Starting phenix.real_space_refine on Sat Jul 4 14:29:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sjo_54950/07_2026/9sjo_54950.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sjo_54950/07_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_54950/07_2026/9sjo_54950.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sjo_54950/07_2026/9sjo_54950.map" model { file = "/net/cci-nas-00/data/ceres_data/9sjo_54950/07_2026/9sjo_54950.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sjo_54950/07_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-6108/lib/python3.11/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: 4.69, per 1000 atoms: 0.22 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: 1.82 Conformation dependent library (CDL) restraints added in 801.3 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: 2.39 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: 3.09 Time building geometry restraints manager: 2.36 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: 5.320 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: 0.460 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 20.880 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 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= 0.272 Angle : 0.717 17.042 29499 Z= 0.436 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/Z covalent geometry : bond 0.00501 / 0.27 (21629) covalent geometry : angle 0.71724 / 0.44 (29499) hydrogen bonds : bond 0.15610 / 10.23 ( 567) hydrogen bonds : angle 7.03498 / 4.76 ( 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 : 0.823 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: 0.1688 time to fit residues: 150.8039 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 : 0.875 ------------------------------------------------------------------------------- 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... A 34 ASN A 71 ASN A 159 HIS B 53 ASN I 4 GLN I 29 HIS I 166 HIS C 18 ASN G 34 GLN H 308 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.157632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.123554 restraints weight = 30957.609| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.04 r_work: 0.3473 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.0807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 21629 Z= 0.201 Angle : 0.614 15.662 29499 Z= 0.324 Chirality : 0.044 0.205 3293 Planarity : 0.005 0.077 3533 Dihedral : 16.419 177.168 3772 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.35 % Favored : 93.32 % Rotamer: Outliers : 5.73 % Allowed : 26.02 % Favored : 68.25 % 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: -0.92 (0.17), residues: 2394 helix: 0.11 (0.20), residues: 695 sheet: 0.37 (0.26), residues: 427 loop : -1.39 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 291 TYR 0.021 0.001 TYR A 171 PHE 0.023 0.002 PHE A 212 TRP 0.011 0.001 TRP A 74 HIS 0.004 0.001 HIS G 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.20 (21629) covalent geometry : angle 0.61407 / 0.32 (29499) hydrogen bonds : bond 0.05000 / 3.28 ( 567) hydrogen bonds : angle 5.96685 / 4.01 ( 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 635 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 511 time to evaluate : 0.613 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: 0.3666 (OUTLIER) cc_final: 0.3457 (pt) REVERT: A 62 MET cc_start: 0.7047 (tmm) cc_final: 0.6615 (tmm) REVERT: A 71 ASN cc_start: 0.8196 (t0) cc_final: 0.7953 (t0) REVERT: A 176 ARG cc_start: 0.6720 (OUTLIER) cc_final: 0.6140 (mmm160) REVERT: B 96 ILE cc_start: 0.7009 (OUTLIER) cc_final: 0.6745 (pt) REVERT: B 97 MET cc_start: 0.6405 (tmm) cc_final: 0.5515 (tmm) REVERT: B 144 LYS cc_start: 0.8366 (mmtt) cc_final: 0.8055 (mmtt) REVERT: B 209 ARG cc_start: 0.6477 (OUTLIER) cc_final: 0.4913 (ttt180) REVERT: B 246 GLU cc_start: 0.6459 (mm-30) cc_final: 0.6079 (mp0) REVERT: I 25 PHE cc_start: 0.7498 (OUTLIER) cc_final: 0.7121 (t80) REVERT: I 58 ILE cc_start: 0.6875 (OUTLIER) cc_final: 0.6601 (mm) REVERT: I 85 LYS cc_start: 0.6442 (OUTLIER) cc_final: 0.6010 (tmtp) REVERT: I 99 PHE cc_start: 0.4533 (OUTLIER) cc_final: 0.4155 (m-80) REVERT: D 210 TYR cc_start: 0.8406 (m-80) cc_final: 0.7754 (m-80) REVERT: D 238 LYS cc_start: 0.8127 (ttmm) cc_final: 0.7807 (tttm) REVERT: E 91 LEU cc_start: 0.8444 (tp) cc_final: 0.8142 (tp) REVERT: E 115 ARG cc_start: 0.8026 (ttp80) cc_final: 0.7795 (ttp80) REVERT: E 119 TYR cc_start: 0.8669 (m-10) cc_final: 0.8346 (m-10) REVERT: E 228 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7720 (mm-30) REVERT: E 279 ASN cc_start: 0.8335 (m-40) cc_final: 0.8118 (m-40) REVERT: E 299 LYS cc_start: 0.8546 (tppt) cc_final: 0.8163 (mmmm) REVERT: F 40 ARG cc_start: 0.8945 (ptt-90) cc_final: 0.8553 (ptt90) REVERT: F 316 LYS cc_start: 0.7847 (mttt) cc_final: 0.7644 (mttt) REVERT: C 184 GLU cc_start: 0.7781 (mp0) cc_final: 0.7328 (mp0) REVERT: G 125 TYR cc_start: 0.8068 (t80) cc_final: 0.7813 (t80) REVERT: G 239 LYS cc_start: 0.8920 (mmmt) cc_final: 0.8655 (mmmt) REVERT: H 114 TYR cc_start: 0.7030 (t80) cc_final: 0.6773 (t80) REVERT: H 120 GLN cc_start: 0.7497 (OUTLIER) cc_final: 0.6784 (pp30) REVERT: H 121 LYS cc_start: 0.8152 (mmmt) cc_final: 0.6826 (mmmt) REVERT: H 125 TYR cc_start: 0.8142 (t80) cc_final: 0.7850 (t80) REVERT: H 192 ILE cc_start: 0.8195 (OUTLIER) cc_final: 0.7955 (mp) REVERT: H 252 GLN cc_start: 0.7855 (mp10) cc_final: 0.7632 (mp10) REVERT: H 271 TYR cc_start: 0.7990 (m-80) cc_final: 0.7373 (m-80) REVERT: H 272 GLU cc_start: 0.6792 (mp0) cc_final: 0.6419 (mp0) outliers start: 124 outliers final: 72 residues processed: 606 average time/residue: 0.1656 time to fit residues: 149.3994 Evaluate side-chains 575 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 493 time to evaluate : 0.747 ------------------------------------------------------------------------------- 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 95 MET 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 161 LEU Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 176 ARG Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain A residue 239 ILE 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 205 VAL Chi-restraints excluded: chain B residue 209 ARG 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 29 HIS 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 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 175 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 226 SER Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 313 ILE Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 166 ASP Chi-restraints excluded: chain F residue 249 MET Chi-restraints excluded: chain F residue 325 ARG Chi-restraints excluded: chain C residue 51 ASP 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 C residue 328 MET Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 105 SER 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 251 SER Chi-restraints excluded: chain G residue 310 ASP Chi-restraints excluded: chain G residue 311 LEU Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain H residue 192 ILE Chi-restraints excluded: chain H residue 205 GLU 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: 0.7980 chunk 131 optimal weight: 0.7980 chunk 61 optimal weight: 10.0000 chunk 95 optimal weight: 1.9990 chunk 157 optimal weight: 0.6980 chunk 3 optimal weight: 5.9990 chunk 96 optimal weight: 0.5980 chunk 187 optimal weight: 1.9990 chunk 198 optimal weight: 0.8980 chunk 200 optimal weight: 0.7980 chunk 189 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 ASN A 159 HIS A 213 GLN I 29 HIS 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 = 0.4033 r_free = 0.4033 target = 0.158121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.124060 restraints weight = 31044.292| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.04 r_work: 0.3478 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 21629 Z= 0.166 Angle : 0.575 14.728 29499 Z= 0.303 Chirality : 0.043 0.198 3293 Planarity : 0.005 0.072 3533 Dihedral : 15.918 178.550 3675 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.10 % Favored : 93.65 % Rotamer: Outliers : 6.19 % Allowed : 26.62 % Favored : 67.19 % 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: -0.86 (0.17), residues: 2394 helix: 0.18 (0.19), residues: 698 sheet: 0.36 (0.27), residues: 420 loop : -1.34 (0.17), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 303 TYR 0.018 0.001 TYR A 171 PHE 0.022 0.001 PHE A 212 TRP 0.014 0.001 TRP A 74 HIS 0.007 0.001 HIS I 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 (21629) covalent geometry : angle 0.57489 / 0.30 (29499) hydrogen bonds : bond 0.04511 / 2.98 ( 567) hydrogen bonds : angle 5.67294 / 3.80 ( 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 631 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 497 time to evaluate : 0.654 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: 0.6921 (tmm) cc_final: 0.6670 (tmm) REVERT: A 176 ARG cc_start: 0.6843 (OUTLIER) cc_final: 0.6331 (mmm160) REVERT: A 230 LYS cc_start: 0.7937 (OUTLIER) cc_final: 0.7430 (mptp) REVERT: B 96 ILE cc_start: 0.6997 (OUTLIER) cc_final: 0.6741 (pt) REVERT: B 97 MET cc_start: 0.6395 (tmm) cc_final: 0.5746 (tmm) REVERT: B 144 LYS cc_start: 0.8346 (mmtt) cc_final: 0.8039 (mmtt) REVERT: B 209 ARG cc_start: 0.6441 (OUTLIER) cc_final: 0.4712 (ttt180) REVERT: B 246 GLU cc_start: 0.6414 (mm-30) cc_final: 0.6019 (mp0) REVERT: I 25 PHE cc_start: 0.7413 (OUTLIER) cc_final: 0.7062 (t80) REVERT: I 38 LYS cc_start: 0.2319 (OUTLIER) cc_final: 0.1794 (tptp) REVERT: I 58 ILE cc_start: 0.6856 (OUTLIER) cc_final: 0.6559 (mm) REVERT: I 85 LYS cc_start: 0.6477 (OUTLIER) cc_final: 0.5965 (tmtp) REVERT: I 99 PHE cc_start: 0.4527 (OUTLIER) cc_final: 0.4130 (m-80) REVERT: D 105 SER cc_start: 0.8225 (OUTLIER) cc_final: 0.7937 (p) REVERT: D 238 LYS cc_start: 0.8119 (ttmm) cc_final: 0.7859 (ttmm) REVERT: E 91 LEU cc_start: 0.8459 (tp) cc_final: 0.8136 (tp) REVERT: E 119 TYR cc_start: 0.8633 (m-10) cc_final: 0.8378 (m-10) REVERT: E 129 ASP cc_start: 0.7971 (t0) cc_final: 0.7734 (t0) REVERT: E 222 GLU cc_start: 0.7873 (tt0) cc_final: 0.7644 (tt0) REVERT: E 228 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7724 (mm-30) REVERT: E 279 ASN cc_start: 0.8342 (m-40) cc_final: 0.8128 (m-40) REVERT: E 299 LYS cc_start: 0.8539 (tppt) cc_final: 0.8148 (mmmm) REVERT: F 40 ARG cc_start: 0.8948 (ptt-90) cc_final: 0.8570 (ptt90) REVERT: F 303 ARG cc_start: 0.8344 (ttp80) cc_final: 0.8132 (mtp85) REVERT: C 169 TYR cc_start: 0.8729 (m-80) cc_final: 0.8411 (m-80) REVERT: C 184 GLU cc_start: 0.7792 (mp0) cc_final: 0.7333 (mp0) REVERT: G 136 LYS cc_start: 0.8297 (mttm) cc_final: 0.7889 (mmtt) REVERT: G 239 LYS cc_start: 0.8913 (mmmt) cc_final: 0.8607 (mmmt) REVERT: H 120 GLN cc_start: 0.7500 (OUTLIER) cc_final: 0.6782 (pp30) REVERT: H 121 LYS cc_start: 0.8126 (mmmt) cc_final: 0.6772 (mmmt) REVERT: H 184 GLU cc_start: 0.6231 (tm-30) cc_final: 0.5785 (tm-30) REVERT: H 192 ILE cc_start: 0.8195 (OUTLIER) cc_final: 0.7957 (mp) REVERT: H 206 TYR cc_start: 0.8424 (p90) cc_final: 0.8104 (p90) REVERT: H 271 TYR cc_start: 0.8002 (m-80) cc_final: 0.7525 (m-80) REVERT: H 272 GLU cc_start: 0.6828 (mp0) cc_final: 0.6488 (mp0) outliers start: 134 outliers final: 79 residues processed: 597 average time/residue: 0.1695 time to fit residues: 150.6279 Evaluate side-chains 575 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 484 time to evaluate : 0.767 ------------------------------------------------------------------------------- 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 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 127 GLU 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 159 HIS 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 222 LYS Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 256 LEU 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 38 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 175 LEU Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 226 SER Chi-restraints excluded: chain D residue 267 ASP 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 90 THR Chi-restraints excluded: chain E residue 171 SER Chi-restraints excluded: chain E residue 176 SER Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 251 SER Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 166 ASP Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 325 ARG Chi-restraints excluded: chain F residue 328 MET Chi-restraints excluded: chain C residue 51 ASP 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 48 LEU 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 310 ASP Chi-restraints excluded: chain G residue 311 LEU 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 205 GLU Chi-restraints excluded: chain H residue 215 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 116 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 214 optimal weight: 0.9990 chunk 202 optimal weight: 1.9990 chunk 124 optimal weight: 0.0670 chunk 143 optimal weight: 1.9990 chunk 220 optimal weight: 0.6980 chunk 208 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 173 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 ASN A 213 GLN D 178 ASN ** G 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.158955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.124718 restraints weight = 30985.154| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.05 r_work: 0.3508 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1331 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= 0.147 Angle : 0.557 14.099 29499 Z= 0.294 Chirality : 0.042 0.194 3293 Planarity : 0.005 0.073 3533 Dihedral : 15.816 179.368 3665 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.81 % Favored : 93.94 % Rotamer: Outliers : 6.01 % Allowed : 26.99 % 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: -0.78 (0.17), residues: 2394 helix: 0.27 (0.19), residues: 698 sheet: 0.43 (0.27), residues: 406 loop : -1.30 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 115 TYR 0.015 0.001 TYR A 171 PHE 0.022 0.001 PHE A 212 TRP 0.011 0.001 TRP A 208 HIS 0.012 0.001 HIS A 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (21629) covalent geometry : angle 0.55681 / 0.29 (29499) hydrogen bonds : bond 0.04201 / 2.77 ( 567) hydrogen bonds : angle 5.53335 / 3.70 ( 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 624 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 494 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.7090 (pttm) cc_final: 0.6787 (pttm) REVERT: A 76 GLU cc_start: 0.6253 (OUTLIER) cc_final: 0.5995 (mp0) REVERT: A 176 ARG cc_start: 0.6858 (OUTLIER) cc_final: 0.6255 (mmm160) REVERT: A 230 LYS cc_start: 0.7949 (OUTLIER) cc_final: 0.7424 (mptp) REVERT: A 241 GLU cc_start: 0.7169 (mp0) cc_final: 0.6677 (mp0) REVERT: A 281 LYS cc_start: 0.6148 (mttp) cc_final: 0.5918 (mttp) REVERT: B 96 ILE cc_start: 0.7028 (OUTLIER) cc_final: 0.6752 (pt) REVERT: B 97 MET cc_start: 0.6325 (tmm) cc_final: 0.5720 (tmm) REVERT: B 144 LYS cc_start: 0.8318 (mmtt) cc_final: 0.8011 (mmtt) REVERT: B 209 ARG cc_start: 0.6424 (OUTLIER) cc_final: 0.4965 (ttt180) REVERT: B 246 GLU cc_start: 0.6352 (mm-30) cc_final: 0.5964 (mp0) REVERT: I 25 PHE cc_start: 0.7432 (OUTLIER) cc_final: 0.7046 (t80) REVERT: I 37 LYS cc_start: 0.5611 (OUTLIER) cc_final: 0.5395 (mttm) REVERT: I 38 LYS cc_start: 0.2628 (OUTLIER) cc_final: 0.1942 (tptp) REVERT: I 58 ILE cc_start: 0.6856 (OUTLIER) cc_final: 0.6551 (mm) REVERT: I 85 LYS cc_start: 0.6576 (OUTLIER) cc_final: 0.6046 (tmtp) REVERT: I 99 PHE cc_start: 0.4554 (OUTLIER) cc_final: 0.4124 (m-80) REVERT: D 102 VAL cc_start: 0.8818 (p) cc_final: 0.8527 (t) REVERT: D 105 SER cc_start: 0.8171 (OUTLIER) cc_final: 0.7873 (p) REVERT: D 238 LYS cc_start: 0.8099 (ttmm) cc_final: 0.7520 (ttmm) REVERT: E 91 LEU cc_start: 0.8459 (tp) cc_final: 0.8142 (tp) REVERT: E 115 ARG cc_start: 0.7972 (ttp80) cc_final: 0.7754 (ttp80) REVERT: E 129 ASP cc_start: 0.7979 (t0) cc_final: 0.7756 (t0) REVERT: E 228 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7779 (mm-30) REVERT: E 279 ASN cc_start: 0.8344 (m-40) cc_final: 0.8122 (m-40) REVERT: E 299 LYS cc_start: 0.8535 (tppt) cc_final: 0.8139 (mmmm) REVERT: F 40 ARG cc_start: 0.8947 (ptt-90) cc_final: 0.8449 (ptt180) REVERT: C 171 SER cc_start: 0.8264 (p) cc_final: 0.8040 (m) REVERT: C 224 TYR cc_start: 0.8399 (m-80) cc_final: 0.8050 (m-80) REVERT: G 136 LYS cc_start: 0.8298 (mttm) cc_final: 0.7876 (mmtt) REVERT: G 239 LYS cc_start: 0.8907 (mmmt) cc_final: 0.8601 (mmmt) REVERT: H 120 GLN cc_start: 0.7537 (OUTLIER) cc_final: 0.6778 (pp30) REVERT: H 121 LYS cc_start: 0.8104 (mmmt) cc_final: 0.6755 (mmmt) REVERT: H 184 GLU cc_start: 0.6229 (tm-30) cc_final: 0.5740 (tm-30) REVERT: H 195 GLN cc_start: 0.7709 (mp10) cc_final: 0.7455 (mp10) REVERT: H 206 TYR cc_start: 0.8374 (p90) cc_final: 0.8166 (p90) REVERT: H 272 GLU cc_start: 0.6885 (mp0) cc_final: 0.6574 (mp0) outliers start: 130 outliers final: 91 residues processed: 585 average time/residue: 0.1709 time to fit residues: 149.6790 Evaluate side-chains 589 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 485 time to evaluate : 0.811 ------------------------------------------------------------------------------- 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 108 GLN Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 145 GLN 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 222 LYS Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 251 ILE 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 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 194 VAL 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 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 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 87 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 175 LEU Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 105 SER 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 296 SER Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 171 SER 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 251 SER 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 249 MET Chi-restraints excluded: chain F residue 325 ARG Chi-restraints excluded: chain F residue 328 MET 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 305 ILE Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 48 LEU 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 249 MET Chi-restraints excluded: chain G residue 275 ILE Chi-restraints excluded: chain G residue 278 GLU 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 215 VAL Chi-restraints excluded: chain H residue 314 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 149 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 222 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 201 optimal weight: 0.0270 chunk 82 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 241 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 58 optimal weight: 6.9990 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 GLN D 178 ASN ** G 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.158553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.124132 restraints weight = 30863.892| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.05 r_work: 0.3499 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 21629 Z= 0.159 Angle : 0.554 13.517 29499 Z= 0.292 Chirality : 0.043 0.194 3293 Planarity : 0.005 0.087 3533 Dihedral : 15.634 179.827 3655 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.72 % Favored : 94.03 % Rotamer: Outliers : 6.33 % Allowed : 27.50 % 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: -0.69 (0.17), residues: 2394 helix: 0.38 (0.19), residues: 692 sheet: 0.43 (0.27), residues: 407 loop : -1.24 (0.17), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 40 TYR 0.021 0.001 TYR A 66 PHE 0.017 0.001 PHE A 212 TRP 0.010 0.001 TRP A 208 HIS 0.005 0.001 HIS I 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (21629) covalent geometry : angle 0.55377 / 0.29 (29499) hydrogen bonds : bond 0.04154 / 2.72 ( 567) hydrogen bonds : angle 5.47875 / 3.67 ( 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 631 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 494 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.6604 (tmm) cc_final: 0.6327 (tmm) REVERT: A 152 PHE cc_start: 0.8528 (t80) cc_final: 0.8053 (t80) REVERT: A 176 ARG cc_start: 0.6878 (OUTLIER) cc_final: 0.6277 (mmm160) REVERT: A 222 LYS cc_start: 0.8065 (OUTLIER) cc_final: 0.7732 (ttmm) REVERT: A 230 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7415 (mptp) REVERT: A 241 GLU cc_start: 0.7351 (mp0) cc_final: 0.6771 (mp0) REVERT: B 97 MET cc_start: 0.6309 (tmm) cc_final: 0.5718 (tmm) REVERT: B 111 GLU cc_start: 0.8344 (tm-30) cc_final: 0.7563 (tm-30) REVERT: B 144 LYS cc_start: 0.8311 (mmtt) cc_final: 0.8005 (mmtt) REVERT: I 25 PHE cc_start: 0.7419 (OUTLIER) cc_final: 0.7022 (t80) REVERT: I 38 LYS cc_start: 0.2486 (OUTLIER) cc_final: 0.1809 (tptp) REVERT: I 58 ILE cc_start: 0.6823 (OUTLIER) cc_final: 0.6509 (mm) REVERT: I 85 LYS cc_start: 0.6576 (OUTLIER) cc_final: 0.6110 (tmtp) REVERT: I 99 PHE cc_start: 0.4612 (OUTLIER) cc_final: 0.4203 (m-80) REVERT: D 102 VAL cc_start: 0.8812 (p) cc_final: 0.8565 (t) REVERT: D 238 LYS cc_start: 0.8114 (ttmm) cc_final: 0.7851 (ttmm) REVERT: E 91 LEU cc_start: 0.8456 (tp) cc_final: 0.8135 (tp) REVERT: E 115 ARG cc_start: 0.8038 (ttp80) cc_final: 0.7699 (ttp80) REVERT: E 119 TYR cc_start: 0.8661 (m-10) cc_final: 0.8256 (m-10) REVERT: E 299 LYS cc_start: 0.8532 (tppt) cc_final: 0.8140 (mmmm) REVERT: F 40 ARG cc_start: 0.8947 (ptt-90) cc_final: 0.8547 (ptt180) REVERT: C 165 GLU cc_start: 0.6560 (OUTLIER) cc_final: 0.5883 (pp20) REVERT: C 171 SER cc_start: 0.8315 (p) cc_final: 0.8091 (m) REVERT: C 224 TYR cc_start: 0.8432 (m-80) cc_final: 0.8139 (m-80) REVERT: C 228 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7241 (mm-30) REVERT: G 136 LYS cc_start: 0.8336 (mttm) cc_final: 0.7925 (mmtt) REVERT: G 204 ARG cc_start: 0.8327 (ttm-80) cc_final: 0.7717 (ttm170) REVERT: G 319 VAL cc_start: 0.7641 (OUTLIER) cc_final: 0.7416 (p) REVERT: H 120 GLN cc_start: 0.7524 (OUTLIER) cc_final: 0.6762 (pp30) REVERT: H 121 LYS cc_start: 0.8097 (mmmt) cc_final: 0.6758 (mmmt) REVERT: H 184 GLU cc_start: 0.6283 (tm-30) cc_final: 0.5779 (tm-30) REVERT: H 272 GLU cc_start: 0.6946 (mp0) cc_final: 0.6637 (mp0) outliers start: 137 outliers final: 93 residues processed: 590 average time/residue: 0.1674 time to fit residues: 148.9200 Evaluate side-chains 596 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 492 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 46 THR 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 97 MET 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 127 GLU Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain A residue 133 LEU 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 176 ARG Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 251 ILE 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 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 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 38 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 87 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 175 LEU Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 104 GLU 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 296 SER Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 322 ILE Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 171 SER Chi-restraints excluded: chain E residue 176 SER Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 251 SER 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 226 SER 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 F residue 328 MET 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 305 ILE Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 48 LEU 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 275 ILE Chi-restraints excluded: chain G residue 278 GLU Chi-restraints excluded: chain G residue 310 ASP 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 153 LYS Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 224 TYR Chi-restraints excluded: chain H residue 314 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 151 optimal weight: 0.6980 chunk 244 optimal weight: 30.0000 chunk 48 optimal weight: 4.9990 chunk 95 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 185 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 160 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 GLN ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 156 ASN D 178 ASN ** G 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 178 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.159858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.125166 restraints weight = 30775.028| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.02 r_work: 0.3520 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1666 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= 0.161 Angle : 0.553 13.129 29499 Z= 0.291 Chirality : 0.043 0.195 3293 Planarity : 0.004 0.069 3533 Dihedral : 15.516 179.986 3650 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.85 % Favored : 93.90 % Rotamer: Outliers : 6.28 % Allowed : 27.45 % 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: -0.67 (0.17), residues: 2394 helix: 0.38 (0.20), residues: 692 sheet: 0.41 (0.27), residues: 421 loop : -1.22 (0.17), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 115 TYR 0.023 0.001 TYR A 171 PHE 0.028 0.001 PHE A 146 TRP 0.009 0.001 TRP H 149 HIS 0.005 0.001 HIS G 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (21629) covalent geometry : angle 0.55291 / 0.29 (29499) hydrogen bonds : bond 0.04080 / 2.67 ( 567) hydrogen bonds : angle 5.42970 / 3.64 ( 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 637 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 501 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.6618 (tmm) cc_final: 0.6387 (tmm) REVERT: A 76 GLU cc_start: 0.6499 (OUTLIER) cc_final: 0.6158 (mp0) REVERT: A 164 LEU cc_start: 0.7590 (mm) cc_final: 0.7227 (mt) REVERT: A 176 ARG cc_start: 0.6967 (OUTLIER) cc_final: 0.6320 (mmm160) REVERT: A 230 LYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7440 (mptp) REVERT: A 241 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.7075 (mp0) REVERT: B 97 MET cc_start: 0.6240 (tmm) cc_final: 0.5639 (tmm) REVERT: B 111 GLU cc_start: 0.8321 (tm-30) cc_final: 0.7544 (tm-30) REVERT: B 144 LYS cc_start: 0.8328 (mmtt) cc_final: 0.8039 (mmtt) REVERT: B 209 ARG cc_start: 0.6433 (OUTLIER) cc_final: 0.5339 (ttt180) REVERT: I 25 PHE cc_start: 0.7293 (OUTLIER) cc_final: 0.6911 (t80) REVERT: I 58 ILE cc_start: 0.6817 (OUTLIER) cc_final: 0.6491 (mm) REVERT: I 85 LYS cc_start: 0.6598 (OUTLIER) cc_final: 0.6074 (tmtp) REVERT: I 99 PHE cc_start: 0.4492 (OUTLIER) cc_final: 0.4043 (m-80) REVERT: I 104 GLU cc_start: 0.1681 (OUTLIER) cc_final: 0.0561 (pm20) REVERT: D 102 VAL cc_start: 0.8783 (p) cc_final: 0.8538 (t) REVERT: D 238 LYS cc_start: 0.8111 (ttmm) cc_final: 0.7865 (ttmm) REVERT: E 91 LEU cc_start: 0.8465 (tp) cc_final: 0.8137 (tp) REVERT: E 299 LYS cc_start: 0.8544 (tppt) cc_final: 0.8175 (mmmm) REVERT: F 40 ARG cc_start: 0.8933 (ptt-90) cc_final: 0.8507 (ptt180) REVERT: F 252 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.8003 (pm20) REVERT: C 51 ASP cc_start: 0.7901 (m-30) cc_final: 0.7698 (m-30) REVERT: C 146 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.8184 (ttp-170) REVERT: C 165 GLU cc_start: 0.6501 (OUTLIER) cc_final: 0.5860 (pp20) REVERT: C 171 SER cc_start: 0.8342 (p) cc_final: 0.8072 (m) REVERT: C 224 TYR cc_start: 0.8462 (m-80) cc_final: 0.8159 (m-80) REVERT: C 228 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7248 (mm-30) REVERT: G 136 LYS cc_start: 0.8299 (mttm) cc_final: 0.7885 (mmtt) REVERT: G 163 THR cc_start: 0.8490 (m) cc_final: 0.8087 (p) REVERT: G 204 ARG cc_start: 0.8337 (ttm-80) cc_final: 0.7770 (ttm170) REVERT: G 210 TYR cc_start: 0.8523 (m-80) cc_final: 0.8269 (m-80) REVERT: G 239 LYS cc_start: 0.8917 (mmmt) cc_final: 0.8699 (mmmt) REVERT: G 319 VAL cc_start: 0.7642 (OUTLIER) cc_final: 0.7420 (p) REVERT: H 120 GLN cc_start: 0.7549 (OUTLIER) cc_final: 0.6781 (pp30) REVERT: H 121 LYS cc_start: 0.8074 (mmmt) cc_final: 0.6757 (mmmt) REVERT: H 184 GLU cc_start: 0.6342 (tm-30) cc_final: 0.5834 (tm-30) REVERT: H 272 GLU cc_start: 0.7016 (mp0) cc_final: 0.6730 (mp0) REVERT: H 279 ASN cc_start: 0.6896 (p0) cc_final: 0.6554 (p0) outliers start: 136 outliers final: 94 residues processed: 590 average time/residue: 0.1677 time to fit residues: 148.6373 Evaluate side-chains 612 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 503 time to evaluate : 0.947 ------------------------------------------------------------------------------- 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 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 133 LEU 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 176 ARG Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 218 LYS 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 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 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 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 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 87 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 175 LEU Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 171 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 D residue 322 ILE Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain E residue 103 LYS Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 171 SER Chi-restraints excluded: chain E residue 176 SER Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 239 LYS Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 251 SER 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 226 SER Chi-restraints excluded: chain F residue 249 MET Chi-restraints excluded: chain F residue 252 GLN Chi-restraints excluded: chain F residue 325 ARG Chi-restraints excluded: chain F residue 328 MET 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 C residue 275 ILE Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 48 LEU 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 275 ILE Chi-restraints excluded: chain G residue 278 GLU 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 153 LYS Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 224 TYR Chi-restraints excluded: chain H residue 323 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 2 optimal weight: 0.6980 chunk 197 optimal weight: 1.9990 chunk 226 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 211 optimal weight: 0.1980 chunk 172 optimal weight: 0.7980 chunk 201 optimal weight: 0.0980 chunk 129 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 198 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 GLN ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 156 ASN D 178 ASN ** E 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.160509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.125986 restraints weight = 30733.687| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.02 r_work: 0.3532 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1755 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= 0.132 Angle : 0.544 12.935 29499 Z= 0.286 Chirality : 0.042 0.188 3293 Planarity : 0.004 0.067 3533 Dihedral : 15.448 179.692 3639 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.39 % Favored : 94.36 % Rotamer: Outliers : 5.50 % Allowed : 28.47 % Favored : 66.04 % 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: -0.59 (0.17), residues: 2394 helix: 0.47 (0.20), residues: 691 sheet: 0.52 (0.27), residues: 411 loop : -1.19 (0.17), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 303 TYR 0.020 0.001 TYR C 114 PHE 0.016 0.001 PHE A 212 TRP 0.009 0.001 TRP H 149 HIS 0.005 0.001 HIS I 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (21629) covalent geometry : angle 0.54434 / 0.29 (29499) hydrogen bonds : bond 0.03956 / 2.59 ( 567) hydrogen bonds : angle 5.37022 / 3.60 ( 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 625 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 506 time to evaluate : 0.765 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 76 GLU cc_start: 0.6495 (OUTLIER) cc_final: 0.6114 (mp0) REVERT: A 104 MET cc_start: 0.6339 (ttp) cc_final: 0.5551 (ttp) REVERT: A 118 MET cc_start: 0.4032 (OUTLIER) cc_final: 0.3611 (tpt) REVERT: A 152 PHE cc_start: 0.8537 (t80) cc_final: 0.8162 (t80) REVERT: A 164 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.7191 (mt) REVERT: A 176 ARG cc_start: 0.6980 (OUTLIER) cc_final: 0.6318 (mmm160) REVERT: A 230 LYS cc_start: 0.8013 (OUTLIER) cc_final: 0.7447 (mptp) REVERT: A 241 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.6940 (mp0) REVERT: B 97 MET cc_start: 0.6193 (tmm) cc_final: 0.5609 (tmm) REVERT: B 111 GLU cc_start: 0.8323 (tm-30) cc_final: 0.7600 (tm-30) REVERT: B 144 LYS cc_start: 0.8303 (mmtt) cc_final: 0.8006 (mmtt) REVERT: B 209 ARG cc_start: 0.6298 (OUTLIER) cc_final: 0.5239 (ttt180) REVERT: I 1 MET cc_start: 0.3837 (tpp) cc_final: 0.2959 (tpt) REVERT: I 25 PHE cc_start: 0.7330 (OUTLIER) cc_final: 0.6963 (t80) REVERT: I 85 LYS cc_start: 0.6557 (OUTLIER) cc_final: 0.6036 (tmtp) REVERT: I 99 PHE cc_start: 0.4457 (OUTLIER) cc_final: 0.3980 (m-80) REVERT: I 104 GLU cc_start: 0.1552 (OUTLIER) cc_final: 0.0493 (pm20) REVERT: D 91 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.7908 (tp) REVERT: D 102 VAL cc_start: 0.8770 (p) cc_final: 0.8534 (t) REVERT: D 238 LYS cc_start: 0.8087 (ttmm) cc_final: 0.7838 (ttmm) REVERT: E 91 LEU cc_start: 0.8464 (tp) cc_final: 0.8140 (tp) REVERT: E 119 TYR cc_start: 0.8602 (m-10) cc_final: 0.8250 (m-10) REVERT: E 138 TYR cc_start: 0.8142 (m-80) cc_final: 0.7712 (m-80) REVERT: E 299 LYS cc_start: 0.8536 (tppt) cc_final: 0.8165 (mmmm) REVERT: F 40 ARG cc_start: 0.8922 (ptt-90) cc_final: 0.8525 (ptt180) REVERT: C 21 PHE cc_start: 0.8057 (m-80) cc_final: 0.7718 (m-80) REVERT: C 146 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.8181 (ttp-170) REVERT: C 165 GLU cc_start: 0.6478 (OUTLIER) cc_final: 0.5846 (pp20) REVERT: C 171 SER cc_start: 0.8309 (p) cc_final: 0.8070 (m) REVERT: C 224 TYR cc_start: 0.8448 (m-80) cc_final: 0.8199 (m-80) REVERT: C 228 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7254 (mm-30) REVERT: G 136 LYS cc_start: 0.8290 (mttm) cc_final: 0.7876 (mmtt) REVERT: G 163 THR cc_start: 0.8503 (m) cc_final: 0.8113 (p) REVERT: G 204 ARG cc_start: 0.8331 (ttm-80) cc_final: 0.7723 (ttm170) REVERT: G 210 TYR cc_start: 0.8518 (m-80) cc_final: 0.8259 (m-80) REVERT: G 239 LYS cc_start: 0.8902 (mmmt) cc_final: 0.8667 (mmmt) REVERT: G 319 VAL cc_start: 0.7621 (OUTLIER) cc_final: 0.7399 (p) REVERT: H 120 GLN cc_start: 0.7550 (OUTLIER) cc_final: 0.6778 (pp30) REVERT: H 121 LYS cc_start: 0.8061 (mmmt) cc_final: 0.6744 (mmmt) REVERT: H 184 GLU cc_start: 0.6327 (tm-30) cc_final: 0.5816 (tm-30) REVERT: H 195 GLN cc_start: 0.7754 (mp10) cc_final: 0.7501 (mp10) REVERT: H 272 GLU cc_start: 0.6963 (mp0) cc_final: 0.6663 (mp0) REVERT: H 279 ASN cc_start: 0.6869 (p0) cc_final: 0.6523 (p0) outliers start: 119 outliers final: 89 residues processed: 587 average time/residue: 0.1689 time to fit residues: 148.6209 Evaluate side-chains 601 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 496 time to evaluate : 0.734 ------------------------------------------------------------------------------- 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 67 LEU 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 97 MET 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 133 LEU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 176 ARG Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 218 LYS 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 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 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 50 LYS Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 85 LYS Chi-restraints excluded: chain I residue 87 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 51 ASP Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain E residue 103 LYS Chi-restraints excluded: chain E residue 171 SER 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 239 LYS Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 251 SER 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 166 ASP Chi-restraints excluded: chain F residue 226 SER Chi-restraints excluded: chain F residue 249 MET 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 C residue 275 ILE Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 48 LEU 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 251 SER Chi-restraints excluded: chain G residue 275 ILE Chi-restraints excluded: chain G residue 278 GLU 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 153 LYS Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 224 TYR Chi-restraints excluded: chain H residue 314 GLU Chi-restraints excluded: chain H residue 323 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 63 optimal weight: 20.0000 chunk 102 optimal weight: 0.3980 chunk 150 optimal weight: 0.5980 chunk 73 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 241 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 7 optimal weight: 30.0000 chunk 166 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 159 HIS A 213 GLN A 296 ASN ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 156 ASN D 178 ASN ** E 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 140 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 = 0.4049 r_free = 0.4049 target = 0.159369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.124686 restraints weight = 30481.028| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.02 r_work: 0.3510 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 21629 Z= 0.192 Angle : 0.570 12.690 29499 Z= 0.299 Chirality : 0.043 0.197 3293 Planarity : 0.005 0.073 3533 Dihedral : 15.388 179.982 3637 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.89 % Favored : 93.90 % Rotamer: Outliers : 6.10 % Allowed : 28.19 % Favored : 65.71 % 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: 0.43 (0.20), residues: 692 sheet: 0.33 (0.27), residues: 426 loop : -1.21 (0.17), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 115 TYR 0.022 0.001 TYR C 114 PHE 0.014 0.001 PHE A 212 TRP 0.011 0.001 TRP A 74 HIS 0.004 0.001 HIS I 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.19 (21629) covalent geometry : angle 0.56982 / 0.30 (29499) hydrogen bonds : bond 0.04135 / 2.70 ( 567) hydrogen bonds : angle 5.43086 / 3.66 ( 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 635 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 503 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.6553 (tmm) cc_final: 0.6153 (tmm) REVERT: A 104 MET cc_start: 0.6263 (ttp) cc_final: 0.5457 (ttp) REVERT: A 118 MET cc_start: 0.3991 (OUTLIER) cc_final: 0.3560 (tpt) REVERT: A 176 ARG cc_start: 0.7099 (OUTLIER) cc_final: 0.6418 (mmm160) REVERT: A 201 ARG cc_start: 0.3757 (OUTLIER) cc_final: 0.3095 (tpt170) REVERT: A 230 LYS cc_start: 0.7994 (OUTLIER) cc_final: 0.7440 (mptp) REVERT: A 241 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.6954 (mp0) REVERT: B 97 MET cc_start: 0.6259 (tmm) cc_final: 0.5579 (tmm) REVERT: B 111 GLU cc_start: 0.8324 (tm-30) cc_final: 0.7540 (tm-30) REVERT: B 144 LYS cc_start: 0.8336 (mmtt) cc_final: 0.8049 (mmtt) REVERT: B 209 ARG cc_start: 0.6431 (OUTLIER) cc_final: 0.5466 (ttt180) REVERT: I 25 PHE cc_start: 0.7294 (OUTLIER) cc_final: 0.6924 (t80) REVERT: I 85 LYS cc_start: 0.6520 (OUTLIER) cc_final: 0.6016 (tmtp) REVERT: I 99 PHE cc_start: 0.4491 (OUTLIER) cc_final: 0.3980 (m-80) REVERT: I 104 GLU cc_start: 0.1627 (OUTLIER) cc_final: 0.0523 (pm20) REVERT: D 91 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.7934 (tp) REVERT: D 102 VAL cc_start: 0.8791 (p) cc_final: 0.8509 (t) REVERT: D 105 SER cc_start: 0.8166 (OUTLIER) cc_final: 0.7876 (p) REVERT: D 238 LYS cc_start: 0.8102 (ttmm) cc_final: 0.7874 (ttmm) REVERT: E 91 LEU cc_start: 0.8489 (tp) cc_final: 0.8166 (tp) REVERT: E 119 TYR cc_start: 0.8640 (m-10) cc_final: 0.8288 (m-10) REVERT: E 138 TYR cc_start: 0.8161 (m-80) cc_final: 0.7730 (m-80) REVERT: E 299 LYS cc_start: 0.8543 (tppt) cc_final: 0.8171 (mmmm) REVERT: F 40 ARG cc_start: 0.8935 (ptt-90) cc_final: 0.8492 (ptt180) REVERT: F 252 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.8007 (pm20) REVERT: C 21 PHE cc_start: 0.8066 (m-80) cc_final: 0.7748 (m-80) REVERT: C 146 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.8229 (ttp-170) REVERT: C 165 GLU cc_start: 0.6507 (OUTLIER) cc_final: 0.5882 (pp20) REVERT: C 171 SER cc_start: 0.8322 (p) cc_final: 0.8052 (m) REVERT: C 224 TYR cc_start: 0.8459 (m-80) cc_final: 0.8247 (m-80) REVERT: C 228 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7342 (mm-30) REVERT: G 115 ARG cc_start: 0.7549 (ttm-80) cc_final: 0.7220 (ttp80) REVERT: G 136 LYS cc_start: 0.8305 (mttm) cc_final: 0.7887 (mmtt) REVERT: G 163 THR cc_start: 0.8507 (m) cc_final: 0.8120 (p) REVERT: G 204 ARG cc_start: 0.8350 (ttm-80) cc_final: 0.7785 (ttm170) REVERT: G 210 TYR cc_start: 0.8554 (m-80) cc_final: 0.8291 (m-80) REVERT: G 239 LYS cc_start: 0.8896 (mmmt) cc_final: 0.8636 (mmmt) REVERT: G 319 VAL cc_start: 0.7647 (OUTLIER) cc_final: 0.7416 (p) REVERT: H 120 GLN cc_start: 0.7553 (OUTLIER) cc_final: 0.6774 (pp30) REVERT: H 121 LYS cc_start: 0.8067 (mmmt) cc_final: 0.6739 (mmmt) REVERT: H 184 GLU cc_start: 0.6387 (tm-30) cc_final: 0.5884 (tm-30) REVERT: H 195 GLN cc_start: 0.7770 (mp10) cc_final: 0.7475 (mp10) REVERT: H 272 GLU cc_start: 0.7051 (mp0) cc_final: 0.6753 (mp0) REVERT: H 279 ASN cc_start: 0.6913 (p0) cc_final: 0.6540 (p0) REVERT: H 324 ILE cc_start: 0.8253 (OUTLIER) cc_final: 0.7930 (mp) outliers start: 132 outliers final: 89 residues processed: 595 average time/residue: 0.1724 time to fit residues: 153.2618 Evaluate side-chains 600 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 493 time to evaluate : 0.765 ------------------------------------------------------------------------------- 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 97 MET 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 133 LEU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 176 ARG Chi-restraints excluded: chain A residue 201 ARG Chi-restraints excluded: chain A residue 218 LYS 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 251 ILE 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 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 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 50 LYS Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 85 LYS Chi-restraints excluded: chain I residue 87 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 51 ASP Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 171 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 D residue 322 ILE Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain E residue 103 LYS Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 171 SER Chi-restraints excluded: chain E residue 176 SER Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 251 SER 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 226 SER Chi-restraints excluded: chain F residue 249 MET Chi-restraints excluded: chain F residue 252 GLN 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 C residue 275 ILE Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 48 LEU 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 275 ILE Chi-restraints excluded: chain G residue 278 GLU 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 153 LYS Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 224 TYR Chi-restraints excluded: chain H residue 323 LEU Chi-restraints excluded: chain H residue 324 ILE 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: 0.5980 chunk 220 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 83 optimal weight: 0.1980 chunk 9 optimal weight: 0.6980 chunk 172 optimal weight: 0.5980 chunk 162 optimal weight: 0.0570 chunk 86 optimal weight: 0.5980 chunk 64 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** G 140 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.161028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.126503 restraints weight = 30588.369| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.02 r_work: 0.3530 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1963 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= 0.124 Angle : 0.553 12.708 29499 Z= 0.289 Chirality : 0.042 0.177 3293 Planarity : 0.004 0.071 3533 Dihedral : 15.349 179.294 3637 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.56 % Favored : 94.24 % Rotamer: Outliers : 5.04 % Allowed : 29.48 % Favored : 65.48 % 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: -0.53 (0.17), residues: 2394 helix: 0.55 (0.20), residues: 686 sheet: 0.56 (0.28), residues: 400 loop : -1.16 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 204 TYR 0.019 0.001 TYR C 114 PHE 0.024 0.001 PHE A 146 TRP 0.011 0.001 TRP H 149 HIS 0.005 0.001 HIS I 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (21629) covalent geometry : angle 0.55286 / 0.29 (29499) hydrogen bonds : bond 0.03856 / 2.53 ( 567) hydrogen bonds : angle 5.34316 / 3.60 ( 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 603 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 494 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.6596 (tmm) cc_final: 0.6150 (tmm) REVERT: A 76 GLU cc_start: 0.6507 (OUTLIER) cc_final: 0.6091 (mp0) REVERT: A 104 MET cc_start: 0.6229 (ttp) cc_final: 0.5389 (ttp) REVERT: A 118 MET cc_start: 0.3996 (OUTLIER) cc_final: 0.3608 (tpt) REVERT: A 152 PHE cc_start: 0.8522 (t80) cc_final: 0.8250 (t80) REVERT: A 176 ARG cc_start: 0.7073 (OUTLIER) cc_final: 0.6366 (mmm160) REVERT: A 201 ARG cc_start: 0.3815 (OUTLIER) cc_final: 0.3146 (tpt170) REVERT: A 230 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7431 (mptp) REVERT: A 241 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.6911 (mp0) REVERT: A 266 LYS cc_start: 0.8504 (mmmt) cc_final: 0.8228 (mttm) REVERT: B 96 ILE cc_start: 0.6971 (OUTLIER) cc_final: 0.6689 (pt) REVERT: B 97 MET cc_start: 0.6139 (tmm) cc_final: 0.5603 (tmm) REVERT: B 111 GLU cc_start: 0.8299 (tm-30) cc_final: 0.7604 (tm-30) REVERT: B 144 LYS cc_start: 0.8321 (mmtt) cc_final: 0.8039 (mmtt) REVERT: B 209 ARG cc_start: 0.6228 (OUTLIER) cc_final: 0.5244 (ttt180) REVERT: I 25 PHE cc_start: 0.7319 (OUTLIER) cc_final: 0.6921 (t80) REVERT: I 85 LYS cc_start: 0.6503 (OUTLIER) cc_final: 0.5996 (tmtp) REVERT: I 99 PHE cc_start: 0.4456 (OUTLIER) cc_final: 0.3938 (m-80) REVERT: I 104 GLU cc_start: 0.1472 (OUTLIER) cc_final: 0.0489 (pm20) REVERT: D 102 VAL cc_start: 0.8787 (p) cc_final: 0.8505 (t) REVERT: D 105 SER cc_start: 0.8153 (OUTLIER) cc_final: 0.7861 (p) REVERT: D 238 LYS cc_start: 0.8078 (ttmm) cc_final: 0.7844 (ttmm) REVERT: E 91 LEU cc_start: 0.8473 (tp) cc_final: 0.8157 (tp) REVERT: E 119 TYR cc_start: 0.8606 (m-10) cc_final: 0.8316 (m-10) REVERT: E 299 LYS cc_start: 0.8554 (tppt) cc_final: 0.8190 (mmmm) REVERT: F 40 ARG cc_start: 0.8920 (ptt-90) cc_final: 0.8514 (ptt180) REVERT: F 229 MET cc_start: 0.6106 (ttt) cc_final: 0.5718 (mtt) REVERT: F 252 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.8037 (pm20) REVERT: C 21 PHE cc_start: 0.8048 (m-80) cc_final: 0.7729 (m-80) REVERT: C 146 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.8225 (ttp-170) REVERT: C 165 GLU cc_start: 0.6452 (OUTLIER) cc_final: 0.5837 (pp20) REVERT: C 171 SER cc_start: 0.8333 (p) cc_final: 0.8040 (m) REVERT: C 224 TYR cc_start: 0.8408 (m-80) cc_final: 0.8175 (m-80) REVERT: C 228 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7269 (mm-30) REVERT: G 115 ARG cc_start: 0.7546 (ttm-80) cc_final: 0.7197 (ttp80) REVERT: G 136 LYS cc_start: 0.8316 (mttm) cc_final: 0.7904 (mmtt) REVERT: G 163 THR cc_start: 0.8491 (m) cc_final: 0.8120 (p) REVERT: G 204 ARG cc_start: 0.8326 (ttm-80) cc_final: 0.7728 (ttm170) REVERT: G 210 TYR cc_start: 0.8515 (m-80) cc_final: 0.8255 (m-80) REVERT: G 239 LYS cc_start: 0.8908 (mmmt) cc_final: 0.8663 (mmmt) REVERT: G 319 VAL cc_start: 0.7624 (OUTLIER) cc_final: 0.7407 (p) REVERT: H 120 GLN cc_start: 0.7525 (OUTLIER) cc_final: 0.6769 (pp30) REVERT: H 121 LYS cc_start: 0.8094 (mmmt) cc_final: 0.6780 (mmmt) REVERT: H 184 GLU cc_start: 0.6360 (tm-30) cc_final: 0.5849 (tm-30) REVERT: H 195 GLN cc_start: 0.7751 (mp10) cc_final: 0.7470 (mp10) REVERT: H 272 GLU cc_start: 0.6994 (mp0) cc_final: 0.6693 (mp0) REVERT: H 324 ILE cc_start: 0.8235 (OUTLIER) cc_final: 0.7885 (mp) outliers start: 109 outliers final: 80 residues processed: 568 average time/residue: 0.1730 time to fit residues: 146.4785 Evaluate side-chains 591 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 492 time to evaluate : 0.745 ------------------------------------------------------------------------------- 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 67 LEU 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 118 MET Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 176 ARG Chi-restraints excluded: chain A residue 201 ARG Chi-restraints excluded: chain A residue 218 LYS 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 251 ILE 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 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 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 50 LYS Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 85 LYS Chi-restraints excluded: chain I residue 87 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 51 ASP Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain E residue 103 LYS Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 171 SER Chi-restraints excluded: chain E residue 176 SER Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 313 ILE Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 166 ASP Chi-restraints excluded: chain F residue 226 SER Chi-restraints excluded: chain F residue 249 MET Chi-restraints excluded: chain F residue 252 GLN Chi-restraints excluded: chain F residue 325 ARG Chi-restraints excluded: chain C residue 28 THR 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 35 THR 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 249 MET Chi-restraints excluded: chain G residue 251 SER Chi-restraints excluded: chain G residue 278 GLU 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 205 GLU Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 224 TYR Chi-restraints excluded: chain H residue 314 GLU Chi-restraints excluded: chain H residue 323 LEU Chi-restraints excluded: chain H residue 324 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 22 optimal weight: 3.9990 chunk 191 optimal weight: 0.1980 chunk 46 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 140 optimal weight: 0.0980 chunk 193 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 159 HIS A 213 GLN B 15 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.160659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.126134 restraints weight = 30803.212| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 2.03 r_work: 0.3520 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21629 Z= 0.147 Angle : 0.559 12.515 29499 Z= 0.293 Chirality : 0.042 0.181 3293 Planarity : 0.004 0.073 3533 Dihedral : 15.290 179.115 3631 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.81 % Favored : 93.98 % Rotamer: Outliers : 4.85 % Allowed : 29.62 % Favored : 65.53 % 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: -0.57 (0.17), residues: 2394 helix: 0.48 (0.20), residues: 692 sheet: 0.48 (0.27), residues: 413 loop : -1.16 (0.17), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 291 TYR 0.020 0.001 TYR C 114 PHE 0.018 0.001 PHE A 146 TRP 0.011 0.001 TRP H 149 HIS 0.004 0.001 HIS I 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (21629) covalent geometry : angle 0.55855 / 0.29 (29499) hydrogen bonds : bond 0.03948 / 2.57 ( 567) hydrogen bonds : angle 5.35421 / 3.61 ( 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 599 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 494 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ILE cc_start: 0.3686 (OUTLIER) cc_final: 0.3413 (pt) REVERT: A 62 MET cc_start: 0.6569 (tmm) cc_final: 0.6065 (tmm) REVERT: A 76 GLU cc_start: 0.6577 (OUTLIER) cc_final: 0.6112 (mp0) REVERT: A 104 MET cc_start: 0.6192 (ttp) cc_final: 0.5358 (ttp) REVERT: A 118 MET cc_start: 0.4041 (OUTLIER) cc_final: 0.3637 (tpt) REVERT: A 152 PHE cc_start: 0.8519 (t80) cc_final: 0.8276 (t80) REVERT: A 176 ARG cc_start: 0.7096 (OUTLIER) cc_final: 0.6399 (mmm160) REVERT: A 201 ARG cc_start: 0.3863 (OUTLIER) cc_final: 0.3200 (tpt170) REVERT: A 230 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7453 (mptp) REVERT: A 241 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.6928 (mp0) REVERT: A 266 LYS cc_start: 0.8523 (mmmt) cc_final: 0.8261 (mttm) REVERT: B 96 ILE cc_start: 0.6992 (OUTLIER) cc_final: 0.6710 (pt) REVERT: B 97 MET cc_start: 0.6191 (tmm) cc_final: 0.5623 (tmm) REVERT: B 111 GLU cc_start: 0.8314 (tm-30) cc_final: 0.7603 (tm-30) REVERT: B 144 LYS cc_start: 0.8331 (mmtt) cc_final: 0.8048 (mmtt) REVERT: B 209 ARG cc_start: 0.6285 (OUTLIER) cc_final: 0.5375 (ttt180) REVERT: I 25 PHE cc_start: 0.7356 (OUTLIER) cc_final: 0.6962 (t80) REVERT: I 85 LYS cc_start: 0.6468 (OUTLIER) cc_final: 0.5978 (tmtp) REVERT: I 99 PHE cc_start: 0.4521 (OUTLIER) cc_final: 0.3965 (m-80) REVERT: I 104 GLU cc_start: 0.1412 (OUTLIER) cc_final: 0.0454 (pm20) REVERT: D 91 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.7923 (tp) REVERT: D 102 VAL cc_start: 0.8795 (p) cc_final: 0.8521 (t) REVERT: D 105 SER cc_start: 0.8180 (OUTLIER) cc_final: 0.7895 (p) REVERT: D 238 LYS cc_start: 0.8078 (ttmm) cc_final: 0.7854 (ttmm) REVERT: E 91 LEU cc_start: 0.8491 (tp) cc_final: 0.8181 (tp) REVERT: E 119 TYR cc_start: 0.8612 (m-10) cc_final: 0.8241 (m-10) REVERT: E 299 LYS cc_start: 0.8548 (tppt) cc_final: 0.8186 (mmmm) REVERT: F 40 ARG cc_start: 0.8922 (ptt-90) cc_final: 0.8544 (ptt180) REVERT: F 229 MET cc_start: 0.6227 (ttt) cc_final: 0.5822 (mtt) REVERT: F 252 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.8049 (pm20) REVERT: C 21 PHE cc_start: 0.8062 (m-80) cc_final: 0.7741 (m-80) REVERT: C 146 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8220 (ttp-170) REVERT: C 165 GLU cc_start: 0.6453 (OUTLIER) cc_final: 0.5844 (pp20) REVERT: C 171 SER cc_start: 0.8357 (p) cc_final: 0.8061 (m) REVERT: C 228 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7277 (mm-30) REVERT: G 114 TYR cc_start: 0.8202 (t80) cc_final: 0.7343 (t80) REVERT: G 115 ARG cc_start: 0.7534 (ttm-80) cc_final: 0.7201 (ttp80) REVERT: G 136 LYS cc_start: 0.8378 (mttm) cc_final: 0.7963 (mmtt) REVERT: G 163 THR cc_start: 0.8490 (m) cc_final: 0.8115 (p) REVERT: G 204 ARG cc_start: 0.8347 (ttm-80) cc_final: 0.7762 (ttm170) REVERT: G 239 LYS cc_start: 0.8910 (mmmt) cc_final: 0.8662 (mmmt) REVERT: G 319 VAL cc_start: 0.7632 (OUTLIER) cc_final: 0.7406 (p) REVERT: H 115 ARG cc_start: 0.7776 (tpp80) cc_final: 0.7553 (tpp80) REVERT: H 120 GLN cc_start: 0.7519 (OUTLIER) cc_final: 0.6760 (pp30) REVERT: H 121 LYS cc_start: 0.8103 (mmmt) cc_final: 0.6786 (mmmt) REVERT: H 184 GLU cc_start: 0.6401 (tm-30) cc_final: 0.5894 (tm-30) REVERT: H 195 GLN cc_start: 0.7748 (mp10) cc_final: 0.7474 (mp10) REVERT: H 272 GLU cc_start: 0.7021 (mp0) cc_final: 0.6706 (mp0) REVERT: H 324 ILE cc_start: 0.8259 (OUTLIER) cc_final: 0.7907 (mp) outliers start: 105 outliers final: 78 residues processed: 566 average time/residue: 0.1717 time to fit residues: 145.1608 Evaluate side-chains 589 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 490 time to evaluate : 0.798 ------------------------------------------------------------------------------- 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 67 LEU 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 118 MET Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 176 ARG Chi-restraints excluded: chain A residue 201 ARG Chi-restraints excluded: chain A residue 218 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 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 129 MET Chi-restraints excluded: chain B residue 147 LEU 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 205 VAL Chi-restraints excluded: chain B residue 209 ARG 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 50 LYS Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 85 LYS Chi-restraints excluded: chain I residue 87 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 51 ASP Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 171 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 87 GLU Chi-restraints excluded: chain E residue 103 LYS Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 171 SER Chi-restraints excluded: chain E residue 176 SER Chi-restraints excluded: chain E residue 217 ILE 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 166 ASP Chi-restraints excluded: chain F residue 226 SER Chi-restraints excluded: chain F residue 249 MET Chi-restraints excluded: chain F residue 252 GLN Chi-restraints excluded: chain C residue 28 THR 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 35 THR 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 249 MET Chi-restraints excluded: chain G residue 278 GLU 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 215 VAL Chi-restraints excluded: chain H residue 224 TYR Chi-restraints excluded: chain H residue 286 ILE Chi-restraints excluded: chain H residue 324 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 48 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 64 optimal weight: 9.9990 chunk 221 optimal weight: 2.9990 chunk 142 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 86 optimal weight: 0.9980 chunk 52 optimal weight: 0.0980 chunk 67 optimal weight: 6.9990 chunk 184 optimal weight: 0.9990 chunk 93 optimal weight: 0.0870 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 139 GLN A 159 HIS A 213 GLN ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 15 ASN ** 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 = 0.4068 r_free = 0.4068 target = 0.161005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.126561 restraints weight = 30630.018| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.02 r_work: 0.3532 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2105 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= 0.136 Angle : 0.554 12.517 29499 Z= 0.291 Chirality : 0.042 0.173 3293 Planarity : 0.004 0.072 3533 Dihedral : 15.248 178.820 3631 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.68 % Favored : 94.11 % Rotamer: Outliers : 4.85 % Allowed : 29.76 % Favored : 65.39 % 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: -0.53 (0.17), residues: 2394 helix: 0.54 (0.20), residues: 686 sheet: 0.47 (0.27), residues: 413 loop : -1.14 (0.17), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG C 150 TYR 0.020 0.001 TYR C 114 PHE 0.017 0.001 PHE C 243 TRP 0.010 0.001 TRP H 149 HIS 0.004 0.001 HIS I 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (21629) covalent geometry : angle 0.55437 / 0.29 (29499) hydrogen bonds : bond 0.03873 / 2.53 ( 567) hydrogen bonds : angle 5.30562 / 3.59 ( 1542) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7348.24 seconds wall clock time: 126 minutes 34.00 seconds (7594.00 seconds total)