Starting phenix.real_space_refine on Thu Mar 5 10:17:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sjo_54950/03_2026/9sjo_54950.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sjo_54950/03_2026/9sjo_54950.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9sjo_54950/03_2026/9sjo_54950.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sjo_54950/03_2026/9sjo_54950.map" model { file = "/net/cci-nas-00/data/ceres_data/9sjo_54950/03_2026/9sjo_54950.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sjo_54950/03_2026/9sjo_54950.cif" } resolution = 3.07 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= 0.002 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 59 5.49 5 S 104 5.16 5 C 13254 2.51 5 N 3514 2.21 5 O 4116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21047 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2422 Classifications: {'peptide': 302} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 285} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 1901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1901 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 7, 'TRANS': 233} Chain breaks: 1 Chain: "I" Number of atoms: 1141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1141 Classifications: {'peptide': 144} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 5, 'TRANS': 138} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 2381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2381 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 11, 'TRANS': 280} Chain breaks: 2 Chain: "E" Number of atoms: 2419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2419 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 12, 'TRANS': 284} Chain breaks: 2 Chain: "F" Number of atoms: 2425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2425 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 12, 'TRANS': 285} Chain breaks: 2 Chain: "C" Number of atoms: 2461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2461 Classifications: {'peptide': 302} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 288} Chain breaks: 1 Chain: "G" Number of atoms: 2355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2355 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 11, 'TRANS': 276} Chain breaks: 2 Chain: "H" Number of atoms: 2254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2254 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 264} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 1288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1288 Classifications: {'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 17, 'rna2p_pyr': 10, 'rna3p_pur': 20, 'rna3p_pyr': 13} Link IDs: {'rna2p': 27, 'rna3p': 32} Time building chain proxies: 4.92, per 1000 atoms: 0.23 Number of scatterers: 21047 At special positions: 0 Unit cell: (117.45, 149.35, 149.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 104 16.00 P 59 15.00 O 4116 8.00 N 3514 7.00 C 13254 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.05 Conformation dependent library (CDL) restraints added in 895.2 milliseconds 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4642 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 34 sheets defined 32.6% alpha, 8.3% beta 6 base pairs and 26 stacking pairs defined. Time for finding SS restraints: 2.88 Creating SS restraints... Processing helix chain 'A' and resid 36 through 40 removed outlier: 3.972A pdb=" N HIS A 39 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL A 40 " --> pdb=" O ALA A 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 36 through 40' Processing helix chain 'A' and resid 111 through 116 Processing helix chain 'A' and resid 124 through 130 removed outlier: 3.839A pdb=" N ILE A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 178 removed outlier: 4.533A pdb=" N SER A 174 " --> pdb=" O ASN A 170 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ASP A 175 " --> pdb=" O TYR A 171 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG A 176 " --> pdb=" O GLU A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 221 Processing helix chain 'A' and resid 223 through 230 removed outlier: 3.555A pdb=" N ALA A 227 " --> pdb=" O ASN A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 254 No H-bonds generated for 'chain 'A' and resid 252 through 254' Processing helix chain 'A' and resid 255 through 267 Processing helix chain 'A' and resid 281 through 293 removed outlier: 3.526A pdb=" N VAL A 285 " --> pdb=" O LYS A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 312 Processing helix chain 'A' and resid 324 through 340 Processing helix chain 'B' and resid 28 through 46 removed outlier: 3.579A pdb=" N PHE B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 130 removed outlier: 3.972A pdb=" N GLU B 130 " --> pdb=" O LYS B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 154 Processing helix chain 'B' and resid 163 through 170 removed outlier: 3.665A pdb=" N LEU B 167 " --> pdb=" O ARG B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 186 Processing helix chain 'B' and resid 235 through 240 removed outlier: 3.788A pdb=" N LEU B 240 " --> pdb=" O ASN B 237 " (cutoff:3.500A) Processing helix chain 'I' and resid 15 through 24 removed outlier: 3.917A pdb=" N SER I 21 " --> pdb=" O ASN I 17 " (cutoff:3.500A) Processing helix chain 'I' and resid 24 through 35 Processing helix chain 'I' and resid 65 through 70 Processing helix chain 'I' and resid 72 through 77 Processing helix chain 'I' and resid 78 through 81 Processing helix chain 'D' and resid 111 through 129 Processing helix chain 'D' and resid 131 through 144 Processing helix chain 'D' and resid 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' Processing helix chain 'D' and resid 186 through 201 Processing helix chain 'D' and resid 250 through 259 Processing helix chain 'D' and resid 267 through 272 Processing helix chain 'D' and resid 296 through 306 Processing helix chain 'D' and resid 312 through 326 Processing helix chain 'E' and resid 111 through 129 Processing helix chain 'E' and resid 131 through 144 Processing helix chain 'E' and resid 175 through 177 No H-bonds generated for 'chain 'E' and resid 175 through 177' Processing helix chain 'E' and resid 186 through 201 Processing helix chain 'E' and resid 250 through 260 removed outlier: 3.521A pdb=" N ALA E 257 " --> pdb=" O LYS E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 272 Processing helix chain 'E' and resid 296 through 306 Processing helix chain 'E' and resid 312 through 326 Processing helix chain 'F' and resid 102 through 104 No H-bonds generated for 'chain 'F' and resid 102 through 104' Processing helix chain 'F' and resid 111 through 129 Processing helix chain 'F' and resid 131 through 144 Processing helix chain 'F' and resid 175 through 177 No H-bonds generated for 'chain 'F' and resid 175 through 177' Processing helix chain 'F' and resid 186 through 201 removed outlier: 3.686A pdb=" N GLN F 195 " --> pdb=" O GLU F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 259 removed outlier: 3.542A pdb=" N ALA F 257 " --> pdb=" O LYS F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 272 Processing helix chain 'F' and resid 296 through 306 removed outlier: 3.753A pdb=" N ASP F 302 " --> pdb=" O TYR F 298 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ARG F 303 " --> pdb=" O LYS F 299 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 326 Processing helix chain 'C' and resid 36 through 40 Processing helix chain 'C' and resid 102 through 104 No H-bonds generated for 'chain 'C' and resid 102 through 104' Processing helix chain 'C' and resid 111 through 129 removed outlier: 3.701A pdb=" N ALA C 127 " --> pdb=" O ASP C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 144 Processing helix chain 'C' and resid 175 through 177 No H-bonds generated for 'chain 'C' and resid 175 through 177' Processing helix chain 'C' and resid 186 through 201 removed outlier: 3.693A pdb=" N GLN C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 259 Processing helix chain 'C' and resid 267 through 272 removed outlier: 3.627A pdb=" N TYR C 271 " --> pdb=" O ASP C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 306 Processing helix chain 'C' and resid 312 through 326 Processing helix chain 'G' and resid 36 through 40 Processing helix chain 'G' and resid 102 through 106 removed outlier: 3.886A pdb=" N MET G 106 " --> pdb=" O LYS G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 129 Processing helix chain 'G' and resid 131 through 144 Processing helix chain 'G' and resid 186 through 201 Processing helix chain 'G' and resid 250 through 259 removed outlier: 3.505A pdb=" N ILE G 254 " --> pdb=" O HIS G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 267 through 272 removed outlier: 3.645A pdb=" N TYR G 271 " --> pdb=" O ASP G 267 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 306 Processing helix chain 'G' and resid 312 through 326 removed outlier: 3.687A pdb=" N TYR G 318 " --> pdb=" O GLU G 314 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU G 323 " --> pdb=" O VAL G 319 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 104 No H-bonds generated for 'chain 'H' and resid 102 through 104' Processing helix chain 'H' and resid 111 through 129 Processing helix chain 'H' and resid 131 through 144 Processing helix chain 'H' and resid 145 through 153 removed outlier: 3.764A pdb=" N LEU H 148 " --> pdb=" O ALA H 145 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ARG H 150 " --> pdb=" O PHE H 147 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LYS H 153 " --> pdb=" O ARG H 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 186 through 202 removed outlier: 3.636A pdb=" N GLN H 195 " --> pdb=" O GLU H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 250 through 259 removed outlier: 3.655A pdb=" N ILE H 254 " --> pdb=" O HIS H 250 " (cutoff:3.500A) Processing helix chain 'H' and resid 265 through 271 removed outlier: 4.479A pdb=" N THR H 269 " --> pdb=" O PRO H 266 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR H 271 " --> pdb=" O TYR H 268 " (cutoff:3.500A) Processing helix chain 'H' and resid 292 through 295 Processing helix chain 'H' and resid 296 through 306 Processing helix chain 'H' and resid 312 through 326 removed outlier: 3.869A pdb=" N HIS H 317 " --> pdb=" O ILE H 313 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N TYR H 318 " --> pdb=" O GLU H 314 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL H 319 " --> pdb=" O ASP H 315 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU H 323 " --> pdb=" O VAL H 319 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 149 through 150 Processing sheet with id=AA2, first strand: chain 'A' and resid 212 through 214 Processing sheet with id=AA3, first strand: chain 'A' and resid 302 through 305 Processing sheet with id=AA4, first strand: chain 'B' and resid 4 through 17 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 4 through 17 current: chain 'B' and resid 101 through 113 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 101 through 113 current: chain 'B' and resid 137 through 139 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 137 through 139 current: chain 'B' and resid 218 through 229 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 218 through 229 current: chain 'B' and resid 249 through 253 No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 66 through 68 Processing sheet with id=AA6, first strand: chain 'I' and resid 5 through 7 removed outlier: 3.834A pdb=" N ILE I 7 " --> pdb=" O LYS I 85 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 40 through 42 removed outlier: 3.821A pdb=" N GLU I 59 " --> pdb=" O THR I 42 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 143 through 148 Processing sheet with id=AA9, first strand: chain 'D' and resid 106 through 109 removed outlier: 3.909A pdb=" N LEU D 19 " --> pdb=" O PHE D 329 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 25 through 27 current: chain 'D' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 45 through 46 current: chain 'D' and resid 172 through 173 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 172 through 173 current: chain 'D' and resid 246 through 249 No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 50 through 51 Processing sheet with id=AB3, first strand: chain 'D' and resid 227 through 228 removed outlier: 4.505A pdb=" N LYS D 239 " --> pdb=" O GLU D 228 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 260 through 262 Processing sheet with id=AB5, first strand: chain 'E' and resid 106 through 109 removed outlier: 3.588A pdb=" N SER E 108 " --> pdb=" O SER E 20 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 25 through 27 current: chain 'E' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 45 through 46 current: chain 'E' and resid 167 through 168 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 167 through 168 current: chain 'E' and resid 246 through 249 No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'E' and resid 50 through 54 removed outlier: 4.271A pdb=" N CYS E 82 " --> pdb=" O VAL E 223 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 19 through 21 removed outlier: 3.795A pdb=" N SER F 108 " --> pdb=" O SER F 20 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 25 through 27 current: chain 'F' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 45 through 46 current: chain 'F' and resid 167 through 168 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 167 through 168 current: chain 'F' and resid 246 through 249 No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'F' and resid 50 through 54 removed outlier: 4.165A pdb=" N CYS F 82 " --> pdb=" O VAL F 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 227 through 228 removed outlier: 4.576A pdb=" N LYS F 239 " --> pdb=" O GLU F 228 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 260 through 262 Processing sheet with id=AC4, first strand: chain 'F' and resid 282 through 283 removed outlier: 3.920A pdb=" N ALA F 283 " --> pdb=" O ILE F 288 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE F 288 " --> pdb=" O ALA F 283 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'C' and resid 106 through 109 removed outlier: 3.635A pdb=" N SER C 108 " --> pdb=" O SER C 20 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 25 through 27 current: chain 'C' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 45 through 46 current: chain 'C' and resid 167 through 168 No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'C' and resid 50 through 54 Processing sheet with id=AC8, first strand: chain 'C' and resid 242 through 243 Processing sheet with id=AC9, first strand: chain 'G' and resid 108 through 109 removed outlier: 4.036A pdb=" N SER G 108 " --> pdb=" O SER G 20 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER G 20 " --> pdb=" O SER G 108 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 25 through 27 current: chain 'G' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 45 through 46 current: chain 'G' and resid 167 through 168 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 167 through 168 current: chain 'G' and resid 246 through 249 No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'G' and resid 82 through 83 removed outlier: 4.139A pdb=" N CYS G 82 " --> pdb=" O VAL G 223 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 260 through 262 Processing sheet with id=AD4, first strand: chain 'G' and resid 282 through 283 removed outlier: 3.654A pdb=" N ILE G 288 " --> pdb=" O ALA G 283 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 106 through 109 removed outlier: 3.539A pdb=" N SER H 108 " --> pdb=" O SER H 20 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 25 through 27 current: chain 'H' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 45 through 46 current: chain 'H' and resid 167 through 168 No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'H' and resid 260 through 262 550 hydrogen bonds defined for protein. 1512 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 17 hydrogen bonds 30 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 26 stacking parallelities Total time for adding SS restraints: 3.51 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 6045 1.33 - 1.45: 3931 1.45 - 1.57: 11374 1.57 - 1.69: 118 1.69 - 1.81: 161 Bond restraints: 21629 Sorted by residual: bond pdb=" N ILE E 286 " pdb=" CA ILE E 286 " ideal model delta sigma weight residual 1.459 1.497 -0.038 9.10e-03 1.21e+04 1.77e+01 bond pdb=" N ASP D 267 " pdb=" CA ASP D 267 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.12e-02 7.97e+03 9.68e+00 bond pdb=" N TYR A 232 " pdb=" CA TYR A 232 " ideal model delta sigma weight residual 1.457 1.496 -0.038 1.29e-02 6.01e+03 8.90e+00 bond pdb=" N ILE A 239 " pdb=" CA ILE A 239 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.53e+00 bond pdb=" N PHE H 21 " pdb=" CA PHE H 21 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.15e-02 7.56e+03 8.10e+00 ... (remaining 21624 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.41: 29349 3.41 - 6.82: 142 6.82 - 10.22: 6 10.22 - 13.63: 0 13.63 - 17.04: 2 Bond angle restraints: 29499 Sorted by residual: angle pdb=" N ILE E 286 " pdb=" CA ILE E 286 " pdb=" C ILE E 286 " ideal model delta sigma weight residual 113.47 108.51 4.96 1.01e+00 9.80e-01 2.42e+01 angle pdb=" CA LEU A 202 " pdb=" CB LEU A 202 " pdb=" CG LEU A 202 " ideal model delta sigma weight residual 116.30 133.34 -17.04 3.50e+00 8.16e-02 2.37e+01 angle pdb=" C TYR A 232 " pdb=" CA TYR A 232 " pdb=" CB TYR A 232 " ideal model delta sigma weight residual 110.42 119.41 -8.99 1.99e+00 2.53e-01 2.04e+01 angle pdb=" C GLY E 287 " pdb=" N ILE E 288 " pdb=" CA ILE E 288 " ideal model delta sigma weight residual 123.02 118.64 4.38 1.04e+00 9.25e-01 1.77e+01 angle pdb=" CA LEU I 175 " pdb=" CB LEU I 175 " pdb=" CG LEU I 175 " ideal model delta sigma weight residual 116.30 130.52 -14.22 3.50e+00 8.16e-02 1.65e+01 ... (remaining 29494 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.20: 12338 35.20 - 70.41: 706 70.41 - 105.61: 46 105.61 - 140.81: 2 140.81 - 176.02: 1 Dihedral angle restraints: 13093 sinusoidal: 5908 harmonic: 7185 Sorted by residual: dihedral pdb=" O4' U J 42 " pdb=" C1' U J 42 " pdb=" N1 U J 42 " pdb=" C2 U J 42 " ideal model delta sinusoidal sigma weight residual 232.00 55.98 176.02 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" CD ARG A 265 " pdb=" NE ARG A 265 " pdb=" CZ ARG A 265 " pdb=" NH1 ARG A 265 " ideal model delta sinusoidal sigma weight residual 0.00 -49.37 49.37 1 1.00e+01 1.00e-02 3.35e+01 dihedral pdb=" CA LEU C 148 " pdb=" C LEU C 148 " pdb=" N TRP C 149 " pdb=" CA TRP C 149 " ideal model delta harmonic sigma weight residual 180.00 -153.21 -26.79 0 5.00e+00 4.00e-02 2.87e+01 ... (remaining 13090 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2672 0.056 - 0.113: 522 0.113 - 0.169: 83 0.169 - 0.225: 14 0.225 - 0.282: 2 Chirality restraints: 3293 Sorted by residual: chirality pdb=" CA VAL A 245 " pdb=" N VAL A 245 " pdb=" C VAL A 245 " pdb=" CB VAL A 245 " both_signs ideal model delta sigma weight residual False 2.44 2.72 -0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CA VAL C 223 " pdb=" N VAL C 223 " pdb=" C VAL C 223 " pdb=" CB VAL C 223 " both_signs ideal model delta sigma weight residual False 2.44 2.71 -0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" C1' A J 4 " pdb=" O4' A J 4 " pdb=" C2' A J 4 " pdb=" N9 A J 4 " both_signs ideal model delta sigma weight residual False 2.46 2.23 0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 3290 not shown) Planarity restraints: 3533 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 265 " -0.826 9.50e-02 1.11e+02 3.70e-01 8.34e+01 pdb=" NE ARG A 265 " 0.050 2.00e-02 2.50e+03 pdb=" CZ ARG A 265 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 265 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 265 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 209 " -0.518 9.50e-02 1.11e+02 2.32e-01 3.30e+01 pdb=" NE ARG B 209 " 0.031 2.00e-02 2.50e+03 pdb=" CZ ARG B 209 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG B 209 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 209 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN G 308 " 0.015 2.00e-02 2.50e+03 3.10e-02 9.62e+00 pdb=" C ASN G 308 " -0.054 2.00e-02 2.50e+03 pdb=" O ASN G 308 " 0.021 2.00e-02 2.50e+03 pdb=" N GLU G 309 " 0.018 2.00e-02 2.50e+03 ... (remaining 3530 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 396 2.64 - 3.20: 19666 3.20 - 3.77: 34333 3.77 - 4.33: 49647 4.33 - 4.90: 78976 Nonbonded interactions: 183018 Sorted by model distance: nonbonded pdb=" OD1 ASP B 118 " pdb=" N MET B 119 " model vdw 2.074 3.120 nonbonded pdb=" OH TYR G 265 " pdb=" O PHE G 273 " model vdw 2.201 3.040 nonbonded pdb=" NZ LYS F 253 " pdb=" OP1 C J 28 " model vdw 2.208 3.120 nonbonded pdb=" O SER I 70 " pdb=" OG SER I 70 " model vdw 2.215 3.040 nonbonded pdb=" O GLU C 278 " pdb=" OH TYR C 318 " model vdw 2.216 3.040 ... (remaining 183013 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 15 through 16 or (resid 17 and (name N or name CA or name \ C or name O or name CB )) or resid 18 through 50 or resid 80 through 228 or resi \ d 240 through 329)) selection = (chain 'D' and (resid 15 through 16 or (resid 17 and (name N or name CA or name \ C or name O or name CB )) or resid 18 through 50 or resid 80 through 228 or resi \ d 240 through 329)) selection = (chain 'E' and (resid 15 through 16 or (resid 17 and (name N or name CA or name \ C or name O or name CB )) or resid 18 through 50 or resid 80 through 228 or resi \ d 240 through 329)) selection = (chain 'F' and (resid 15 through 16 or (resid 17 and (name N or name CA or name \ C or name O or name CB )) or resid 18 through 50 or resid 80 through 228 or resi \ d 240 through 329)) selection = (chain 'G' and (resid 15 through 16 or (resid 17 and (name N or name CA or name \ C or name O or name CB )) or resid 18 through 50 or resid 80 through 228 or resi \ d 240 through 329)) selection = (chain 'H' and resid 15 through 329) } 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: 7.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 22.090 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 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 : 0.005 0.052 21629 Z= 0.262 Angle : 0.717 17.042 29499 Z= 0.421 Chirality : 0.047 0.282 3293 Planarity : 0.009 0.370 3533 Dihedral : 19.852 176.018 8451 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.77 % Favored : 92.77 % Rotamer: Outliers : 5.59 % Allowed : 27.31 % Favored : 67.10 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: -0.96 (0.17), residues: 2394 helix: 0.06 (0.20), residues: 677 sheet: 0.45 (0.27), residues: 406 loop : -1.40 (0.17), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 150 TYR 0.028 0.002 TYR F 318 PHE 0.020 0.002 PHE A 212 TRP 0.013 0.002 TRP A 74 HIS 0.005 0.001 HIS G 317 Details of bonding type rmsd covalent geometry : bond 0.00501 (21629) covalent geometry : angle 0.71723 (29499) hydrogen bonds : bond 0.15610 ( 567) hydrogen bonds : angle 7.03498 ( 1542) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 515 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 96 ILE cc_start: 0.6987 (OUTLIER) cc_final: 0.6688 (pt) REVERT: B 97 MET cc_start: 0.6252 (tmm) cc_final: 0.5991 (tmm) REVERT: B 144 LYS cc_start: 0.7814 (mmtt) cc_final: 0.7610 (mmtt) REVERT: B 209 ARG cc_start: 0.4960 (OUTLIER) cc_final: 0.4242 (ttt90) REVERT: B 224 LEU cc_start: 0.7341 (OUTLIER) cc_final: 0.7072 (mt) REVERT: I 103 ARG cc_start: 0.1315 (OUTLIER) cc_final: -0.0078 (tpp-160) REVERT: D 210 TYR cc_start: 0.7832 (m-80) cc_final: 0.7409 (m-80) REVERT: E 119 TYR cc_start: 0.8089 (m-10) cc_final: 0.7874 (m-10) REVERT: F 40 ARG cc_start: 0.8535 (ptt-90) cc_final: 0.8318 (ptt90) REVERT: C 184 GLU cc_start: 0.6902 (mp0) cc_final: 0.6558 (mp0) REVERT: C 228 GLU cc_start: 0.7388 (mm-30) cc_final: 0.7180 (mm-30) REVERT: H 192 ILE cc_start: 0.7821 (OUTLIER) cc_final: 0.7586 (mp) REVERT: H 206 TYR cc_start: 0.7329 (p90) cc_final: 0.6683 (p90) REVERT: H 258 LEU cc_start: 0.8106 (mp) cc_final: 0.7906 (mt) outliers start: 121 outliers final: 83 residues processed: 600 average time/residue: 0.1658 time to fit residues: 147.8552 Evaluate side-chains 590 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 502 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 101 ARG Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 209 ARG Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain I residue 2 PHE Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain I residue 20 ILE Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 50 LYS Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 87 LYS Chi-restraints excluded: chain I residue 88 LYS Chi-restraints excluded: chain I residue 101 ARG Chi-restraints excluded: chain I residue 103 ARG Chi-restraints excluded: chain I residue 104 GLU Chi-restraints excluded: chain I residue 143 TYR Chi-restraints excluded: chain I residue 145 LYS Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 155 TYR Chi-restraints excluded: chain I residue 159 LEU Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain E residue 103 LYS Chi-restraints excluded: chain E residue 171 SER Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 251 SER Chi-restraints excluded: chain E residue 313 ILE Chi-restraints excluded: chain E residue 328 MET Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 166 ASP Chi-restraints excluded: chain F residue 226 SER Chi-restraints excluded: chain F residue 267 ASP Chi-restraints excluded: chain F residue 328 MET Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 219 CYS Chi-restraints excluded: chain G residue 267 ASP Chi-restraints excluded: chain G residue 278 GLU Chi-restraints excluded: chain G residue 310 ASP Chi-restraints excluded: chain G residue 311 LEU Chi-restraints excluded: chain H residue 15 ARG Chi-restraints excluded: chain H residue 144 ASN Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain H residue 192 ILE Chi-restraints excluded: chain H residue 215 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.6980 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 235 optimal weight: 0.0670 overall best weight: 0.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 71 ASN A 159 HIS B 53 ASN I 4 GLN I 29 HIS I 166 HIS G 34 GLN H 144 ASN H 308 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.158142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.123968 restraints weight = 30880.369| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.03 r_work: 0.3486 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 21629 Z= 0.196 Angle : 0.599 15.013 29499 Z= 0.312 Chirality : 0.043 0.191 3293 Planarity : 0.005 0.073 3533 Dihedral : 16.147 176.832 3772 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.27 % Favored : 93.40 % Rotamer: Outliers : 5.64 % Allowed : 25.65 % Favored : 68.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: -0.87 (0.17), residues: 2394 helix: 0.20 (0.19), residues: 697 sheet: 0.41 (0.27), residues: 418 loop : -1.39 (0.17), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 291 TYR 0.022 0.001 TYR A 171 PHE 0.019 0.002 PHE A 212 TRP 0.013 0.001 TRP A 74 HIS 0.004 0.001 HIS G 317 Details of bonding type rmsd covalent geometry : bond 0.00454 (21629) covalent geometry : angle 0.59923 (29499) hydrogen bonds : bond 0.04480 ( 567) hydrogen bonds : angle 5.68584 ( 1542) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 518 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ILE cc_start: 0.3733 (OUTLIER) cc_final: 0.3509 (pt) REVERT: A 62 MET cc_start: 0.6952 (tmm) cc_final: 0.6159 (tmm) REVERT: A 71 ASN cc_start: 0.8323 (t0) cc_final: 0.8094 (t0) REVERT: A 104 MET cc_start: 0.6022 (ttp) cc_final: 0.5554 (ttp) REVERT: A 152 PHE cc_start: 0.8585 (t80) cc_final: 0.8010 (t80) REVERT: A 176 ARG cc_start: 0.6866 (OUTLIER) cc_final: 0.6391 (mmm160) REVERT: A 210 LEU cc_start: 0.5262 (OUTLIER) cc_final: 0.4987 (mm) REVERT: A 222 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7755 (ttmm) REVERT: A 238 ASN cc_start: 0.6525 (t0) cc_final: 0.6167 (t0) REVERT: B 96 ILE cc_start: 0.7055 (OUTLIER) cc_final: 0.6781 (pt) REVERT: B 97 MET cc_start: 0.6432 (tmm) cc_final: 0.5710 (tmm) REVERT: B 144 LYS cc_start: 0.8320 (mmtt) cc_final: 0.8008 (mmtt) REVERT: B 209 ARG cc_start: 0.6528 (OUTLIER) cc_final: 0.4925 (ttt180) REVERT: B 246 GLU cc_start: 0.6446 (mm-30) cc_final: 0.6093 (mp0) REVERT: I 25 PHE cc_start: 0.7481 (OUTLIER) cc_final: 0.7125 (t80) REVERT: I 37 LYS cc_start: 0.6236 (OUTLIER) cc_final: 0.6027 (mmtm) REVERT: I 58 ILE cc_start: 0.6853 (OUTLIER) cc_final: 0.6557 (mm) REVERT: I 85 LYS cc_start: 0.6404 (OUTLIER) cc_final: 0.6011 (tmtp) REVERT: I 99 PHE cc_start: 0.4560 (OUTLIER) cc_final: 0.4178 (m-80) REVERT: D 121 LYS cc_start: 0.7055 (mmtp) cc_final: 0.6831 (mmtp) REVERT: D 238 LYS cc_start: 0.8118 (ttmm) cc_final: 0.7799 (tttm) REVERT: E 91 LEU cc_start: 0.8442 (tp) cc_final: 0.8156 (tp) REVERT: E 115 ARG cc_start: 0.7994 (ttp80) cc_final: 0.7735 (ttp80) REVERT: E 119 TYR cc_start: 0.8639 (m-10) cc_final: 0.8307 (m-10) REVERT: E 138 TYR cc_start: 0.8195 (m-80) cc_final: 0.7664 (m-80) REVERT: E 228 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7777 (mm-30) REVERT: E 279 ASN cc_start: 0.8345 (m-40) cc_final: 0.8132 (m-40) REVERT: E 299 LYS cc_start: 0.8541 (tppt) cc_final: 0.8239 (mmtp) REVERT: F 40 ARG cc_start: 0.8967 (ptt-90) cc_final: 0.8587 (ptt90) REVERT: F 226 SER cc_start: 0.8618 (m) cc_final: 0.8371 (t) REVERT: F 303 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7877 (ttp80) REVERT: C 184 GLU cc_start: 0.7800 (mp0) cc_final: 0.7279 (mp0) REVERT: C 224 TYR cc_start: 0.8483 (m-80) cc_final: 0.8193 (m-80) REVERT: G 116 THR cc_start: 0.8315 (m) cc_final: 0.8059 (t) REVERT: G 239 LYS cc_start: 0.8899 (mmmt) cc_final: 0.8619 (mmmt) REVERT: H 120 GLN cc_start: 0.7577 (OUTLIER) cc_final: 0.6832 (pp30) REVERT: H 121 LYS cc_start: 0.8125 (mmmt) cc_final: 0.6804 (mmmt) REVERT: H 165 GLU cc_start: 0.7455 (pp20) cc_final: 0.7249 (pp20) REVERT: H 184 GLU cc_start: 0.6253 (tm-30) cc_final: 0.5862 (tm-30) REVERT: H 192 ILE cc_start: 0.8153 (OUTLIER) cc_final: 0.7919 (mp) REVERT: H 271 TYR cc_start: 0.8050 (m-80) cc_final: 0.7439 (m-80) REVERT: H 272 GLU cc_start: 0.6971 (mp0) cc_final: 0.6542 (mp0) REVERT: H 308 ASN cc_start: 0.7515 (t0) cc_final: 0.7302 (t0) outliers start: 122 outliers final: 56 residues processed: 611 average time/residue: 0.1629 time to fit residues: 147.7814 Evaluate side-chains 561 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 491 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 74 TRP Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 101 ARG Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 176 ARG Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 209 ARG Chi-restraints excluded: chain I residue 2 PHE Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 25 PHE Chi-restraints excluded: chain I residue 29 HIS Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 50 LYS Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 85 LYS Chi-restraints excluded: chain I residue 88 LYS Chi-restraints excluded: chain I residue 99 PHE Chi-restraints excluded: chain I residue 101 ARG Chi-restraints excluded: chain I residue 104 GLU Chi-restraints excluded: chain I residue 141 HIS Chi-restraints excluded: chain I residue 143 TYR Chi-restraints excluded: chain I residue 145 LYS Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 155 TYR Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 159 LEU Chi-restraints excluded: chain I residue 169 PHE Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 226 SER Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 322 ILE Chi-restraints excluded: chain E residue 239 LYS Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain F residue 166 ASP Chi-restraints excluded: chain F residue 303 ARG Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 310 ASP Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain H residue 192 ILE Chi-restraints excluded: chain H residue 215 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 13 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 95 optimal weight: 0.6980 chunk 157 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 96 optimal weight: 0.5980 chunk 187 optimal weight: 1.9990 chunk 198 optimal weight: 0.0980 chunk 200 optimal weight: 0.5980 chunk 189 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 HIS A 213 GLN I 29 HIS ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 178 ASN D 195 GLN G 34 GLN G 195 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.160982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.126559 restraints weight = 30928.585| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.02 r_work: 0.3535 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21629 Z= 0.137 Angle : 0.541 14.246 29499 Z= 0.284 Chirality : 0.041 0.183 3293 Planarity : 0.005 0.068 3533 Dihedral : 15.603 178.145 3663 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.76 % Favored : 93.94 % Rotamer: Outliers : 5.27 % Allowed : 26.57 % Favored : 68.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: -0.65 (0.17), residues: 2394 helix: 0.48 (0.19), residues: 692 sheet: 0.48 (0.27), residues: 417 loop : -1.29 (0.17), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 137 TYR 0.019 0.001 TYR C 114 PHE 0.016 0.001 PHE A 212 TRP 0.012 0.001 TRP A 74 HIS 0.011 0.001 HIS A 159 Details of bonding type rmsd covalent geometry : bond 0.00314 (21629) covalent geometry : angle 0.54141 (29499) hydrogen bonds : bond 0.03958 ( 567) hydrogen bonds : angle 5.39357 ( 1542) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 509 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ILE cc_start: 0.3636 (OUTLIER) cc_final: 0.3404 (pt) REVERT: A 62 MET cc_start: 0.6841 (tmm) cc_final: 0.6516 (tmm) REVERT: A 104 MET cc_start: 0.5909 (ttp) cc_final: 0.5451 (ttp) REVERT: A 152 PHE cc_start: 0.8569 (t80) cc_final: 0.8066 (t80) REVERT: A 176 ARG cc_start: 0.6813 (OUTLIER) cc_final: 0.6199 (mmm160) REVERT: A 222 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7741 (ttmm) REVERT: A 230 LYS cc_start: 0.7934 (OUTLIER) cc_final: 0.7398 (mptp) REVERT: A 238 ASN cc_start: 0.6621 (t0) cc_final: 0.6166 (t0) REVERT: A 266 LYS cc_start: 0.8431 (mmmt) cc_final: 0.8177 (mmmt) REVERT: A 281 LYS cc_start: 0.6149 (mttp) cc_final: 0.5920 (mttp) REVERT: B 97 MET cc_start: 0.6285 (tmm) cc_final: 0.5712 (tmm) REVERT: B 144 LYS cc_start: 0.8340 (mmtt) cc_final: 0.8044 (mmtt) REVERT: B 209 ARG cc_start: 0.6389 (OUTLIER) cc_final: 0.5248 (ttt180) REVERT: I 25 PHE cc_start: 0.7340 (OUTLIER) cc_final: 0.7017 (t80) REVERT: I 85 LYS cc_start: 0.6531 (OUTLIER) cc_final: 0.6078 (tmtp) REVERT: I 99 PHE cc_start: 0.4616 (OUTLIER) cc_final: 0.4167 (m-80) REVERT: I 104 GLU cc_start: 0.1705 (OUTLIER) cc_final: 0.0606 (pm20) REVERT: D 102 VAL cc_start: 0.8792 (p) cc_final: 0.8538 (t) REVERT: D 224 TYR cc_start: 0.8234 (m-80) cc_final: 0.7986 (m-80) REVERT: D 238 LYS cc_start: 0.8107 (ttmm) cc_final: 0.7820 (ttmm) REVERT: E 279 ASN cc_start: 0.8297 (m-40) cc_final: 0.8083 (m-40) REVERT: E 299 LYS cc_start: 0.8534 (tppt) cc_final: 0.8153 (mmmm) REVERT: F 40 ARG cc_start: 0.8947 (ptt-90) cc_final: 0.8443 (ptt180) REVERT: F 226 SER cc_start: 0.8652 (m) cc_final: 0.8347 (t) REVERT: C 164 ILE cc_start: 0.8350 (mp) cc_final: 0.8140 (mt) REVERT: C 171 SER cc_start: 0.8238 (p) cc_final: 0.7985 (m) REVERT: C 184 GLU cc_start: 0.7757 (mp0) cc_final: 0.7334 (mp0) REVERT: C 224 TYR cc_start: 0.8453 (m-80) cc_final: 0.8105 (m-80) REVERT: G 136 LYS cc_start: 0.8272 (mttm) cc_final: 0.7879 (mmtt) REVERT: G 191 GLU cc_start: 0.7066 (tt0) cc_final: 0.6862 (tt0) REVERT: G 239 LYS cc_start: 0.8866 (mmmt) cc_final: 0.8582 (mmmt) REVERT: H 120 GLN cc_start: 0.7595 (OUTLIER) cc_final: 0.6837 (pp30) REVERT: H 121 LYS cc_start: 0.8060 (mmmt) cc_final: 0.6792 (mmmt) REVERT: H 165 GLU cc_start: 0.7384 (pp20) cc_final: 0.7007 (pp20) REVERT: H 184 GLU cc_start: 0.6261 (tm-30) cc_final: 0.5780 (tm-30) REVERT: H 272 GLU cc_start: 0.6884 (mp0) cc_final: 0.6548 (mp0) outliers start: 114 outliers final: 66 residues processed: 593 average time/residue: 0.1601 time to fit residues: 142.5797 Evaluate side-chains 555 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 479 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 101 ARG Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 176 ARG Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 209 ARG Chi-restraints excluded: chain I residue 2 PHE Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 25 PHE Chi-restraints excluded: chain I residue 50 LYS Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 85 LYS Chi-restraints excluded: chain I residue 88 LYS Chi-restraints excluded: chain I residue 99 PHE Chi-restraints excluded: chain I residue 101 ARG Chi-restraints excluded: chain I residue 104 GLU Chi-restraints excluded: chain I residue 141 HIS Chi-restraints excluded: chain I residue 143 TYR Chi-restraints excluded: chain I residue 145 LYS Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 155 TYR Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 159 LEU Chi-restraints excluded: chain I residue 169 PHE Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 226 SER Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 239 LYS Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 313 ILE Chi-restraints excluded: chain F residue 166 ASP Chi-restraints excluded: chain F residue 249 MET Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 325 ARG Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 109 CYS Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 171 SER Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 229 MET Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain G residue 275 ILE Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 314 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 116 optimal weight: 2.9990 chunk 58 optimal weight: 9.9990 chunk 214 optimal weight: 5.9990 chunk 202 optimal weight: 0.7980 chunk 124 optimal weight: 0.0870 chunk 143 optimal weight: 1.9990 chunk 220 optimal weight: 2.9990 chunk 208 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 173 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 159 HIS A 213 GLN A 296 ASN ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 178 ASN ** C 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 34 GLN H 308 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.158870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.124288 restraints weight = 30715.282| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.02 r_work: 0.3506 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21629 Z= 0.190 Angle : 0.558 13.510 29499 Z= 0.292 Chirality : 0.043 0.200 3293 Planarity : 0.005 0.074 3533 Dihedral : 15.441 177.443 3651 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.97 % Favored : 93.78 % Rotamer: Outliers : 5.64 % Allowed : 26.66 % Favored : 67.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: -0.66 (0.17), residues: 2394 helix: 0.49 (0.20), residues: 686 sheet: 0.37 (0.27), residues: 423 loop : -1.25 (0.17), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 152 TYR 0.025 0.001 TYR C 114 PHE 0.016 0.001 PHE A 212 TRP 0.013 0.001 TRP A 74 HIS 0.004 0.001 HIS G 317 Details of bonding type rmsd covalent geometry : bond 0.00443 (21629) covalent geometry : angle 0.55778 (29499) hydrogen bonds : bond 0.04150 ( 567) hydrogen bonds : angle 5.40186 ( 1542) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 503 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ILE cc_start: 0.3689 (OUTLIER) cc_final: 0.3417 (pt) REVERT: A 62 MET cc_start: 0.6853 (tmm) cc_final: 0.6578 (tmm) REVERT: A 104 MET cc_start: 0.5913 (ttp) cc_final: 0.5467 (ttp) REVERT: A 152 PHE cc_start: 0.8640 (t80) cc_final: 0.8143 (t80) REVERT: A 176 ARG cc_start: 0.6994 (OUTLIER) cc_final: 0.6328 (mmm160) REVERT: A 226 LYS cc_start: 0.8184 (mttm) cc_final: 0.7537 (mtpp) REVERT: A 230 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7472 (mptp) REVERT: B 97 MET cc_start: 0.6321 (tmm) cc_final: 0.5639 (tmm) REVERT: B 144 LYS cc_start: 0.8328 (mmtt) cc_final: 0.8055 (mmtt) REVERT: B 209 ARG cc_start: 0.6480 (OUTLIER) cc_final: 0.5724 (ttt180) REVERT: I 25 PHE cc_start: 0.7345 (OUTLIER) cc_final: 0.6992 (t80) REVERT: I 65 LYS cc_start: 0.6609 (OUTLIER) cc_final: 0.6348 (mttm) REVERT: I 85 LYS cc_start: 0.6441 (OUTLIER) cc_final: 0.5974 (tmtp) REVERT: I 99 PHE cc_start: 0.4510 (OUTLIER) cc_final: 0.4014 (m-80) REVERT: I 104 GLU cc_start: 0.1674 (OUTLIER) cc_final: 0.0565 (pm20) REVERT: D 224 TYR cc_start: 0.8246 (m-80) cc_final: 0.8009 (m-80) REVERT: D 238 LYS cc_start: 0.8079 (ttmm) cc_final: 0.7801 (ttmm) REVERT: E 138 TYR cc_start: 0.8160 (m-80) cc_final: 0.7710 (m-80) REVERT: E 299 LYS cc_start: 0.8550 (tppt) cc_final: 0.8246 (mmtp) REVERT: F 40 ARG cc_start: 0.8939 (ptt-90) cc_final: 0.8528 (ptt180) REVERT: F 55 LEU cc_start: 0.7731 (tp) cc_final: 0.7510 (tp) REVERT: F 119 TYR cc_start: 0.8097 (m-10) cc_final: 0.7811 (m-10) REVERT: F 226 SER cc_start: 0.8674 (m) cc_final: 0.8421 (t) REVERT: F 229 MET cc_start: 0.6141 (ttt) cc_final: 0.5705 (mtt) REVERT: F 252 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.8179 (pm20) REVERT: F 291 ARG cc_start: 0.8735 (mtt180) cc_final: 0.8534 (mtt180) REVERT: C 21 PHE cc_start: 0.8084 (m-80) cc_final: 0.7797 (m-80) REVERT: C 164 ILE cc_start: 0.8334 (mp) cc_final: 0.8108 (mt) REVERT: C 165 GLU cc_start: 0.6508 (OUTLIER) cc_final: 0.5831 (pp20) REVERT: C 171 SER cc_start: 0.8211 (p) cc_final: 0.7989 (m) REVERT: C 224 TYR cc_start: 0.8438 (m-80) cc_final: 0.8063 (m-80) REVERT: G 136 LYS cc_start: 0.8285 (mttm) cc_final: 0.7880 (mmtt) REVERT: G 163 THR cc_start: 0.8517 (m) cc_final: 0.8135 (p) REVERT: G 204 ARG cc_start: 0.8355 (ttm-80) cc_final: 0.7782 (ttm170) REVERT: H 29 GLU cc_start: 0.8276 (mp0) cc_final: 0.7934 (mt-10) REVERT: H 120 GLN cc_start: 0.7576 (OUTLIER) cc_final: 0.6824 (pp30) REVERT: H 121 LYS cc_start: 0.8076 (mmmt) cc_final: 0.6772 (mmmt) REVERT: H 165 GLU cc_start: 0.7378 (pp20) cc_final: 0.6992 (pp20) REVERT: H 184 GLU cc_start: 0.6375 (tm-30) cc_final: 0.5893 (tm-30) REVERT: H 272 GLU cc_start: 0.7043 (mp0) cc_final: 0.6652 (mp0) REVERT: H 290 PHE cc_start: 0.7567 (m-10) cc_final: 0.7366 (m-10) outliers start: 122 outliers final: 73 residues processed: 596 average time/residue: 0.1583 time to fit residues: 141.2724 Evaluate side-chains 577 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 492 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 74 TRP Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 101 ARG Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain A residue 139 GLN Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 176 ARG Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 209 ARG Chi-restraints excluded: chain I residue 2 PHE Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 25 PHE Chi-restraints excluded: chain I residue 50 LYS Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain I residue 85 LYS Chi-restraints excluded: chain I residue 88 LYS Chi-restraints excluded: chain I residue 99 PHE Chi-restraints excluded: chain I residue 101 ARG Chi-restraints excluded: chain I residue 104 GLU Chi-restraints excluded: chain I residue 141 HIS Chi-restraints excluded: chain I residue 143 TYR Chi-restraints excluded: chain I residue 145 LYS Chi-restraints excluded: chain I residue 155 TYR Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 159 LEU Chi-restraints excluded: chain I residue 169 PHE Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 322 ILE Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 313 ILE Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 166 ASP Chi-restraints excluded: chain F residue 249 MET Chi-restraints excluded: chain F residue 251 SER Chi-restraints excluded: chain F residue 252 GLN Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 325 ARG Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 109 CYS Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 229 MET Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain G residue 275 ILE Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain H residue 215 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 149 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 222 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 201 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 241 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 58 optimal weight: 10.0000 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 HIS A 213 GLN ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 156 ASN ** E 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 34 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.156126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.121886 restraints weight = 30760.962| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.03 r_work: 0.3455 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 21629 Z= 0.253 Angle : 0.599 12.889 29499 Z= 0.311 Chirality : 0.045 0.215 3293 Planarity : 0.005 0.076 3533 Dihedral : 15.375 176.131 3643 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.14 % Favored : 93.61 % Rotamer: Outliers : 6.15 % Allowed : 26.76 % Favored : 67.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.77 (0.17), residues: 2394 helix: 0.33 (0.19), residues: 685 sheet: 0.26 (0.26), residues: 430 loop : -1.27 (0.17), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 152 TYR 0.030 0.002 TYR C 114 PHE 0.023 0.002 PHE A 146 TRP 0.014 0.002 TRP A 74 HIS 0.014 0.001 HIS A 159 Details of bonding type rmsd covalent geometry : bond 0.00590 (21629) covalent geometry : angle 0.59857 (29499) hydrogen bonds : bond 0.04452 ( 567) hydrogen bonds : angle 5.53083 ( 1542) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 497 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ILE cc_start: 0.3717 (OUTLIER) cc_final: 0.3480 (pt) REVERT: A 62 MET cc_start: 0.7060 (tmm) cc_final: 0.6778 (tmm) REVERT: A 104 MET cc_start: 0.6046 (ttp) cc_final: 0.5633 (ttp) REVERT: A 176 ARG cc_start: 0.7178 (OUTLIER) cc_final: 0.6539 (mmm160) REVERT: A 226 LYS cc_start: 0.8250 (mttm) cc_final: 0.7565 (mtpp) REVERT: A 230 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7460 (mptp) REVERT: A 232 TYR cc_start: 0.7323 (m-10) cc_final: 0.7050 (m-10) REVERT: B 14 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7137 (mt-10) REVERT: B 96 ILE cc_start: 0.7100 (OUTLIER) cc_final: 0.6818 (pt) REVERT: B 97 MET cc_start: 0.6423 (tmm) cc_final: 0.5459 (tmm) REVERT: B 111 GLU cc_start: 0.8338 (tm-30) cc_final: 0.7500 (tm-30) REVERT: B 144 LYS cc_start: 0.8378 (mmtt) cc_final: 0.8082 (mmtt) REVERT: B 209 ARG cc_start: 0.6588 (OUTLIER) cc_final: 0.5736 (ttt180) REVERT: I 25 PHE cc_start: 0.7444 (OUTLIER) cc_final: 0.7143 (t80) REVERT: I 38 LYS cc_start: 0.2535 (OUTLIER) cc_final: 0.2137 (mmmt) REVERT: I 65 LYS cc_start: 0.6534 (OUTLIER) cc_final: 0.6267 (mttm) REVERT: I 85 LYS cc_start: 0.6567 (OUTLIER) cc_final: 0.6074 (tmtp) REVERT: I 99 PHE cc_start: 0.4458 (OUTLIER) cc_final: 0.3900 (m-80) REVERT: I 104 GLU cc_start: 0.1708 (OUTLIER) cc_final: 0.0494 (pm20) REVERT: I 143 TYR cc_start: -0.0464 (OUTLIER) cc_final: -0.1796 (p90) REVERT: D 224 TYR cc_start: 0.8271 (m-80) cc_final: 0.7986 (m-80) REVERT: D 238 LYS cc_start: 0.8155 (ttmm) cc_final: 0.7876 (ttmm) REVERT: E 119 TYR cc_start: 0.8682 (m-10) cc_final: 0.8394 (m-10) REVERT: F 40 ARG cc_start: 0.8956 (ptt-90) cc_final: 0.8529 (ptt180) REVERT: F 226 SER cc_start: 0.8693 (m) cc_final: 0.8429 (t) REVERT: F 229 MET cc_start: 0.6314 (ttt) cc_final: 0.5912 (mtt) REVERT: F 252 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.8096 (pm20) REVERT: C 21 PHE cc_start: 0.8110 (m-80) cc_final: 0.7775 (m-80) REVERT: C 29 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7252 (mt-10) REVERT: C 165 GLU cc_start: 0.6621 (OUTLIER) cc_final: 0.5983 (pp20) REVERT: C 224 TYR cc_start: 0.8463 (m-80) cc_final: 0.8199 (m-80) REVERT: G 114 TYR cc_start: 0.8210 (t80) cc_final: 0.7349 (t80) REVERT: G 204 ARG cc_start: 0.8385 (ttm-80) cc_final: 0.7835 (ttm170) REVERT: G 239 LYS cc_start: 0.8942 (mmmt) cc_final: 0.8711 (mmmt) REVERT: H 115 ARG cc_start: 0.7706 (tpp80) cc_final: 0.7271 (tpp80) REVERT: H 120 GLN cc_start: 0.7538 (OUTLIER) cc_final: 0.6765 (pp30) REVERT: H 121 LYS cc_start: 0.8140 (mmmt) cc_final: 0.6763 (mmmt) REVERT: H 165 GLU cc_start: 0.7416 (pp20) cc_final: 0.6999 (pp20) REVERT: H 184 GLU cc_start: 0.6472 (tm-30) cc_final: 0.6024 (tm-30) REVERT: H 252 GLN cc_start: 0.7872 (mp10) cc_final: 0.7657 (mp10) REVERT: H 271 TYR cc_start: 0.7926 (m-80) cc_final: 0.7508 (m-80) REVERT: H 272 GLU cc_start: 0.7164 (mp0) cc_final: 0.6707 (mp0) REVERT: H 279 ASN cc_start: 0.6928 (p0) cc_final: 0.6441 (p0) REVERT: H 290 PHE cc_start: 0.7672 (m-10) cc_final: 0.7434 (m-10) outliers start: 133 outliers final: 81 residues processed: 594 average time/residue: 0.1608 time to fit residues: 143.0151 Evaluate side-chains 584 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 487 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 74 TRP Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 101 ARG Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 176 ARG Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 209 ARG Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain I residue 2 PHE Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 25 PHE Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 38 LYS Chi-restraints excluded: chain I residue 50 LYS Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain I residue 85 LYS Chi-restraints excluded: chain I residue 88 LYS Chi-restraints excluded: chain I residue 99 PHE Chi-restraints excluded: chain I residue 101 ARG Chi-restraints excluded: chain I residue 104 GLU Chi-restraints excluded: chain I residue 141 HIS Chi-restraints excluded: chain I residue 143 TYR Chi-restraints excluded: chain I residue 145 LYS Chi-restraints excluded: chain I residue 155 TYR Chi-restraints excluded: chain I residue 156 ASN Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 159 LEU Chi-restraints excluded: chain I residue 169 PHE Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 226 SER Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 322 ILE Chi-restraints excluded: chain E residue 106 MET Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 313 ILE Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 166 ASP Chi-restraints excluded: chain F residue 249 MET Chi-restraints excluded: chain F residue 251 SER Chi-restraints excluded: chain F residue 252 GLN Chi-restraints excluded: chain F residue 272 GLU Chi-restraints excluded: chain F residue 322 ILE Chi-restraints excluded: chain F residue 325 ARG Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 109 CYS Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 229 MET Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain G residue 278 GLU Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain H residue 215 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 151 optimal weight: 0.7980 chunk 244 optimal weight: 20.0000 chunk 48 optimal weight: 0.9980 chunk 95 optimal weight: 0.5980 chunk 49 optimal weight: 0.0060 chunk 101 optimal weight: 0.5980 chunk 185 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 160 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 108 GLN A 159 HIS A 213 GLN ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 178 ASN ** E 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.160107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.125562 restraints weight = 30681.320| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.03 r_work: 0.3521 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3380 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21629 Z= 0.135 Angle : 0.543 12.594 29499 Z= 0.281 Chirality : 0.042 0.178 3293 Planarity : 0.004 0.068 3533 Dihedral : 15.243 178.578 3643 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.43 % Favored : 94.28 % Rotamer: Outliers : 5.36 % Allowed : 27.63 % Favored : 67.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: -0.56 (0.17), residues: 2394 helix: 0.57 (0.20), residues: 685 sheet: 0.42 (0.27), residues: 425 loop : -1.19 (0.17), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 259 TYR 0.020 0.001 TYR C 114 PHE 0.014 0.001 PHE A 146 TRP 0.009 0.001 TRP A 74 HIS 0.004 0.001 HIS B 215 Details of bonding type rmsd covalent geometry : bond 0.00308 (21629) covalent geometry : angle 0.54317 (29499) hydrogen bonds : bond 0.03818 ( 567) hydrogen bonds : angle 5.28285 ( 1542) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 515 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.6939 (tmm) cc_final: 0.6659 (tmm) REVERT: A 78 ASP cc_start: 0.6706 (m-30) cc_final: 0.6478 (m-30) REVERT: A 104 MET cc_start: 0.5941 (ttp) cc_final: 0.5536 (ttp) REVERT: A 152 PHE cc_start: 0.8488 (t80) cc_final: 0.8256 (t80) REVERT: A 176 ARG cc_start: 0.7172 (OUTLIER) cc_final: 0.6522 (mmm160) REVERT: A 230 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7431 (mptp) REVERT: A 283 GLU cc_start: 0.5944 (tm-30) cc_final: 0.5735 (tm-30) REVERT: B 96 ILE cc_start: 0.7024 (OUTLIER) cc_final: 0.6750 (pt) REVERT: B 97 MET cc_start: 0.6213 (tmm) cc_final: 0.5685 (tmm) REVERT: B 111 GLU cc_start: 0.8359 (tm-30) cc_final: 0.7566 (tm-30) REVERT: B 144 LYS cc_start: 0.8321 (mmtt) cc_final: 0.8036 (mmtt) REVERT: B 234 GLU cc_start: 0.7476 (pm20) cc_final: 0.7247 (pm20) REVERT: I 25 PHE cc_start: 0.7229 (OUTLIER) cc_final: 0.6896 (t80) REVERT: I 38 LYS cc_start: 0.2645 (OUTLIER) cc_final: 0.2343 (mmmt) REVERT: I 65 LYS cc_start: 0.6513 (OUTLIER) cc_final: 0.6258 (mttm) REVERT: I 85 LYS cc_start: 0.6485 (OUTLIER) cc_final: 0.5999 (tmtp) REVERT: I 99 PHE cc_start: 0.4417 (OUTLIER) cc_final: 0.3811 (t80) REVERT: I 104 GLU cc_start: 0.1531 (OUTLIER) cc_final: 0.0536 (pm20) REVERT: D 102 VAL cc_start: 0.8794 (p) cc_final: 0.8538 (t) REVERT: D 224 TYR cc_start: 0.8289 (m-80) cc_final: 0.8018 (m-80) REVERT: D 238 LYS cc_start: 0.8074 (ttmm) cc_final: 0.7867 (ttmm) REVERT: E 119 TYR cc_start: 0.8562 (m-10) cc_final: 0.8293 (m-10) REVERT: E 224 TYR cc_start: 0.8443 (m-80) cc_final: 0.8208 (m-80) REVERT: E 292 PRO cc_start: 0.8090 (Cg_endo) cc_final: 0.7888 (Cg_exo) REVERT: E 299 LYS cc_start: 0.8550 (tppt) cc_final: 0.8155 (mmmm) REVERT: F 40 ARG cc_start: 0.8927 (ptt-90) cc_final: 0.8511 (ptt180) REVERT: F 119 TYR cc_start: 0.8120 (m-10) cc_final: 0.7882 (m-10) REVERT: F 229 MET cc_start: 0.6355 (ttt) cc_final: 0.6071 (mtt) REVERT: F 252 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.8134 (pm20) REVERT: C 21 PHE cc_start: 0.8066 (m-80) cc_final: 0.7801 (m-80) REVERT: C 165 GLU cc_start: 0.6476 (OUTLIER) cc_final: 0.5838 (pp20) REVERT: G 114 TYR cc_start: 0.8197 (t80) cc_final: 0.7347 (t80) REVERT: G 136 LYS cc_start: 0.8263 (mttm) cc_final: 0.7841 (mmtt) REVERT: G 163 THR cc_start: 0.8498 (m) cc_final: 0.8107 (p) REVERT: G 204 ARG cc_start: 0.8335 (ttm-80) cc_final: 0.7757 (ttm170) REVERT: G 239 LYS cc_start: 0.8893 (mmmt) cc_final: 0.8622 (mmmt) REVERT: G 303 ARG cc_start: 0.8343 (mtm110) cc_final: 0.8125 (mtm110) REVERT: G 319 VAL cc_start: 0.7622 (OUTLIER) cc_final: 0.7395 (p) REVERT: H 120 GLN cc_start: 0.7557 (OUTLIER) cc_final: 0.6785 (pp30) REVERT: H 121 LYS cc_start: 0.8074 (mmmt) cc_final: 0.6769 (mmmt) REVERT: H 165 GLU cc_start: 0.7366 (pp20) cc_final: 0.6908 (pp20) REVERT: H 184 GLU cc_start: 0.6486 (tm-30) cc_final: 0.6012 (tm-30) REVERT: H 272 GLU cc_start: 0.7042 (mp0) cc_final: 0.6632 (mp0) REVERT: H 279 ASN cc_start: 0.6839 (p0) cc_final: 0.6316 (p0) outliers start: 116 outliers final: 70 residues processed: 600 average time/residue: 0.1605 time to fit residues: 144.7727 Evaluate side-chains 580 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 497 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 101 ARG Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 176 ARG Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain I residue 2 PHE Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain I residue 25 PHE Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 38 LYS Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain I residue 85 LYS Chi-restraints excluded: chain I residue 88 LYS Chi-restraints excluded: chain I residue 99 PHE Chi-restraints excluded: chain I residue 101 ARG Chi-restraints excluded: chain I residue 104 GLU Chi-restraints excluded: chain I residue 141 HIS Chi-restraints excluded: chain I residue 143 TYR Chi-restraints excluded: chain I residue 145 LYS Chi-restraints excluded: chain I residue 155 TYR Chi-restraints excluded: chain I residue 159 LEU Chi-restraints excluded: chain I residue 169 PHE Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 226 SER Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 313 ILE Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 166 ASP Chi-restraints excluded: chain F residue 249 MET Chi-restraints excluded: chain F residue 252 GLN Chi-restraints excluded: chain F residue 272 GLU Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 325 ARG Chi-restraints excluded: chain C residue 146 ARG Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain G residue 39 LYS Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 109 CYS Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 229 MET Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 215 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 2 optimal weight: 0.5980 chunk 197 optimal weight: 2.9990 chunk 226 optimal weight: 0.7980 chunk 65 optimal weight: 10.0000 chunk 211 optimal weight: 0.7980 chunk 172 optimal weight: 0.8980 chunk 201 optimal weight: 0.9980 chunk 129 optimal weight: 0.0470 chunk 106 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 198 optimal weight: 0.7980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 159 HIS I 35 HIS D 178 ASN ** E 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 308 ASN C 195 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.160327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.125683 restraints weight = 30598.781| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.03 r_work: 0.3518 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21629 Z= 0.142 Angle : 0.546 12.321 29499 Z= 0.283 Chirality : 0.042 0.176 3293 Planarity : 0.005 0.074 3533 Dihedral : 15.037 179.281 3622 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.76 % Favored : 93.98 % Rotamer: Outliers : 5.13 % Allowed : 28.65 % Favored : 66.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: -0.49 (0.17), residues: 2394 helix: 0.64 (0.20), residues: 683 sheet: 0.48 (0.27), residues: 430 loop : -1.16 (0.17), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 291 TYR 0.020 0.001 TYR C 114 PHE 0.015 0.001 PHE H 200 TRP 0.009 0.001 TRP H 149 HIS 0.004 0.001 HIS I 141 Details of bonding type rmsd covalent geometry : bond 0.00329 (21629) covalent geometry : angle 0.54639 (29499) hydrogen bonds : bond 0.03847 ( 567) hydrogen bonds : angle 5.26140 ( 1542) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 491 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.6881 (tmm) cc_final: 0.6606 (tmm) REVERT: A 76 GLU cc_start: 0.5850 (OUTLIER) cc_final: 0.5523 (mp0) REVERT: A 104 MET cc_start: 0.5934 (ttp) cc_final: 0.5543 (ttp) REVERT: A 152 PHE cc_start: 0.8476 (t80) cc_final: 0.8260 (t80) REVERT: A 176 ARG cc_start: 0.7167 (OUTLIER) cc_final: 0.6555 (mmm160) REVERT: A 226 LYS cc_start: 0.8061 (mttm) cc_final: 0.7490 (mttm) REVERT: A 230 LYS cc_start: 0.8008 (OUTLIER) cc_final: 0.7421 (mptp) REVERT: A 283 GLU cc_start: 0.5950 (tm-30) cc_final: 0.5717 (tm-30) REVERT: B 96 ILE cc_start: 0.7016 (OUTLIER) cc_final: 0.6741 (pt) REVERT: B 97 MET cc_start: 0.6259 (tmm) cc_final: 0.5734 (tmm) REVERT: B 111 GLU cc_start: 0.8341 (tm-30) cc_final: 0.7555 (tm-30) REVERT: B 144 LYS cc_start: 0.8285 (mmtt) cc_final: 0.7987 (mmtt) REVERT: B 224 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7673 (mp) REVERT: B 234 GLU cc_start: 0.7510 (pm20) cc_final: 0.7293 (pm20) REVERT: I 1 MET cc_start: 0.4005 (tpt) cc_final: 0.3373 (tpt) REVERT: I 25 PHE cc_start: 0.7244 (OUTLIER) cc_final: 0.6913 (t80) REVERT: I 38 LYS cc_start: 0.2644 (OUTLIER) cc_final: 0.2363 (mmmt) REVERT: I 65 LYS cc_start: 0.6474 (OUTLIER) cc_final: 0.6224 (mttm) REVERT: I 85 LYS cc_start: 0.6467 (OUTLIER) cc_final: 0.5956 (tmtp) REVERT: I 99 PHE cc_start: 0.4322 (OUTLIER) cc_final: 0.3786 (t80) REVERT: I 104 GLU cc_start: 0.1416 (OUTLIER) cc_final: 0.0500 (pm20) REVERT: D 91 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.7938 (tp) REVERT: D 102 VAL cc_start: 0.8789 (OUTLIER) cc_final: 0.8562 (t) REVERT: D 224 TYR cc_start: 0.8293 (m-80) cc_final: 0.7998 (m-80) REVERT: D 238 LYS cc_start: 0.8094 (ttmm) cc_final: 0.7827 (ttmm) REVERT: E 119 TYR cc_start: 0.8583 (m-10) cc_final: 0.8294 (m-10) REVERT: E 125 TYR cc_start: 0.8170 (t80) cc_final: 0.7960 (t80) REVERT: E 292 PRO cc_start: 0.8127 (Cg_endo) cc_final: 0.7919 (Cg_exo) REVERT: E 299 LYS cc_start: 0.8512 (tppt) cc_final: 0.8130 (mmmm) REVERT: F 40 ARG cc_start: 0.8929 (ptt-90) cc_final: 0.8515 (ptt180) REVERT: F 119 TYR cc_start: 0.8115 (m-10) cc_final: 0.7906 (m-10) REVERT: F 252 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.8052 (pm20) REVERT: C 21 PHE cc_start: 0.8088 (m-80) cc_final: 0.7779 (m-80) REVERT: C 159 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8145 (mt-10) REVERT: C 165 GLU cc_start: 0.6457 (OUTLIER) cc_final: 0.5828 (pp20) REVERT: C 166 ASP cc_start: 0.6988 (p0) cc_final: 0.6701 (p0) REVERT: C 227 GLN cc_start: 0.8491 (tt0) cc_final: 0.8271 (mt0) REVERT: C 228 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7325 (mm-30) REVERT: G 114 TYR cc_start: 0.8214 (t80) cc_final: 0.7337 (t80) REVERT: G 136 LYS cc_start: 0.8270 (mttm) cc_final: 0.7863 (mmtt) REVERT: G 163 THR cc_start: 0.8486 (m) cc_final: 0.8086 (p) REVERT: G 204 ARG cc_start: 0.8343 (ttm-80) cc_final: 0.7767 (ttm170) REVERT: G 239 LYS cc_start: 0.8886 (mmmt) cc_final: 0.8649 (mmmt) REVERT: G 319 VAL cc_start: 0.7617 (OUTLIER) cc_final: 0.7388 (p) REVERT: H 120 GLN cc_start: 0.7575 (OUTLIER) cc_final: 0.6797 (pp30) REVERT: H 121 LYS cc_start: 0.8060 (mmmt) cc_final: 0.6752 (mmmt) REVERT: H 165 GLU cc_start: 0.7338 (pp20) cc_final: 0.6876 (pp20) REVERT: H 184 GLU cc_start: 0.6462 (tm-30) cc_final: 0.5973 (tm-30) REVERT: H 241 PHE cc_start: 0.7813 (t80) cc_final: 0.7610 (t80) REVERT: H 272 GLU cc_start: 0.7040 (mp0) cc_final: 0.6651 (mp0) REVERT: H 279 ASN cc_start: 0.6825 (p0) cc_final: 0.6306 (p0) outliers start: 111 outliers final: 71 residues processed: 574 average time/residue: 0.1615 time to fit residues: 138.7231 Evaluate side-chains 572 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 483 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 101 ARG Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 176 ARG Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain I residue 2 PHE Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 25 PHE Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 38 LYS Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain I residue 85 LYS Chi-restraints excluded: chain I residue 88 LYS Chi-restraints excluded: chain I residue 99 PHE Chi-restraints excluded: chain I residue 101 ARG Chi-restraints excluded: chain I residue 104 GLU Chi-restraints excluded: chain I residue 141 HIS Chi-restraints excluded: chain I residue 143 TYR Chi-restraints excluded: chain I residue 145 LYS Chi-restraints excluded: chain I residue 155 TYR Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 159 LEU Chi-restraints excluded: chain I residue 169 PHE Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 226 SER Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 313 ILE Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 166 ASP Chi-restraints excluded: chain F residue 249 MET Chi-restraints excluded: chain F residue 252 GLN Chi-restraints excluded: chain F residue 272 GLU Chi-restraints excluded: chain F residue 325 ARG Chi-restraints excluded: chain C residue 146 ARG Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 108 SER Chi-restraints excluded: chain G residue 109 CYS Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 229 MET Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 215 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 63 optimal weight: 0.7980 chunk 102 optimal weight: 0.5980 chunk 150 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 59 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 241 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 chunk 166 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN A 159 HIS B 73 GLN D 178 ASN E 208 ASN E 308 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.159350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.124785 restraints weight = 30471.874| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.02 r_work: 0.3509 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 21629 Z= 0.159 Angle : 0.561 14.461 29499 Z= 0.288 Chirality : 0.042 0.171 3293 Planarity : 0.005 0.071 3533 Dihedral : 14.987 179.191 3622 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.64 % Favored : 94.11 % Rotamer: Outliers : 5.08 % Allowed : 28.65 % Favored : 66.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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 (0.17), residues: 2394 helix: 0.63 (0.20), residues: 683 sheet: 0.57 (0.27), residues: 421 loop : -1.14 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 291 TYR 0.020 0.001 TYR C 114 PHE 0.017 0.001 PHE H 200 TRP 0.016 0.001 TRP A 208 HIS 0.004 0.001 HIS I 141 Details of bonding type rmsd covalent geometry : bond 0.00373 (21629) covalent geometry : angle 0.56061 (29499) hydrogen bonds : bond 0.03853 ( 567) hydrogen bonds : angle 5.27886 ( 1542) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 486 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.6922 (tmm) cc_final: 0.6611 (tmm) REVERT: A 104 MET cc_start: 0.5937 (ttp) cc_final: 0.5568 (ttp) REVERT: A 152 PHE cc_start: 0.8500 (t80) cc_final: 0.8300 (t80) REVERT: A 176 ARG cc_start: 0.7214 (OUTLIER) cc_final: 0.6638 (mmm160) REVERT: A 226 LYS cc_start: 0.8100 (mttm) cc_final: 0.7519 (mttm) REVERT: A 230 LYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7462 (mptp) REVERT: A 241 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7203 (mp0) REVERT: A 283 GLU cc_start: 0.6005 (tm-30) cc_final: 0.5755 (tm-30) REVERT: A 294 TYR cc_start: 0.6086 (m-80) cc_final: 0.5586 (m-80) REVERT: B 96 ILE cc_start: 0.7062 (OUTLIER) cc_final: 0.6785 (pt) REVERT: B 97 MET cc_start: 0.6279 (tmm) cc_final: 0.5776 (tmm) REVERT: B 111 GLU cc_start: 0.8370 (tm-30) cc_final: 0.7588 (tm-30) REVERT: B 144 LYS cc_start: 0.8332 (mmtt) cc_final: 0.8060 (mmtt) REVERT: B 209 ARG cc_start: 0.6299 (OUTLIER) cc_final: 0.5784 (ttt180) REVERT: B 213 LYS cc_start: 0.8225 (mttp) cc_final: 0.8017 (mttp) REVERT: B 224 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7715 (mp) REVERT: B 234 GLU cc_start: 0.7551 (pm20) cc_final: 0.7337 (pm20) REVERT: I 1 MET cc_start: 0.4002 (tpt) cc_final: 0.3349 (tpt) REVERT: I 25 PHE cc_start: 0.7306 (OUTLIER) cc_final: 0.6976 (t80) REVERT: I 38 LYS cc_start: 0.2637 (OUTLIER) cc_final: 0.2355 (mmmt) REVERT: I 65 LYS cc_start: 0.6405 (OUTLIER) cc_final: 0.6122 (mttm) REVERT: I 85 LYS cc_start: 0.6428 (OUTLIER) cc_final: 0.5920 (tmtp) REVERT: I 99 PHE cc_start: 0.4322 (OUTLIER) cc_final: 0.3797 (t80) REVERT: I 104 GLU cc_start: 0.1317 (OUTLIER) cc_final: 0.0431 (pm20) REVERT: D 91 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7926 (tp) REVERT: D 102 VAL cc_start: 0.8829 (OUTLIER) cc_final: 0.8586 (t) REVERT: D 224 TYR cc_start: 0.8278 (m-80) cc_final: 0.7997 (m-80) REVERT: D 238 LYS cc_start: 0.8091 (ttmm) cc_final: 0.7832 (ttmm) REVERT: E 119 TYR cc_start: 0.8622 (m-10) cc_final: 0.8318 (m-10) REVERT: E 292 PRO cc_start: 0.8126 (Cg_endo) cc_final: 0.7922 (Cg_exo) REVERT: E 299 LYS cc_start: 0.8560 (tppt) cc_final: 0.8191 (mmmm) REVERT: F 40 ARG cc_start: 0.8936 (ptt-90) cc_final: 0.8584 (ptt180) REVERT: F 252 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.8089 (pm20) REVERT: C 21 PHE cc_start: 0.8100 (m-80) cc_final: 0.7802 (m-80) REVERT: C 165 GLU cc_start: 0.6482 (OUTLIER) cc_final: 0.5858 (pp20) REVERT: C 166 ASP cc_start: 0.6966 (p0) cc_final: 0.6661 (p0) REVERT: C 228 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7354 (mm-30) REVERT: G 114 TYR cc_start: 0.8207 (t80) cc_final: 0.7337 (t80) REVERT: G 136 LYS cc_start: 0.8315 (mttm) cc_final: 0.7906 (mmtt) REVERT: G 163 THR cc_start: 0.8484 (m) cc_final: 0.8083 (p) REVERT: G 204 ARG cc_start: 0.8356 (ttm-80) cc_final: 0.7791 (ttm170) REVERT: G 239 LYS cc_start: 0.8900 (mmmt) cc_final: 0.8683 (mmmt) REVERT: G 319 VAL cc_start: 0.7646 (OUTLIER) cc_final: 0.7429 (p) REVERT: H 115 ARG cc_start: 0.7840 (tpp80) cc_final: 0.7413 (tpp80) REVERT: H 120 GLN cc_start: 0.7577 (OUTLIER) cc_final: 0.6808 (pp30) REVERT: H 121 LYS cc_start: 0.8092 (mmmt) cc_final: 0.6803 (mmmt) REVERT: H 165 GLU cc_start: 0.7339 (pp20) cc_final: 0.6872 (pp20) REVERT: H 184 GLU cc_start: 0.6503 (tm-30) cc_final: 0.6024 (tm-30) REVERT: H 259 ARG cc_start: 0.6723 (ttp-170) cc_final: 0.6279 (ttp80) REVERT: H 272 GLU cc_start: 0.7093 (mp0) cc_final: 0.6698 (mp0) REVERT: H 279 ASN cc_start: 0.6893 (p0) cc_final: 0.6382 (p0) REVERT: H 325 ARG cc_start: 0.7356 (OUTLIER) cc_final: 0.7136 (ttt-90) outliers start: 110 outliers final: 79 residues processed: 571 average time/residue: 0.1667 time to fit residues: 141.7618 Evaluate side-chains 573 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 475 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 101 ARG Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 176 ARG Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 209 ARG Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain I residue 2 PHE Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 25 PHE Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 38 LYS Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain I residue 85 LYS Chi-restraints excluded: chain I residue 88 LYS Chi-restraints excluded: chain I residue 99 PHE Chi-restraints excluded: chain I residue 101 ARG Chi-restraints excluded: chain I residue 104 GLU Chi-restraints excluded: chain I residue 141 HIS Chi-restraints excluded: chain I residue 143 TYR Chi-restraints excluded: chain I residue 145 LYS Chi-restraints excluded: chain I residue 155 TYR Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 159 LEU Chi-restraints excluded: chain I residue 169 PHE Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 226 SER Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 176 SER Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 313 ILE Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 166 ASP Chi-restraints excluded: chain F residue 249 MET Chi-restraints excluded: chain F residue 252 GLN Chi-restraints excluded: chain F residue 272 GLU Chi-restraints excluded: chain F residue 325 ARG Chi-restraints excluded: chain C residue 146 ARG Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 108 SER Chi-restraints excluded: chain G residue 109 CYS Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 229 MET Chi-restraints excluded: chain G residue 249 MET Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain G residue 275 ILE Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 261 ILE Chi-restraints excluded: chain H residue 325 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 56 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 220 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 chunk 9 optimal weight: 9.9990 chunk 172 optimal weight: 0.8980 chunk 162 optimal weight: 0.2980 chunk 86 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 HIS A 213 GLN D 178 ASN E 308 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.159251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.124701 restraints weight = 30542.172| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.03 r_work: 0.3514 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 21629 Z= 0.161 Angle : 0.560 14.243 29499 Z= 0.288 Chirality : 0.042 0.167 3293 Planarity : 0.005 0.074 3533 Dihedral : 14.953 179.288 3622 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.85 % Favored : 93.90 % Rotamer: Outliers : 5.41 % Allowed : 28.42 % Favored : 66.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: -0.44 (0.17), residues: 2394 helix: 0.69 (0.20), residues: 670 sheet: 0.56 (0.27), residues: 423 loop : -1.13 (0.17), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 291 TYR 0.020 0.001 TYR A 171 PHE 0.018 0.001 PHE A 146 TRP 0.017 0.001 TRP A 208 HIS 0.004 0.001 HIS I 141 Details of bonding type rmsd covalent geometry : bond 0.00377 (21629) covalent geometry : angle 0.56018 (29499) hydrogen bonds : bond 0.03871 ( 567) hydrogen bonds : angle 5.27128 ( 1542) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 475 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.6886 (tmm) cc_final: 0.6565 (tmm) REVERT: A 104 MET cc_start: 0.5882 (ttp) cc_final: 0.5570 (ttp) REVERT: A 176 ARG cc_start: 0.7163 (OUTLIER) cc_final: 0.6582 (mmm160) REVERT: A 226 LYS cc_start: 0.8114 (mttm) cc_final: 0.7548 (mttm) REVERT: A 230 LYS cc_start: 0.8012 (OUTLIER) cc_final: 0.7486 (mptp) REVERT: A 241 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7215 (mp0) REVERT: A 283 GLU cc_start: 0.6059 (tm-30) cc_final: 0.5810 (tm-30) REVERT: B 97 MET cc_start: 0.6244 (tmm) cc_final: 0.5746 (tmm) REVERT: B 111 GLU cc_start: 0.8372 (tm-30) cc_final: 0.7597 (tm-30) REVERT: B 144 LYS cc_start: 0.8298 (mmtt) cc_final: 0.8021 (mmtt) REVERT: B 209 ARG cc_start: 0.6343 (OUTLIER) cc_final: 0.5970 (ttt180) REVERT: B 213 LYS cc_start: 0.8233 (mttp) cc_final: 0.8010 (mttp) REVERT: B 224 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7700 (mp) REVERT: B 234 GLU cc_start: 0.7569 (pm20) cc_final: 0.7356 (pm20) REVERT: I 25 PHE cc_start: 0.7237 (OUTLIER) cc_final: 0.6917 (t80) REVERT: I 65 LYS cc_start: 0.6416 (OUTLIER) cc_final: 0.6131 (mttm) REVERT: I 85 LYS cc_start: 0.6409 (OUTLIER) cc_final: 0.5909 (tmtp) REVERT: I 99 PHE cc_start: 0.4349 (OUTLIER) cc_final: 0.3817 (t80) REVERT: I 104 GLU cc_start: 0.1389 (OUTLIER) cc_final: 0.0494 (pm20) REVERT: D 91 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.7931 (tp) REVERT: D 102 VAL cc_start: 0.8831 (OUTLIER) cc_final: 0.8587 (t) REVERT: D 224 TYR cc_start: 0.8279 (m-80) cc_final: 0.7996 (m-80) REVERT: D 238 LYS cc_start: 0.8077 (ttmm) cc_final: 0.7822 (ttmm) REVERT: E 119 TYR cc_start: 0.8613 (m-10) cc_final: 0.8316 (m-10) REVERT: E 125 TYR cc_start: 0.8217 (t80) cc_final: 0.8004 (t80) REVERT: E 292 PRO cc_start: 0.8121 (Cg_endo) cc_final: 0.7916 (Cg_exo) REVERT: E 299 LYS cc_start: 0.8551 (tppt) cc_final: 0.8181 (mmmm) REVERT: F 40 ARG cc_start: 0.8941 (ptt-90) cc_final: 0.8595 (ptt180) REVERT: F 150 ARG cc_start: 0.8458 (ttt180) cc_final: 0.8226 (mtp180) REVERT: F 252 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.8090 (pm20) REVERT: C 21 PHE cc_start: 0.8100 (m-80) cc_final: 0.7809 (m-80) REVERT: C 165 GLU cc_start: 0.6383 (OUTLIER) cc_final: 0.5790 (pp20) REVERT: C 166 ASP cc_start: 0.6947 (p0) cc_final: 0.6651 (p0) REVERT: C 228 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7324 (mm-30) REVERT: G 114 TYR cc_start: 0.8212 (t80) cc_final: 0.7345 (t80) REVERT: G 204 ARG cc_start: 0.8339 (ttm-80) cc_final: 0.7764 (ttm170) REVERT: G 239 LYS cc_start: 0.8903 (mmmt) cc_final: 0.8682 (mmmt) REVERT: G 319 VAL cc_start: 0.7681 (OUTLIER) cc_final: 0.7467 (p) REVERT: H 115 ARG cc_start: 0.7795 (tpp80) cc_final: 0.7191 (tpp80) REVERT: H 120 GLN cc_start: 0.7588 (OUTLIER) cc_final: 0.6832 (pp30) REVERT: H 121 LYS cc_start: 0.8096 (mmmt) cc_final: 0.6807 (mmmt) REVERT: H 165 GLU cc_start: 0.7277 (pp20) cc_final: 0.6797 (pp20) REVERT: H 184 GLU cc_start: 0.6539 (tm-30) cc_final: 0.6071 (tm-30) REVERT: H 259 ARG cc_start: 0.6755 (ttp-170) cc_final: 0.6317 (ttp80) REVERT: H 272 GLU cc_start: 0.7105 (mp0) cc_final: 0.6691 (mp0) REVERT: H 279 ASN cc_start: 0.6917 (p0) cc_final: 0.6420 (p0) REVERT: H 308 ASN cc_start: 0.7342 (t0) cc_final: 0.7107 (t0) REVERT: H 325 ARG cc_start: 0.7380 (OUTLIER) cc_final: 0.7141 (ttt-90) outliers start: 117 outliers final: 84 residues processed: 569 average time/residue: 0.1633 time to fit residues: 138.6631 Evaluate side-chains 572 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 471 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 101 ARG Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 176 ARG Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 209 ARG Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain I residue 2 PHE Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain I residue 25 PHE Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain I residue 85 LYS Chi-restraints excluded: chain I residue 88 LYS Chi-restraints excluded: chain I residue 99 PHE Chi-restraints excluded: chain I residue 101 ARG Chi-restraints excluded: chain I residue 104 GLU Chi-restraints excluded: chain I residue 141 HIS Chi-restraints excluded: chain I residue 143 TYR Chi-restraints excluded: chain I residue 145 LYS Chi-restraints excluded: chain I residue 155 TYR Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 159 LEU Chi-restraints excluded: chain I residue 169 PHE Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 226 SER Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 176 SER Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 313 ILE Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 166 ASP Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 249 MET Chi-restraints excluded: chain F residue 252 GLN Chi-restraints excluded: chain F residue 272 GLU Chi-restraints excluded: chain F residue 325 ARG Chi-restraints excluded: chain C residue 146 ARG Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 108 SER Chi-restraints excluded: chain G residue 109 CYS Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 229 MET Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain G residue 275 ILE Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 261 ILE Chi-restraints excluded: chain H residue 286 ILE Chi-restraints excluded: chain H residue 325 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 22 optimal weight: 4.9990 chunk 191 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 140 optimal weight: 0.2980 chunk 193 optimal weight: 0.5980 chunk 109 optimal weight: 1.9990 chunk 1 optimal weight: 0.3980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 HIS A 213 GLN ** B 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 178 ASN E 308 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.160611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.126093 restraints weight = 30726.165| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.04 r_work: 0.3525 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21629 Z= 0.131 Angle : 0.554 14.125 29499 Z= 0.284 Chirality : 0.042 0.167 3293 Planarity : 0.005 0.072 3533 Dihedral : 14.885 179.669 3622 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.68 % Favored : 94.07 % Rotamer: Outliers : 4.81 % Allowed : 29.25 % Favored : 65.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: -0.38 (0.17), residues: 2394 helix: 0.77 (0.20), residues: 671 sheet: 0.60 (0.27), residues: 417 loop : -1.11 (0.17), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 92 TYR 0.018 0.001 TYR I 83 PHE 0.017 0.001 PHE H 95 TRP 0.016 0.001 TRP A 208 HIS 0.003 0.001 HIS I 35 Details of bonding type rmsd covalent geometry : bond 0.00306 (21629) covalent geometry : angle 0.55384 (29499) hydrogen bonds : bond 0.03692 ( 567) hydrogen bonds : angle 5.16122 ( 1542) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 473 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.6873 (tmm) cc_final: 0.6526 (tmm) REVERT: A 104 MET cc_start: 0.5937 (ttp) cc_final: 0.5619 (ttp) REVERT: A 152 PHE cc_start: 0.8413 (t80) cc_final: 0.7684 (t80) REVERT: A 176 ARG cc_start: 0.7170 (OUTLIER) cc_final: 0.6638 (mmm160) REVERT: A 226 LYS cc_start: 0.8028 (mttm) cc_final: 0.7472 (mttm) REVERT: A 230 LYS cc_start: 0.8014 (OUTLIER) cc_final: 0.7459 (mptp) REVERT: A 241 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7226 (mp0) REVERT: A 283 GLU cc_start: 0.6035 (tm-30) cc_final: 0.5772 (tm-30) REVERT: B 97 MET cc_start: 0.6195 (tmm) cc_final: 0.5820 (tmm) REVERT: B 111 GLU cc_start: 0.8369 (tm-30) cc_final: 0.7613 (tm-30) REVERT: B 144 LYS cc_start: 0.8295 (mmtt) cc_final: 0.8041 (mmtt) REVERT: B 209 ARG cc_start: 0.6129 (OUTLIER) cc_final: 0.5863 (ttt180) REVERT: B 213 LYS cc_start: 0.8172 (mttp) cc_final: 0.7947 (mttp) REVERT: B 224 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7660 (mp) REVERT: I 25 PHE cc_start: 0.7274 (OUTLIER) cc_final: 0.6952 (t80) REVERT: I 65 LYS cc_start: 0.6393 (OUTLIER) cc_final: 0.6088 (mttm) REVERT: I 85 LYS cc_start: 0.6374 (OUTLIER) cc_final: 0.5880 (tmtp) REVERT: I 99 PHE cc_start: 0.4329 (OUTLIER) cc_final: 0.3797 (t80) REVERT: I 104 GLU cc_start: 0.1199 (OUTLIER) cc_final: 0.0437 (pm20) REVERT: D 91 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7919 (tp) REVERT: D 102 VAL cc_start: 0.8821 (OUTLIER) cc_final: 0.8597 (t) REVERT: D 224 TYR cc_start: 0.8289 (m-80) cc_final: 0.8010 (m-80) REVERT: E 18 ASN cc_start: 0.7967 (t0) cc_final: 0.7505 (t0) REVERT: E 119 TYR cc_start: 0.8588 (m-10) cc_final: 0.8341 (m-10) REVERT: E 125 TYR cc_start: 0.8207 (t80) cc_final: 0.7993 (t80) REVERT: E 265 TYR cc_start: 0.8297 (p90) cc_final: 0.7493 (p90) REVERT: E 292 PRO cc_start: 0.8090 (Cg_endo) cc_final: 0.7876 (Cg_exo) REVERT: F 40 ARG cc_start: 0.8934 (ptt-90) cc_final: 0.8597 (ptt180) REVERT: F 252 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.8165 (pm20) REVERT: C 21 PHE cc_start: 0.8094 (m-80) cc_final: 0.7798 (m-80) REVERT: C 165 GLU cc_start: 0.6391 (OUTLIER) cc_final: 0.5796 (pp20) REVERT: C 166 ASP cc_start: 0.6933 (p0) cc_final: 0.6644 (p0) REVERT: C 228 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7287 (mm-30) REVERT: G 114 TYR cc_start: 0.8190 (t80) cc_final: 0.7308 (t80) REVERT: G 163 THR cc_start: 0.8479 (m) cc_final: 0.8075 (p) REVERT: G 204 ARG cc_start: 0.8391 (ttm-80) cc_final: 0.7778 (ttm170) REVERT: G 319 VAL cc_start: 0.7667 (OUTLIER) cc_final: 0.7441 (p) REVERT: H 115 ARG cc_start: 0.7792 (tpp80) cc_final: 0.7119 (tpp80) REVERT: H 120 GLN cc_start: 0.7563 (OUTLIER) cc_final: 0.6807 (pp30) REVERT: H 121 LYS cc_start: 0.8105 (mmmt) cc_final: 0.6816 (mmmt) REVERT: H 165 GLU cc_start: 0.7266 (pp20) cc_final: 0.6775 (pp20) REVERT: H 184 GLU cc_start: 0.6529 (tm-30) cc_final: 0.6039 (tm-30) REVERT: H 272 GLU cc_start: 0.7073 (mp0) cc_final: 0.6631 (mp0) REVERT: H 279 ASN cc_start: 0.6903 (p0) cc_final: 0.6410 (p0) REVERT: H 308 ASN cc_start: 0.7322 (t0) cc_final: 0.7074 (t0) outliers start: 104 outliers final: 82 residues processed: 552 average time/residue: 0.1701 time to fit residues: 139.4912 Evaluate side-chains 568 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 470 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 101 ARG Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 176 ARG Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 209 ARG Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain I residue 25 PHE Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain I residue 85 LYS Chi-restraints excluded: chain I residue 88 LYS Chi-restraints excluded: chain I residue 99 PHE Chi-restraints excluded: chain I residue 101 ARG Chi-restraints excluded: chain I residue 104 GLU Chi-restraints excluded: chain I residue 141 HIS Chi-restraints excluded: chain I residue 143 TYR Chi-restraints excluded: chain I residue 145 LYS Chi-restraints excluded: chain I residue 155 TYR Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 159 LEU Chi-restraints excluded: chain I residue 169 PHE Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 226 SER Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 176 SER Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 313 ILE Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 166 ASP Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 249 MET Chi-restraints excluded: chain F residue 252 GLN Chi-restraints excluded: chain F residue 272 GLU Chi-restraints excluded: chain F residue 325 ARG Chi-restraints excluded: chain C residue 146 ARG Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 108 SER Chi-restraints excluded: chain G residue 109 CYS Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 229 MET Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain G residue 275 ILE Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 286 ILE Chi-restraints excluded: chain H residue 300 LEU Chi-restraints excluded: chain H residue 325 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 48 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 64 optimal weight: 8.9990 chunk 221 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 184 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 HIS D 26 ASN D 178 ASN D 195 GLN E 308 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.159354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.124838 restraints weight = 30537.627| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.03 r_work: 0.3507 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 21629 Z= 0.168 Angle : 0.571 13.844 29499 Z= 0.293 Chirality : 0.043 0.164 3293 Planarity : 0.005 0.074 3533 Dihedral : 14.837 179.730 3620 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.97 % Favored : 93.82 % Rotamer: Outliers : 4.94 % Allowed : 28.93 % Favored : 66.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: -0.41 (0.17), residues: 2394 helix: 0.71 (0.20), residues: 670 sheet: 0.53 (0.27), residues: 423 loop : -1.10 (0.17), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 92 TYR 0.019 0.001 TYR C 114 PHE 0.018 0.001 PHE H 95 TRP 0.014 0.001 TRP A 208 HIS 0.009 0.001 HIS G 41 Details of bonding type rmsd covalent geometry : bond 0.00395 (21629) covalent geometry : angle 0.57080 (29499) hydrogen bonds : bond 0.03900 ( 567) hydrogen bonds : angle 5.19811 ( 1542) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7131.80 seconds wall clock time: 122 minutes 24.13 seconds (7344.13 seconds total)