0.0770 chunk 163 optimal weight: 0.9980 chunk 33 optimal weight: 10.0000 chunk 176 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 158 optimal weight: 7.9990 chunk 128 optimal weight: 5.9990 chunk 127 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 overall best weight: 1.1340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.234534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.173132 restraints weight = 17268.833| |-----------------------------------------------------------------------------| r_work (start): 0.4071 rms_B_bonded: 2.18 r_work: 0.3978 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3866 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 14555 Z= 0.136 Angle : 0.615 9.128 19763 Z= 0.319 Chirality : 0.043 0.178 2136 Planarity : 0.005 0.055 2535 Dihedral : 5.100 57.406 2031 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.75 % Allowed : 18.44 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.20), residues: 1812 helix: 0.42 (0.52), residues: 104 sheet: 0.55 (0.21), residues: 640 loop : -0.88 (0.20), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 67 TYR 0.022 0.002 TYR B 152 PHE 0.024 0.002 PHE D 68 TRP 0.035 0.002 TRP D 99 HIS 0.006 0.001 HIS E 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (14531) covalent geometry : angle 0.60882 / 0.32 (19713) SS BOND : bond 0.00795 / 0.53 ( 22) SS BOND : angle 1.61846 / 1.03 ( 44) hydrogen bonds : bond 0.03624 / 2.35 ( 469) hydrogen bonds : angle 5.55486 / 3.83 ( 1323) link_NAG-ASN : bond 0.00110 / 0.06 ( 2) link_NAG-ASN : angle 2.95991 / 1.65 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5207.53 seconds wall clock time: 89 minutes 18.78 seconds (5358.78 seconds total)