Starting phenix.real_space_refine on Thu Mar 5 07:13:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w6s_32334/03_2026/7w6s_32334.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w6s_32334/03_2026/7w6s_32334.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7w6s_32334/03_2026/7w6s_32334.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w6s_32334/03_2026/7w6s_32334.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7w6s_32334/03_2026/7w6s_32334.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w6s_32334/03_2026/7w6s_32334.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 136 5.16 5 C 13040 2.51 5 N 3408 2.21 5 O 3684 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 117 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20268 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1465 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 174} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3602 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 19, 'TRANS': 428} Chain breaks: 2 Chain: "C" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1465 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 174} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 3602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3602 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 19, 'TRANS': 428} Chain breaks: 2 Chain: "E" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1465 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 174} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 3602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3602 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 19, 'TRANS': 428} Chain breaks: 2 Chain: "G" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1465 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 174} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 3602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3602 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 19, 'TRANS': 428} Chain breaks: 2 Time building chain proxies: 4.56, per 1000 atoms: 0.22 Number of scatterers: 20268 At special positions: 0 Unit cell: (161.226, 161.226, 127.764, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 136 16.00 O 3684 8.00 N 3408 7.00 C 13040 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: 1.39 Conformation dependent library (CDL) restraints added in 942.8 milliseconds 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4752 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 8 sheets defined 70.9% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 92 through 100 Processing helix chain 'A' and resid 103 through 118 Processing helix chain 'A' and resid 124 through 133 removed outlier: 3.947A pdb=" N LYS A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 153 removed outlier: 3.719A pdb=" N ASN A 150 " --> pdb=" O THR A 146 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA A 151 " --> pdb=" O PHE A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 174 Processing helix chain 'A' and resid 176 through 189 Processing helix chain 'A' and resid 197 through 211 removed outlier: 3.645A pdb=" N ILE A 204 " --> pdb=" O GLU A 200 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N MET A 211 " --> pdb=" O SER A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 236 Processing helix chain 'A' and resid 246 through 255 removed outlier: 3.932A pdb=" N LYS A 255 " --> pdb=" O GLU A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 263 Processing helix chain 'A' and resid 264 through 268 removed outlier: 3.746A pdb=" N ASP A 267 " --> pdb=" O GLN A 264 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN A 268 " --> pdb=" O LEU A 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 264 through 268' Processing helix chain 'B' and resid 8 through 16 Processing helix chain 'B' and resid 17 through 19 No H-bonds generated for 'chain 'B' and resid 17 through 19' Processing helix chain 'B' and resid 55 through 59 Processing helix chain 'B' and resid 69 through 73 Processing helix chain 'B' and resid 90 through 100 Processing helix chain 'B' and resid 110 through 122 Processing helix chain 'B' and resid 124 through 128 removed outlier: 3.610A pdb=" N ILE B 128 " --> pdb=" O PRO B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 132 Processing helix chain 'B' and resid 133 through 148 Processing helix chain 'B' and resid 166 through 174 removed outlier: 3.531A pdb=" N GLU B 174 " --> pdb=" O TRP B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 203 removed outlier: 4.023A pdb=" N PHE B 191 " --> pdb=" O TYR B 187 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE B 192 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE B 193 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ALA B 194 " --> pdb=" O GLY B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 222 Processing helix chain 'B' and resid 222 through 247 removed outlier: 3.667A pdb=" N LEU B 229 " --> pdb=" O ALA B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 276 removed outlier: 3.519A pdb=" N ILE B 261 " --> pdb=" O SER B 257 " (cutoff:3.500A) Proline residue: B 269 - end of helix removed outlier: 3.632A pdb=" N GLY B 273 " --> pdb=" O PRO B 269 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET B 276 " --> pdb=" O ILE B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 281 removed outlier: 4.004A pdb=" N ASP B 281 " --> pdb=" O ASN B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 292 Processing helix chain 'B' and resid 293 through 303 removed outlier: 3.914A pdb=" N ARG B 296 " --> pdb=" O ARG B 293 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG B 302 " --> pdb=" O LYS B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 317 removed outlier: 3.595A pdb=" N ARG B 308 " --> pdb=" O SER B 304 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY B 311 " --> pdb=" O LEU B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 344 removed outlier: 3.634A pdb=" N PHE B 323 " --> pdb=" O SER B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 366 removed outlier: 4.136A pdb=" N TRP B 359 " --> pdb=" O PRO B 355 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N TYR B 360 " --> pdb=" O ALA B 356 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR B 366 " --> pdb=" O ILE B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 396 removed outlier: 3.847A pdb=" N LEU B 389 " --> pdb=" O SER B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 446 removed outlier: 4.448A pdb=" N VAL B 401 " --> pdb=" O LEU B 397 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS B 424 " --> pdb=" O ARG B 420 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA B 425 " --> pdb=" O ALA B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 484 Processing helix chain 'C' and resid 93 through 100 Processing helix chain 'C' and resid 103 through 118 Processing helix chain 'C' and resid 124 through 133 removed outlier: 3.938A pdb=" N LYS C 129 " --> pdb=" O GLU C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 153 removed outlier: 3.714A pdb=" N ASN C 150 " --> pdb=" O THR C 146 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA C 151 " --> pdb=" O PHE C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 174 Processing helix chain 'C' and resid 176 through 189 Processing helix chain 'C' and resid 197 through 211 removed outlier: 3.556A pdb=" N ILE C 204 " --> pdb=" O GLU C 200 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N MET C 211 " --> pdb=" O SER C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 236 Processing helix chain 'C' and resid 246 through 255 removed outlier: 3.937A pdb=" N LYS C 255 " --> pdb=" O GLU C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 263 Processing helix chain 'C' and resid 264 through 268 removed outlier: 3.757A pdb=" N ASP C 267 " --> pdb=" O GLN C 264 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN C 268 " --> pdb=" O LEU C 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 264 through 268' Processing helix chain 'D' and resid 8 through 16 Processing helix chain 'D' and resid 17 through 19 No H-bonds generated for 'chain 'D' and resid 17 through 19' Processing helix chain 'D' and resid 55 through 59 Processing helix chain 'D' and resid 69 through 73 Processing helix chain 'D' and resid 90 through 100 Processing helix chain 'D' and resid 110 through 122 Processing helix chain 'D' and resid 124 through 128 removed outlier: 3.607A pdb=" N ILE D 128 " --> pdb=" O PRO D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 132 Processing helix chain 'D' and resid 133 through 148 Processing helix chain 'D' and resid 166 through 174 Processing helix chain 'D' and resid 179 through 203 removed outlier: 4.068A pdb=" N PHE D 191 " --> pdb=" O TYR D 187 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE D 192 " --> pdb=" O VAL D 188 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE D 193 " --> pdb=" O THR D 189 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ALA D 194 " --> pdb=" O GLY D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 222 Processing helix chain 'D' and resid 222 through 247 removed outlier: 3.657A pdb=" N LEU D 229 " --> pdb=" O ALA D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 276 removed outlier: 3.523A pdb=" N ILE D 261 " --> pdb=" O SER D 257 " (cutoff:3.500A) Proline residue: D 269 - end of helix removed outlier: 3.594A pdb=" N GLY D 273 " --> pdb=" O PRO D 269 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET D 276 " --> pdb=" O ILE D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 281 removed outlier: 3.971A pdb=" N ASP D 281 " --> pdb=" O ASN D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 292 Processing helix chain 'D' and resid 293 through 303 removed outlier: 3.927A pdb=" N ARG D 296 " --> pdb=" O ARG D 293 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG D 302 " --> pdb=" O LYS D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 317 removed outlier: 3.595A pdb=" N ARG D 308 " --> pdb=" O SER D 304 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY D 311 " --> pdb=" O LEU D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 344 removed outlier: 3.631A pdb=" N PHE D 323 " --> pdb=" O SER D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 366 removed outlier: 4.135A pdb=" N TRP D 359 " --> pdb=" O PRO D 355 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N TYR D 360 " --> pdb=" O ALA D 356 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR D 366 " --> pdb=" O ILE D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 396 removed outlier: 3.846A pdb=" N LEU D 389 " --> pdb=" O SER D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 446 removed outlier: 4.448A pdb=" N VAL D 401 " --> pdb=" O LEU D 397 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS D 424 " --> pdb=" O ARG D 420 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA D 425 " --> pdb=" O ALA D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'E' and resid 93 through 100 Processing helix chain 'E' and resid 103 through 118 Processing helix chain 'E' and resid 124 through 133 removed outlier: 3.924A pdb=" N LYS E 129 " --> pdb=" O GLU E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 153 removed outlier: 3.752A pdb=" N ASN E 150 " --> pdb=" O THR E 146 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA E 151 " --> pdb=" O PHE E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 174 Processing helix chain 'E' and resid 176 through 189 Processing helix chain 'E' and resid 197 through 211 removed outlier: 3.544A pdb=" N ILE E 204 " --> pdb=" O GLU E 200 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET E 211 " --> pdb=" O SER E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 236 Processing helix chain 'E' and resid 246 through 255 removed outlier: 3.940A pdb=" N LYS E 255 " --> pdb=" O GLU E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 263 Processing helix chain 'E' and resid 264 through 268 removed outlier: 3.754A pdb=" N ASP E 267 " --> pdb=" O GLN E 264 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN E 268 " --> pdb=" O LEU E 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 264 through 268' Processing helix chain 'F' and resid 8 through 16 Processing helix chain 'F' and resid 17 through 19 No H-bonds generated for 'chain 'F' and resid 17 through 19' Processing helix chain 'F' and resid 55 through 59 Processing helix chain 'F' and resid 69 through 73 Processing helix chain 'F' and resid 90 through 100 Processing helix chain 'F' and resid 110 through 122 Processing helix chain 'F' and resid 124 through 128 removed outlier: 3.596A pdb=" N ILE F 128 " --> pdb=" O PRO F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 129 through 132 Processing helix chain 'F' and resid 133 through 148 Processing helix chain 'F' and resid 166 through 174 removed outlier: 3.532A pdb=" N GLU F 174 " --> pdb=" O TRP F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 203 removed outlier: 4.015A pdb=" N PHE F 191 " --> pdb=" O TYR F 187 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE F 192 " --> pdb=" O VAL F 188 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE F 193 " --> pdb=" O THR F 189 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ALA F 194 " --> pdb=" O GLY F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 217 through 222 Processing helix chain 'F' and resid 222 through 247 removed outlier: 3.655A pdb=" N LEU F 229 " --> pdb=" O ALA F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 276 removed outlier: 3.514A pdb=" N ILE F 261 " --> pdb=" O SER F 257 " (cutoff:3.500A) Proline residue: F 269 - end of helix removed outlier: 3.632A pdb=" N GLY F 273 " --> pdb=" O PRO F 269 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET F 276 " --> pdb=" O ILE F 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 277 through 281 removed outlier: 3.991A pdb=" N ASP F 281 " --> pdb=" O ASN F 278 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 292 Processing helix chain 'F' and resid 293 through 303 removed outlier: 3.930A pdb=" N ARG F 296 " --> pdb=" O ARG F 293 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG F 302 " --> pdb=" O LYS F 299 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 317 removed outlier: 3.582A pdb=" N ARG F 308 " --> pdb=" O SER F 304 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY F 311 " --> pdb=" O LEU F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 344 removed outlier: 3.653A pdb=" N PHE F 323 " --> pdb=" O SER F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 366 removed outlier: 4.144A pdb=" N TRP F 359 " --> pdb=" O PRO F 355 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N TYR F 360 " --> pdb=" O ALA F 356 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR F 366 " --> pdb=" O ILE F 362 " (cutoff:3.500A) Processing helix chain 'F' and resid 377 through 396 removed outlier: 3.876A pdb=" N LEU F 389 " --> pdb=" O SER F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 446 removed outlier: 4.443A pdb=" N VAL F 401 " --> pdb=" O LEU F 397 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LYS F 424 " --> pdb=" O ARG F 420 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA F 425 " --> pdb=" O ALA F 421 " (cutoff:3.500A) Processing helix chain 'F' and resid 472 through 484 Processing helix chain 'G' and resid 93 through 100 Processing helix chain 'G' and resid 103 through 118 Processing helix chain 'G' and resid 124 through 133 removed outlier: 3.969A pdb=" N LYS G 129 " --> pdb=" O GLU G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 153 removed outlier: 3.708A pdb=" N ASN G 150 " --> pdb=" O THR G 146 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA G 151 " --> pdb=" O PHE G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 161 through 174 Processing helix chain 'G' and resid 176 through 189 Processing helix chain 'G' and resid 197 through 211 removed outlier: 3.613A pdb=" N ILE G 204 " --> pdb=" O GLU G 200 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET G 211 " --> pdb=" O SER G 207 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 236 Processing helix chain 'G' and resid 246 through 255 removed outlier: 3.932A pdb=" N LYS G 255 " --> pdb=" O GLU G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 257 through 263 Processing helix chain 'G' and resid 264 through 268 removed outlier: 3.751A pdb=" N ASP G 267 " --> pdb=" O GLN G 264 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN G 268 " --> pdb=" O LEU G 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 264 through 268' Processing helix chain 'H' and resid 8 through 16 Processing helix chain 'H' and resid 17 through 19 No H-bonds generated for 'chain 'H' and resid 17 through 19' Processing helix chain 'H' and resid 55 through 59 Processing helix chain 'H' and resid 69 through 73 Processing helix chain 'H' and resid 90 through 100 Processing helix chain 'H' and resid 110 through 122 Processing helix chain 'H' and resid 124 through 128 removed outlier: 3.621A pdb=" N ILE H 128 " --> pdb=" O PRO H 125 " (cutoff:3.500A) Processing helix chain 'H' and resid 129 through 132 Processing helix chain 'H' and resid 133 through 148 Processing helix chain 'H' and resid 166 through 174 removed outlier: 3.536A pdb=" N GLU H 174 " --> pdb=" O TRP H 170 " (cutoff:3.500A) Processing helix chain 'H' and resid 179 through 203 removed outlier: 4.003A pdb=" N PHE H 191 " --> pdb=" O TYR H 187 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE H 192 " --> pdb=" O VAL H 188 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE H 193 " --> pdb=" O THR H 189 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ALA H 194 " --> pdb=" O GLY H 190 " (cutoff:3.500A) Processing helix chain 'H' and resid 217 through 222 Processing helix chain 'H' and resid 222 through 247 removed outlier: 3.660A pdb=" N LEU H 229 " --> pdb=" O ALA H 225 " (cutoff:3.500A) Processing helix chain 'H' and resid 257 through 276 removed outlier: 3.529A pdb=" N ILE H 261 " --> pdb=" O SER H 257 " (cutoff:3.500A) Proline residue: H 269 - end of helix removed outlier: 3.639A pdb=" N GLY H 273 " --> pdb=" O PRO H 269 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N MET H 276 " --> pdb=" O ILE H 272 " (cutoff:3.500A) Processing helix chain 'H' and resid 277 through 281 removed outlier: 4.004A pdb=" N ASP H 281 " --> pdb=" O ASN H 278 " (cutoff:3.500A) Processing helix chain 'H' and resid 286 through 292 Processing helix chain 'H' and resid 293 through 303 removed outlier: 3.930A pdb=" N ARG H 296 " --> pdb=" O ARG H 293 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG H 302 " --> pdb=" O LYS H 299 " (cutoff:3.500A) Processing helix chain 'H' and resid 304 through 317 removed outlier: 3.636A pdb=" N ARG H 308 " --> pdb=" O SER H 304 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY H 311 " --> pdb=" O LEU H 307 " (cutoff:3.500A) Processing helix chain 'H' and resid 317 through 344 removed outlier: 3.648A pdb=" N PHE H 323 " --> pdb=" O SER H 319 " (cutoff:3.500A) Processing helix chain 'H' and resid 355 through 366 removed outlier: 4.138A pdb=" N TRP H 359 " --> pdb=" O PRO H 355 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N TYR H 360 " --> pdb=" O ALA H 356 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR H 366 " --> pdb=" O ILE H 362 " (cutoff:3.500A) Processing helix chain 'H' and resid 377 through 396 removed outlier: 3.864A pdb=" N LEU H 389 " --> pdb=" O SER H 385 " (cutoff:3.500A) Processing helix chain 'H' and resid 397 through 446 removed outlier: 4.442A pdb=" N VAL H 401 " --> pdb=" O LEU H 397 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS H 424 " --> pdb=" O ARG H 420 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA H 425 " --> pdb=" O ALA H 421 " (cutoff:3.500A) Processing helix chain 'H' and resid 472 through 484 Processing sheet with id=AA1, first strand: chain 'A' and resid 195 through 196 Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 54 removed outlier: 3.595A pdb=" N GLU B 81 " --> pdb=" O ASN B 76 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 195 through 196 Processing sheet with id=AA4, first strand: chain 'D' and resid 49 through 54 removed outlier: 3.617A pdb=" N GLU D 81 " --> pdb=" O ASN D 76 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 195 through 196 Processing sheet with id=AA6, first strand: chain 'F' and resid 49 through 54 removed outlier: 3.607A pdb=" N GLU F 81 " --> pdb=" O ASN F 76 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 195 through 196 Processing sheet with id=AA8, first strand: chain 'H' and resid 49 through 54 removed outlier: 3.552A pdb=" N GLU H 81 " --> pdb=" O ASN H 76 " (cutoff:3.500A) 1174 hydrogen bonds defined for protein. 3366 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.53 Time building geometry restraints manager: 1.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6460 1.34 - 1.46: 3692 1.46 - 1.57: 10380 1.57 - 1.69: 0 1.69 - 1.81: 212 Bond restraints: 20744 Sorted by residual: bond pdb=" C MET D 268 " pdb=" N PRO D 269 " ideal model delta sigma weight residual 1.336 1.361 -0.025 1.08e-02 8.57e+03 5.45e+00 bond pdb=" C MET H 268 " pdb=" N PRO H 269 " ideal model delta sigma weight residual 1.336 1.361 -0.025 1.08e-02 8.57e+03 5.41e+00 bond pdb=" C MET F 268 " pdb=" N PRO F 269 " ideal model delta sigma weight residual 1.336 1.360 -0.024 1.08e-02 8.57e+03 4.91e+00 bond pdb=" C MET B 268 " pdb=" N PRO B 269 " ideal model delta sigma weight residual 1.336 1.359 -0.024 1.08e-02 8.57e+03 4.78e+00 bond pdb=" C GLY E 213 " pdb=" O GLY E 213 " ideal model delta sigma weight residual 1.237 1.227 0.010 7.00e-03 2.04e+04 2.08e+00 ... (remaining 20739 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 27271 1.70 - 3.39: 650 3.39 - 5.09: 70 5.09 - 6.79: 30 6.79 - 8.48: 7 Bond angle restraints: 28028 Sorted by residual: angle pdb=" N GLY C 121 " pdb=" CA GLY C 121 " pdb=" C GLY C 121 " ideal model delta sigma weight residual 113.18 104.70 8.48 2.37e+00 1.78e-01 1.28e+01 angle pdb=" N GLY E 121 " pdb=" CA GLY E 121 " pdb=" C GLY E 121 " ideal model delta sigma weight residual 113.18 104.72 8.46 2.37e+00 1.78e-01 1.27e+01 angle pdb=" N GLY A 121 " pdb=" CA GLY A 121 " pdb=" C GLY A 121 " ideal model delta sigma weight residual 113.18 104.73 8.45 2.37e+00 1.78e-01 1.27e+01 angle pdb=" N GLY G 121 " pdb=" CA GLY G 121 " pdb=" C GLY G 121 " ideal model delta sigma weight residual 113.18 104.79 8.39 2.37e+00 1.78e-01 1.25e+01 angle pdb=" N VAL B 22 " pdb=" CA VAL B 22 " pdb=" C VAL B 22 " ideal model delta sigma weight residual 112.80 108.85 3.95 1.15e+00 7.56e-01 1.18e+01 ... (remaining 28023 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 11160 17.61 - 35.22: 1033 35.22 - 52.83: 136 52.83 - 70.44: 11 70.44 - 88.05: 16 Dihedral angle restraints: 12356 sinusoidal: 4996 harmonic: 7360 Sorted by residual: dihedral pdb=" CA GLY G 121 " pdb=" C GLY G 121 " pdb=" N ILE G 122 " pdb=" CA ILE G 122 " ideal model delta harmonic sigma weight residual -180.00 -143.86 -36.14 0 5.00e+00 4.00e-02 5.22e+01 dihedral pdb=" CA GLY E 121 " pdb=" C GLY E 121 " pdb=" N ILE E 122 " pdb=" CA ILE E 122 " ideal model delta harmonic sigma weight residual 180.00 -143.99 -36.01 0 5.00e+00 4.00e-02 5.19e+01 dihedral pdb=" CA GLY A 121 " pdb=" C GLY A 121 " pdb=" N ILE A 122 " pdb=" CA ILE A 122 " ideal model delta harmonic sigma weight residual -180.00 -144.09 -35.91 0 5.00e+00 4.00e-02 5.16e+01 ... (remaining 12353 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1677 0.031 - 0.063: 915 0.063 - 0.094: 370 0.094 - 0.126: 82 0.126 - 0.157: 24 Chirality restraints: 3068 Sorted by residual: chirality pdb=" CG LEU D 44 " pdb=" CB LEU D 44 " pdb=" CD1 LEU D 44 " pdb=" CD2 LEU D 44 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.16e-01 chirality pdb=" CG LEU B 44 " pdb=" CB LEU B 44 " pdb=" CD1 LEU B 44 " pdb=" CD2 LEU B 44 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.03e-01 chirality pdb=" CG LEU F 44 " pdb=" CB LEU F 44 " pdb=" CD1 LEU F 44 " pdb=" CD2 LEU F 44 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.75e-01 ... (remaining 3065 not shown) Planarity restraints: 3576 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR E 217 " -0.033 5.00e-02 4.00e+02 4.95e-02 3.93e+00 pdb=" N PRO E 218 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO E 218 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 218 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR G 217 " 0.033 5.00e-02 4.00e+02 4.93e-02 3.90e+00 pdb=" N PRO G 218 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO G 218 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO G 218 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 354 " 0.033 5.00e-02 4.00e+02 4.89e-02 3.82e+00 pdb=" N PRO D 355 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO D 355 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 355 " 0.028 5.00e-02 4.00e+02 ... (remaining 3573 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1757 2.73 - 3.27: 21825 3.27 - 3.82: 33309 3.82 - 4.36: 40298 4.36 - 4.90: 67372 Nonbonded interactions: 164561 Sorted by model distance: nonbonded pdb=" O GLU C 248 " pdb=" OG SER C 252 " model vdw 2.191 3.040 nonbonded pdb=" O GLU G 248 " pdb=" OG SER G 252 " model vdw 2.196 3.040 nonbonded pdb=" NH2 ARG A 104 " pdb=" OE1 GLU H 77 " model vdw 2.196 3.120 nonbonded pdb=" O GLU E 248 " pdb=" OG SER E 252 " model vdw 2.196 3.040 nonbonded pdb=" O GLU A 248 " pdb=" OG SER A 252 " model vdw 2.198 3.040 ... (remaining 164556 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 18.470 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.070 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:10.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 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 0.042 20744 Z= 0.236 Angle : 0.675 8.484 28028 Z= 0.394 Chirality : 0.044 0.157 3068 Planarity : 0.005 0.050 3576 Dihedral : 13.599 88.051 7604 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 0.18 % Allowed : 5.34 % Favored : 94.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -3.03 (0.14), residues: 2476 helix: -1.49 (0.11), residues: 1668 sheet: None (None), residues: 0 loop : -2.89 (0.18), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG A 112 TYR 0.024 0.002 TYR C 132 PHE 0.021 0.002 PHE A 165 TRP 0.009 0.002 TRP F 359 HIS 0.005 0.001 HIS B 477 Details of bonding type rmsd covalent geometry : bond 0.00536 (20744) covalent geometry : angle 0.67515 (28028) hydrogen bonds : bond 0.14994 ( 1174) hydrogen bonds : angle 5.69490 ( 3366) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 539 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.8426 (mt0) cc_final: 0.8185 (mt0) REVERT: A 125 GLU cc_start: 0.7578 (tm-30) cc_final: 0.7293 (tm-30) REVERT: A 129 LYS cc_start: 0.8379 (mtmt) cc_final: 0.8064 (mtmt) REVERT: A 133 SER cc_start: 0.8739 (m) cc_final: 0.8362 (m) REVERT: A 134 GLN cc_start: 0.8440 (mm110) cc_final: 0.8008 (mm110) REVERT: A 192 LYS cc_start: 0.8452 (mmtm) cc_final: 0.7998 (mmmt) REVERT: B 29 LEU cc_start: 0.8178 (mm) cc_final: 0.7928 (tp) REVERT: B 130 ASP cc_start: 0.7677 (m-30) cc_final: 0.7468 (m-30) REVERT: B 276 MET cc_start: 0.7864 (mpp) cc_final: 0.7306 (mpt) REVERT: B 315 LYS cc_start: 0.8421 (tppt) cc_final: 0.8035 (tttt) REVERT: B 429 ARG cc_start: 0.7577 (ttp-170) cc_final: 0.7349 (mtm-85) REVERT: C 125 GLU cc_start: 0.7575 (tm-30) cc_final: 0.7345 (tm-30) REVERT: C 129 LYS cc_start: 0.8395 (mtmt) cc_final: 0.8044 (mtmt) REVERT: C 133 SER cc_start: 0.8808 (m) cc_final: 0.8442 (m) REVERT: C 134 GLN cc_start: 0.8421 (mm110) cc_final: 0.7948 (mm110) REVERT: C 192 LYS cc_start: 0.8415 (mmtm) cc_final: 0.7964 (mmmt) REVERT: D 29 LEU cc_start: 0.8174 (mm) cc_final: 0.7941 (tp) REVERT: D 130 ASP cc_start: 0.7675 (m-30) cc_final: 0.7472 (m-30) REVERT: D 315 LYS cc_start: 0.8394 (tppt) cc_final: 0.8023 (tttt) REVERT: E 125 GLU cc_start: 0.7608 (tm-30) cc_final: 0.7346 (tm-30) REVERT: E 129 LYS cc_start: 0.8377 (mtmt) cc_final: 0.8019 (mtmt) REVERT: E 133 SER cc_start: 0.8724 (m) cc_final: 0.8337 (m) REVERT: E 134 GLN cc_start: 0.8409 (mm110) cc_final: 0.7963 (mm110) REVERT: E 192 LYS cc_start: 0.8403 (mmtm) cc_final: 0.7959 (mmmt) REVERT: E 232 PHE cc_start: 0.8253 (t80) cc_final: 0.7809 (t80) REVERT: F 29 LEU cc_start: 0.8170 (mm) cc_final: 0.7927 (tp) REVERT: F 315 LYS cc_start: 0.8395 (tppt) cc_final: 0.8044 (tttt) REVERT: F 429 ARG cc_start: 0.7542 (ttp-170) cc_final: 0.7276 (mtm-85) REVERT: G 125 GLU cc_start: 0.7501 (tm-30) cc_final: 0.7228 (tm-30) REVERT: G 129 LYS cc_start: 0.8343 (mtmt) cc_final: 0.8000 (mtmt) REVERT: G 133 SER cc_start: 0.8727 (m) cc_final: 0.8354 (m) REVERT: G 134 GLN cc_start: 0.8430 (mm110) cc_final: 0.8004 (mm110) REVERT: G 192 LYS cc_start: 0.8440 (mmtm) cc_final: 0.7990 (mmmt) REVERT: H 29 LEU cc_start: 0.8168 (mm) cc_final: 0.7915 (tp) REVERT: H 230 ASP cc_start: 0.8134 (p0) cc_final: 0.7925 (p0) REVERT: H 315 LYS cc_start: 0.8394 (tppt) cc_final: 0.8024 (tttt) outliers start: 4 outliers final: 0 residues processed: 543 average time/residue: 0.6444 time to fit residues: 390.1224 Evaluate side-chains 375 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 375 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 7.9990 chunk 227 optimal weight: 0.3980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 235 optimal weight: 0.4980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN A 182 ASN A 264 GLN B 278 ASN B 405 ASN B 443 HIS C 97 GLN C 182 ASN D 278 ASN D 405 ASN D 443 HIS E 97 GLN E 182 ASN F 278 ASN F 405 ASN F 443 HIS G 97 GLN G 182 ASN H 278 ASN H 405 ASN H 443 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.152859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.101805 restraints weight = 31444.395| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.65 r_work: 0.3192 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20744 Z= 0.153 Angle : 0.664 12.717 28028 Z= 0.339 Chirality : 0.043 0.164 3068 Planarity : 0.005 0.055 3576 Dihedral : 5.099 34.910 2772 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.94 % Allowed : 15.04 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -0.95 (0.17), residues: 2476 helix: 0.05 (0.13), residues: 1676 sheet: None (None), residues: 0 loop : -1.97 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 415 TYR 0.020 0.001 TYR H 186 PHE 0.018 0.001 PHE E 165 TRP 0.007 0.001 TRP B 54 HIS 0.009 0.001 HIS B 443 Details of bonding type rmsd covalent geometry : bond 0.00343 (20744) covalent geometry : angle 0.66443 (28028) hydrogen bonds : bond 0.04951 ( 1174) hydrogen bonds : angle 4.28186 ( 3366) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 440 time to evaluate : 0.815 Fit side-chains REVERT: A 125 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7534 (tm-30) REVERT: A 129 LYS cc_start: 0.8298 (mtmt) cc_final: 0.8004 (mtpt) REVERT: A 133 SER cc_start: 0.8573 (m) cc_final: 0.8255 (m) REVERT: A 134 GLN cc_start: 0.8589 (mm110) cc_final: 0.8329 (mm110) REVERT: A 212 MET cc_start: 0.6848 (tpt) cc_final: 0.6629 (mmm) REVERT: A 232 PHE cc_start: 0.8135 (t80) cc_final: 0.7823 (t80) REVERT: A 254 GLN cc_start: 0.9007 (tp40) cc_final: 0.8754 (tp40) REVERT: A 261 ARG cc_start: 0.8399 (tmt170) cc_final: 0.8193 (tpt90) REVERT: B 29 LEU cc_start: 0.7916 (mm) cc_final: 0.7653 (tp) REVERT: B 130 ASP cc_start: 0.8346 (m-30) cc_final: 0.8132 (m-30) REVERT: B 187 TYR cc_start: 0.7958 (m-10) cc_final: 0.7720 (m-10) REVERT: B 292 PHE cc_start: 0.8748 (m-80) cc_final: 0.8529 (m-80) REVERT: B 299 LYS cc_start: 0.9216 (mttt) cc_final: 0.8959 (mtpt) REVERT: B 315 LYS cc_start: 0.8284 (tppt) cc_final: 0.7796 (ttmt) REVERT: C 125 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7594 (tm-30) REVERT: C 129 LYS cc_start: 0.8329 (mtmt) cc_final: 0.8041 (mtpt) REVERT: C 133 SER cc_start: 0.8582 (m) cc_final: 0.8261 (m) REVERT: C 134 GLN cc_start: 0.8578 (mm110) cc_final: 0.8316 (mm110) REVERT: C 212 MET cc_start: 0.6941 (tpt) cc_final: 0.6680 (mmm) REVERT: C 226 ARG cc_start: 0.8246 (mmm-85) cc_final: 0.7910 (mmm-85) REVERT: C 254 GLN cc_start: 0.9002 (tp40) cc_final: 0.8723 (tp40) REVERT: C 262 SER cc_start: 0.9110 (t) cc_final: 0.8807 (p) REVERT: C 263 MET cc_start: 0.8324 (ttm) cc_final: 0.7847 (tpp) REVERT: D 29 LEU cc_start: 0.7891 (mm) cc_final: 0.7652 (tp) REVERT: D 130 ASP cc_start: 0.8400 (m-30) cc_final: 0.8191 (m-30) REVERT: D 142 GLU cc_start: 0.7760 (tm-30) cc_final: 0.7533 (tm-30) REVERT: D 146 ARG cc_start: 0.8094 (ttm170) cc_final: 0.7794 (ttp-170) REVERT: D 170 TRP cc_start: 0.7284 (t-100) cc_final: 0.7000 (t-100) REVERT: D 315 LYS cc_start: 0.8299 (tppt) cc_final: 0.7795 (ttmt) REVERT: E 125 GLU cc_start: 0.7988 (tm-30) cc_final: 0.7528 (tm-30) REVERT: E 129 LYS cc_start: 0.8345 (mtmt) cc_final: 0.8037 (mtpt) REVERT: E 133 SER cc_start: 0.8519 (m) cc_final: 0.8181 (m) REVERT: E 134 GLN cc_start: 0.8529 (mm110) cc_final: 0.8255 (mm110) REVERT: E 226 ARG cc_start: 0.8211 (mmm-85) cc_final: 0.7946 (mmm-85) REVERT: E 236 MET cc_start: 0.7833 (mtt) cc_final: 0.7134 (pp-130) REVERT: E 254 GLN cc_start: 0.9060 (tp40) cc_final: 0.8681 (tp-100) REVERT: E 260 MET cc_start: 0.8003 (tpp) cc_final: 0.7800 (mpp) REVERT: E 263 MET cc_start: 0.8374 (ttm) cc_final: 0.8167 (tpp) REVERT: F 29 LEU cc_start: 0.7912 (mm) cc_final: 0.7648 (tp) REVERT: F 315 LYS cc_start: 0.8267 (tppt) cc_final: 0.7747 (ttmt) REVERT: G 125 GLU cc_start: 0.8036 (tm-30) cc_final: 0.7563 (tm-30) REVERT: G 129 LYS cc_start: 0.8309 (mtmt) cc_final: 0.8017 (mtpt) REVERT: G 133 SER cc_start: 0.8563 (m) cc_final: 0.8242 (m) REVERT: G 134 GLN cc_start: 0.8559 (mm110) cc_final: 0.8284 (mm110) REVERT: G 212 MET cc_start: 0.6881 (tpt) cc_final: 0.6625 (mmm) REVERT: G 254 GLN cc_start: 0.9012 (tp40) cc_final: 0.8745 (tp40) REVERT: G 262 SER cc_start: 0.9172 (t) cc_final: 0.8869 (p) REVERT: H 29 LEU cc_start: 0.7901 (mm) cc_final: 0.7629 (tp) REVERT: H 187 TYR cc_start: 0.8033 (m-10) cc_final: 0.7784 (m-10) REVERT: H 299 LYS cc_start: 0.9207 (mttt) cc_final: 0.8947 (mtpt) REVERT: H 315 LYS cc_start: 0.8261 (tppt) cc_final: 0.7779 (ttmt) outliers start: 65 outliers final: 30 residues processed: 486 average time/residue: 0.5679 time to fit residues: 311.0579 Evaluate side-chains 419 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 389 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 407 SER Chi-restraints excluded: chain D residue 435 THR Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 407 SER Chi-restraints excluded: chain F residue 435 THR Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 163 GLU Chi-restraints excluded: chain G residue 241 ASP Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 407 SER Chi-restraints excluded: chain H residue 435 THR Chi-restraints excluded: chain H residue 444 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 87 optimal weight: 0.8980 chunk 12 optimal weight: 10.0000 chunk 209 optimal weight: 0.4980 chunk 81 optimal weight: 3.9990 chunk 176 optimal weight: 4.9990 chunk 219 optimal weight: 0.9980 chunk 224 optimal weight: 7.9990 chunk 240 optimal weight: 9.9990 chunk 136 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 189 optimal weight: 8.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN A 264 GLN B 443 HIS C 97 GLN D 443 HIS E 97 GLN F 443 HIS G 97 GLN H 443 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.150987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.099685 restraints weight = 31607.095| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.63 r_work: 0.3150 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 20744 Z= 0.202 Angle : 0.687 12.766 28028 Z= 0.346 Chirality : 0.044 0.170 3068 Planarity : 0.005 0.062 3576 Dihedral : 5.042 34.618 2772 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.44 % Allowed : 17.35 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.17), residues: 2476 helix: 0.40 (0.13), residues: 1680 sheet: None (None), residues: 0 loop : -1.74 (0.20), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 415 TYR 0.020 0.002 TYR D 186 PHE 0.023 0.002 PHE E 232 TRP 0.007 0.001 TRP H 54 HIS 0.006 0.001 HIS B 477 Details of bonding type rmsd covalent geometry : bond 0.00479 (20744) covalent geometry : angle 0.68669 (28028) hydrogen bonds : bond 0.05128 ( 1174) hydrogen bonds : angle 4.33566 ( 3366) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 408 time to evaluate : 0.670 Fit side-chains REVERT: A 125 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7523 (tm-30) REVERT: A 129 LYS cc_start: 0.8303 (mtmt) cc_final: 0.8014 (mtpt) REVERT: A 133 SER cc_start: 0.8590 (m) cc_final: 0.8318 (m) REVERT: A 254 GLN cc_start: 0.9037 (tp40) cc_final: 0.8696 (tp-100) REVERT: B 29 LEU cc_start: 0.7939 (mm) cc_final: 0.7669 (tp) REVERT: B 299 LYS cc_start: 0.9250 (mttt) cc_final: 0.8985 (mtpt) REVERT: B 315 LYS cc_start: 0.8310 (tppt) cc_final: 0.7813 (ttmt) REVERT: C 125 GLU cc_start: 0.8087 (tm-30) cc_final: 0.7634 (tm-30) REVERT: C 129 LYS cc_start: 0.8321 (mtmt) cc_final: 0.8037 (mtpt) REVERT: C 133 SER cc_start: 0.8547 (m) cc_final: 0.8272 (m) REVERT: C 212 MET cc_start: 0.6945 (tpt) cc_final: 0.6745 (mmm) REVERT: C 226 ARG cc_start: 0.8261 (mmm-85) cc_final: 0.7897 (mmm-85) REVERT: C 254 GLN cc_start: 0.9081 (tp40) cc_final: 0.8705 (tp-100) REVERT: C 264 GLN cc_start: 0.8594 (pt0) cc_final: 0.8271 (mm-40) REVERT: D 20 MET cc_start: 0.8887 (mmt) cc_final: 0.8531 (mmt) REVERT: D 29 LEU cc_start: 0.7960 (mm) cc_final: 0.7674 (tp) REVERT: D 142 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7609 (tm-30) REVERT: D 146 ARG cc_start: 0.8216 (ttm170) cc_final: 0.7812 (ttp-170) REVERT: D 187 TYR cc_start: 0.7873 (m-10) cc_final: 0.7668 (m-10) REVERT: D 268 MET cc_start: 0.8420 (ptp) cc_final: 0.8176 (ptm) REVERT: D 276 MET cc_start: 0.6991 (mmm) cc_final: 0.6709 (mmt) REVERT: D 315 LYS cc_start: 0.8314 (tppt) cc_final: 0.7793 (ttmt) REVERT: E 125 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7601 (tm-30) REVERT: E 129 LYS cc_start: 0.8306 (mtmt) cc_final: 0.8021 (mtpt) REVERT: E 133 SER cc_start: 0.8542 (m) cc_final: 0.8272 (m) REVERT: E 226 ARG cc_start: 0.8262 (mmm-85) cc_final: 0.7941 (mmm-85) REVERT: E 254 GLN cc_start: 0.9061 (tp40) cc_final: 0.8701 (tp-100) REVERT: E 260 MET cc_start: 0.7912 (tpp) cc_final: 0.7472 (mpp) REVERT: F 29 LEU cc_start: 0.7962 (mm) cc_final: 0.7667 (tp) REVERT: F 171 ARG cc_start: 0.7572 (tmm-80) cc_final: 0.7332 (tmm-80) REVERT: F 268 MET cc_start: 0.8101 (ptm) cc_final: 0.7868 (ptp) REVERT: F 315 LYS cc_start: 0.8299 (tppt) cc_final: 0.7790 (ttmt) REVERT: G 112 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7678 (mtm-85) REVERT: G 125 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7619 (tm-30) REVERT: G 129 LYS cc_start: 0.8344 (mtmt) cc_final: 0.8100 (mtpt) REVERT: G 133 SER cc_start: 0.8542 (m) cc_final: 0.8271 (m) REVERT: G 212 MET cc_start: 0.6853 (tpt) cc_final: 0.6410 (mmm) REVERT: G 254 GLN cc_start: 0.9059 (tp40) cc_final: 0.8731 (tp-100) REVERT: G 262 SER cc_start: 0.9197 (t) cc_final: 0.8922 (p) REVERT: H 20 MET cc_start: 0.8883 (mmt) cc_final: 0.8471 (mpm) REVERT: H 29 LEU cc_start: 0.7911 (mm) cc_final: 0.7613 (tp) REVERT: H 187 TYR cc_start: 0.7978 (m-10) cc_final: 0.7755 (m-10) REVERT: H 315 LYS cc_start: 0.8296 (tppt) cc_final: 0.7796 (ttmt) outliers start: 76 outliers final: 34 residues processed: 467 average time/residue: 0.5734 time to fit residues: 302.1497 Evaluate side-chains 417 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 382 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 407 SER Chi-restraints excluded: chain D residue 435 THR Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 407 SER Chi-restraints excluded: chain F residue 435 THR Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain G residue 112 ARG Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 163 GLU Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 393 LEU Chi-restraints excluded: chain H residue 407 SER Chi-restraints excluded: chain H residue 435 THR Chi-restraints excluded: chain H residue 444 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 227 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 173 optimal weight: 0.7980 chunk 127 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 194 optimal weight: 10.0000 chunk 160 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 208 optimal weight: 0.9990 chunk 158 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN A 264 GLN B 177 HIS B 443 HIS C 97 GLN D 177 HIS D 443 HIS E 97 GLN F 177 HIS F 443 HIS G 97 GLN H 177 HIS H 443 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.152888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.101687 restraints weight = 31653.277| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.65 r_work: 0.3189 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20744 Z= 0.148 Angle : 0.663 11.721 28028 Z= 0.326 Chirality : 0.042 0.156 3068 Planarity : 0.005 0.053 3576 Dihedral : 4.854 32.648 2772 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.62 % Allowed : 19.97 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -0.05 (0.17), residues: 2476 helix: 0.69 (0.13), residues: 1676 sheet: None (None), residues: 0 loop : -1.50 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 415 TYR 0.017 0.001 TYR F 186 PHE 0.016 0.001 PHE C 136 TRP 0.007 0.001 TRP H 54 HIS 0.004 0.001 HIS B 477 Details of bonding type rmsd covalent geometry : bond 0.00338 (20744) covalent geometry : angle 0.66261 (28028) hydrogen bonds : bond 0.04550 ( 1174) hydrogen bonds : angle 4.15980 ( 3366) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 412 time to evaluate : 0.797 Fit side-chains revert: symmetry clash REVERT: A 125 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7565 (tm-30) REVERT: A 129 LYS cc_start: 0.8295 (mtmt) cc_final: 0.8028 (mtpt) REVERT: A 133 SER cc_start: 0.8551 (m) cc_final: 0.8289 (m) REVERT: A 163 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8119 (mp0) REVERT: A 212 MET cc_start: 0.6959 (mmm) cc_final: 0.6666 (mmm) REVERT: A 241 ASP cc_start: 0.7666 (OUTLIER) cc_final: 0.7149 (p0) REVERT: A 254 GLN cc_start: 0.9045 (tp40) cc_final: 0.8719 (tp-100) REVERT: B 20 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.8496 (mpm) REVERT: B 29 LEU cc_start: 0.7933 (mm) cc_final: 0.7597 (tp) REVERT: B 171 ARG cc_start: 0.7581 (tmm-80) cc_final: 0.7352 (tmm-80) REVERT: B 268 MET cc_start: 0.8375 (ptp) cc_final: 0.8136 (ptm) REVERT: B 299 LYS cc_start: 0.9255 (mttt) cc_final: 0.9046 (mtpm) REVERT: B 315 LYS cc_start: 0.8253 (tppt) cc_final: 0.7750 (ttmt) REVERT: C 105 LYS cc_start: 0.8394 (mmmm) cc_final: 0.8077 (mmtp) REVERT: C 125 GLU cc_start: 0.8010 (tm-30) cc_final: 0.7546 (tm-30) REVERT: C 129 LYS cc_start: 0.8345 (mtmt) cc_final: 0.8026 (mtpt) REVERT: C 133 SER cc_start: 0.8516 (m) cc_final: 0.8265 (m) REVERT: C 163 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8093 (mp0) REVERT: C 212 MET cc_start: 0.6925 (tpt) cc_final: 0.6353 (mmm) REVERT: C 226 ARG cc_start: 0.8283 (mmm-85) cc_final: 0.7905 (mmm-85) REVERT: C 254 GLN cc_start: 0.9054 (tp40) cc_final: 0.8761 (tp-100) REVERT: C 264 GLN cc_start: 0.8519 (pt0) cc_final: 0.8221 (mm-40) REVERT: D 29 LEU cc_start: 0.7910 (mm) cc_final: 0.7574 (tp) REVERT: D 142 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7586 (tm-30) REVERT: D 146 ARG cc_start: 0.8187 (ttm170) cc_final: 0.7730 (ttp-170) REVERT: D 238 THR cc_start: 0.8864 (OUTLIER) cc_final: 0.8623 (p) REVERT: D 276 MET cc_start: 0.6930 (mmm) cc_final: 0.6658 (mmt) REVERT: D 315 LYS cc_start: 0.8287 (tppt) cc_final: 0.7771 (ttmt) REVERT: E 125 GLU cc_start: 0.8008 (tm-30) cc_final: 0.7535 (tm-30) REVERT: E 129 LYS cc_start: 0.8336 (mtmt) cc_final: 0.8031 (mtpt) REVERT: E 133 SER cc_start: 0.8502 (m) cc_final: 0.8236 (m) REVERT: E 163 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8141 (mp0) REVERT: E 212 MET cc_start: 0.6834 (mmm) cc_final: 0.6555 (mmm) REVERT: E 226 ARG cc_start: 0.8276 (mmm-85) cc_final: 0.7894 (mmm-85) REVERT: E 236 MET cc_start: 0.7358 (pp-130) cc_final: 0.7107 (pp-130) REVERT: E 254 GLN cc_start: 0.9016 (tp40) cc_final: 0.8801 (tp40) REVERT: E 260 MET cc_start: 0.7938 (tpp) cc_final: 0.7583 (mpp) REVERT: F 29 LEU cc_start: 0.7937 (mm) cc_final: 0.7567 (tp) REVERT: F 146 ARG cc_start: 0.8190 (ttm170) cc_final: 0.7825 (ttp-170) REVERT: F 171 ARG cc_start: 0.7570 (tmm-80) cc_final: 0.7327 (tmm-80) REVERT: F 268 MET cc_start: 0.8019 (ptm) cc_final: 0.7779 (ptp) REVERT: F 315 LYS cc_start: 0.8289 (tppt) cc_final: 0.7804 (ttmt) REVERT: G 105 LYS cc_start: 0.8398 (mmmm) cc_final: 0.8082 (mmtp) REVERT: G 125 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7620 (tm-30) REVERT: G 129 LYS cc_start: 0.8372 (mtmt) cc_final: 0.8102 (mtpt) REVERT: G 133 SER cc_start: 0.8530 (m) cc_final: 0.8261 (m) REVERT: G 163 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8104 (mp0) REVERT: G 212 MET cc_start: 0.6884 (tpt) cc_final: 0.6406 (mmm) REVERT: G 241 ASP cc_start: 0.7706 (OUTLIER) cc_final: 0.7192 (p0) REVERT: G 254 GLN cc_start: 0.9052 (tp40) cc_final: 0.8724 (tp-100) REVERT: H 20 MET cc_start: 0.8842 (mmt) cc_final: 0.8493 (mpm) REVERT: H 29 LEU cc_start: 0.7951 (mm) cc_final: 0.7602 (tp) REVERT: H 171 ARG cc_start: 0.7520 (tmm-80) cc_final: 0.7277 (tmm-80) REVERT: H 315 LYS cc_start: 0.8328 (tppt) cc_final: 0.7826 (ttmt) outliers start: 80 outliers final: 34 residues processed: 472 average time/residue: 0.5837 time to fit residues: 309.7037 Evaluate side-chains 414 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 372 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 407 SER Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 407 SER Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 163 GLU Chi-restraints excluded: chain G residue 241 ASP Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 393 LEU Chi-restraints excluded: chain H residue 407 SER Chi-restraints excluded: chain H residue 444 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 234 optimal weight: 0.8980 chunk 55 optimal weight: 7.9990 chunk 126 optimal weight: 0.3980 chunk 205 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 215 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 84 optimal weight: 0.7980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN A 264 GLN C 97 GLN E 97 GLN G 97 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.153342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.101891 restraints weight = 31356.834| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.64 r_work: 0.3186 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20744 Z= 0.154 Angle : 0.675 13.420 28028 Z= 0.331 Chirality : 0.042 0.181 3068 Planarity : 0.005 0.048 3576 Dihedral : 4.768 32.089 2772 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.26 % Allowed : 21.83 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 0.12 (0.17), residues: 2476 helix: 0.79 (0.13), residues: 1676 sheet: None (None), residues: 0 loop : -1.37 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 415 TYR 0.018 0.001 TYR F 186 PHE 0.020 0.001 PHE G 136 TRP 0.007 0.001 TRP H 54 HIS 0.004 0.001 HIS B 477 Details of bonding type rmsd covalent geometry : bond 0.00356 (20744) covalent geometry : angle 0.67543 (28028) hydrogen bonds : bond 0.04500 ( 1174) hydrogen bonds : angle 4.10574 ( 3366) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 387 time to evaluate : 0.761 Fit side-chains revert: symmetry clash REVERT: A 105 LYS cc_start: 0.8491 (mmmm) cc_final: 0.8133 (mmtm) REVERT: A 125 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7598 (tm-30) REVERT: A 129 LYS cc_start: 0.8385 (mtmt) cc_final: 0.8075 (mtpt) REVERT: A 133 SER cc_start: 0.8553 (m) cc_final: 0.8264 (m) REVERT: A 163 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.8109 (mp0) REVERT: A 254 GLN cc_start: 0.9029 (tp40) cc_final: 0.8699 (tp-100) REVERT: B 20 MET cc_start: 0.8743 (OUTLIER) cc_final: 0.8357 (mpm) REVERT: B 171 ARG cc_start: 0.7547 (tmm-80) cc_final: 0.7307 (tmm-80) REVERT: B 183 LEU cc_start: 0.5782 (OUTLIER) cc_final: 0.5098 (tt) REVERT: B 187 TYR cc_start: 0.7784 (m-10) cc_final: 0.7527 (m-10) REVERT: B 268 MET cc_start: 0.8348 (ptp) cc_final: 0.8140 (ptm) REVERT: B 299 LYS cc_start: 0.9248 (mttt) cc_final: 0.9029 (mtpm) REVERT: B 315 LYS cc_start: 0.8263 (tppt) cc_final: 0.7751 (ttmt) REVERT: C 125 GLU cc_start: 0.8026 (tm-30) cc_final: 0.7682 (tm-30) REVERT: C 133 SER cc_start: 0.8490 (m) cc_final: 0.8189 (m) REVERT: C 163 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.8031 (mp0) REVERT: C 203 ASP cc_start: 0.8740 (m-30) cc_final: 0.8496 (m-30) REVERT: C 212 MET cc_start: 0.6944 (tpt) cc_final: 0.6378 (mmm) REVERT: C 226 ARG cc_start: 0.8138 (mmm-85) cc_final: 0.7860 (mmm-85) REVERT: C 254 GLN cc_start: 0.9038 (tp40) cc_final: 0.8710 (tp-100) REVERT: C 264 GLN cc_start: 0.8490 (pt0) cc_final: 0.8242 (mm-40) REVERT: D 142 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7597 (tm-30) REVERT: D 146 ARG cc_start: 0.8173 (ttm170) cc_final: 0.7692 (ttp-170) REVERT: D 276 MET cc_start: 0.6836 (mmm) cc_final: 0.6534 (mmt) REVERT: D 315 LYS cc_start: 0.8292 (tppt) cc_final: 0.7766 (ttmt) REVERT: E 125 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7755 (tm-30) REVERT: E 133 SER cc_start: 0.8520 (m) cc_final: 0.8219 (m) REVERT: E 163 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.8089 (mp0) REVERT: E 226 ARG cc_start: 0.8233 (mmm-85) cc_final: 0.8000 (mmm-85) REVERT: E 236 MET cc_start: 0.7363 (pp-130) cc_final: 0.7157 (pp-130) REVERT: E 254 GLN cc_start: 0.9068 (tp40) cc_final: 0.8750 (tp-100) REVERT: E 260 MET cc_start: 0.8017 (tpp) cc_final: 0.7392 (mpp) REVERT: E 264 GLN cc_start: 0.8460 (pt0) cc_final: 0.8229 (mm-40) REVERT: F 171 ARG cc_start: 0.7565 (tmm-80) cc_final: 0.7321 (tmm-80) REVERT: F 183 LEU cc_start: 0.5843 (OUTLIER) cc_final: 0.5150 (tt) REVERT: F 187 TYR cc_start: 0.7846 (m-10) cc_final: 0.7627 (m-10) REVERT: F 268 MET cc_start: 0.7947 (ptm) cc_final: 0.7692 (ptp) REVERT: F 315 LYS cc_start: 0.8295 (tppt) cc_final: 0.7803 (ttmt) REVERT: G 105 LYS cc_start: 0.8423 (mmmm) cc_final: 0.8112 (mptt) REVERT: G 125 GLU cc_start: 0.8012 (tm-30) cc_final: 0.7584 (tm-30) REVERT: G 129 LYS cc_start: 0.8406 (mtmt) cc_final: 0.8115 (mtpt) REVERT: G 130 GLN cc_start: 0.8133 (tp-100) cc_final: 0.7922 (tp-100) REVERT: G 133 SER cc_start: 0.8523 (m) cc_final: 0.8236 (m) REVERT: G 163 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.8060 (mp0) REVERT: G 212 MET cc_start: 0.6871 (tpt) cc_final: 0.6435 (mmm) REVERT: G 254 GLN cc_start: 0.9032 (tp40) cc_final: 0.8705 (tp-100) REVERT: H 20 MET cc_start: 0.8784 (mmt) cc_final: 0.8447 (mpm) REVERT: H 171 ARG cc_start: 0.7601 (tmm-80) cc_final: 0.7365 (tmm-80) REVERT: H 183 LEU cc_start: 0.5827 (OUTLIER) cc_final: 0.5160 (tt) REVERT: H 187 TYR cc_start: 0.7910 (m-10) cc_final: 0.7708 (m-10) REVERT: H 315 LYS cc_start: 0.8341 (tppt) cc_final: 0.7823 (ttmt) outliers start: 72 outliers final: 39 residues processed: 440 average time/residue: 0.5893 time to fit residues: 291.8313 Evaluate side-chains 407 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 360 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 407 SER Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 407 SER Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 163 GLU Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain H residue 393 LEU Chi-restraints excluded: chain H residue 407 SER Chi-restraints excluded: chain H residue 444 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 3 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 10 optimal weight: 20.0000 chunk 190 optimal weight: 4.9990 chunk 8 optimal weight: 9.9990 chunk 198 optimal weight: 0.8980 chunk 12 optimal weight: 7.9990 chunk 18 optimal weight: 0.3980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN A 264 GLN C 97 GLN E 97 GLN G 97 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.153897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.102873 restraints weight = 31213.182| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.67 r_work: 0.3189 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20744 Z= 0.146 Angle : 0.685 16.063 28028 Z= 0.334 Chirality : 0.042 0.184 3068 Planarity : 0.004 0.049 3576 Dihedral : 4.682 31.661 2772 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.85 % Allowed : 22.33 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 0.27 (0.17), residues: 2476 helix: 0.91 (0.13), residues: 1672 sheet: None (None), residues: 0 loop : -1.32 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 415 TYR 0.017 0.001 TYR D 186 PHE 0.019 0.001 PHE A 136 TRP 0.007 0.001 TRP H 54 HIS 0.004 0.001 HIS B 477 Details of bonding type rmsd covalent geometry : bond 0.00337 (20744) covalent geometry : angle 0.68526 (28028) hydrogen bonds : bond 0.04400 ( 1174) hydrogen bonds : angle 4.11221 ( 3366) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 388 time to evaluate : 0.724 Fit side-chains revert: symmetry clash REVERT: A 105 LYS cc_start: 0.8497 (mmmm) cc_final: 0.8125 (mmtm) REVERT: A 125 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7626 (tm-30) REVERT: A 129 LYS cc_start: 0.8347 (mtmt) cc_final: 0.8060 (mtpt) REVERT: A 133 SER cc_start: 0.8526 (m) cc_final: 0.8186 (m) REVERT: A 163 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8112 (mp0) REVERT: A 203 ASP cc_start: 0.8754 (m-30) cc_final: 0.8435 (m-30) REVERT: A 254 GLN cc_start: 0.9034 (tp40) cc_final: 0.8678 (tp-100) REVERT: A 260 MET cc_start: 0.8015 (mpp) cc_final: 0.7635 (mmt) REVERT: B 20 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.8310 (mpm) REVERT: B 171 ARG cc_start: 0.7595 (tmm-80) cc_final: 0.7393 (tmm-80) REVERT: B 183 LEU cc_start: 0.5775 (OUTLIER) cc_final: 0.5097 (tt) REVERT: B 187 TYR cc_start: 0.7784 (m-10) cc_final: 0.7519 (m-10) REVERT: B 299 LYS cc_start: 0.9249 (mttt) cc_final: 0.9027 (mtpm) REVERT: B 315 LYS cc_start: 0.8242 (tppt) cc_final: 0.7743 (ttmt) REVERT: C 125 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7697 (tm-30) REVERT: C 133 SER cc_start: 0.8537 (m) cc_final: 0.8237 (m) REVERT: C 138 GLN cc_start: 0.6446 (OUTLIER) cc_final: 0.5820 (pm20) REVERT: C 163 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.8064 (mp0) REVERT: C 203 ASP cc_start: 0.8782 (m-30) cc_final: 0.8559 (m-30) REVERT: C 212 MET cc_start: 0.6862 (tpt) cc_final: 0.6137 (mmm) REVERT: C 226 ARG cc_start: 0.8096 (mmm-85) cc_final: 0.7846 (mmm-85) REVERT: C 254 GLN cc_start: 0.9048 (tp40) cc_final: 0.8703 (tp-100) REVERT: C 260 MET cc_start: 0.7930 (mpp) cc_final: 0.7512 (mmt) REVERT: C 264 GLN cc_start: 0.8440 (pt0) cc_final: 0.8202 (mm-40) REVERT: D 142 GLU cc_start: 0.7885 (tm-30) cc_final: 0.7601 (tm-30) REVERT: D 146 ARG cc_start: 0.8183 (ttm170) cc_final: 0.7724 (ttp-170) REVERT: D 238 THR cc_start: 0.8944 (OUTLIER) cc_final: 0.8697 (p) REVERT: D 276 MET cc_start: 0.6842 (mmm) cc_final: 0.6523 (mmt) REVERT: D 315 LYS cc_start: 0.8272 (tppt) cc_final: 0.7748 (ttmt) REVERT: E 125 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7709 (tm-30) REVERT: E 133 SER cc_start: 0.8583 (m) cc_final: 0.8299 (m) REVERT: E 163 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.8099 (mp0) REVERT: E 226 ARG cc_start: 0.8224 (mmm-85) cc_final: 0.7982 (mmm-85) REVERT: E 254 GLN cc_start: 0.8988 (tp40) cc_final: 0.8689 (tp-100) REVERT: E 260 MET cc_start: 0.8101 (tpp) cc_final: 0.7406 (mpp) REVERT: E 264 GLN cc_start: 0.8468 (pt0) cc_final: 0.8241 (mm-40) REVERT: F 20 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.8425 (mpm) REVERT: F 171 ARG cc_start: 0.7634 (tmm-80) cc_final: 0.7400 (tmm-80) REVERT: F 183 LEU cc_start: 0.5754 (OUTLIER) cc_final: 0.5046 (tt) REVERT: F 187 TYR cc_start: 0.7810 (m-10) cc_final: 0.7586 (m-10) REVERT: F 268 MET cc_start: 0.7822 (ptm) cc_final: 0.7576 (ptp) REVERT: F 315 LYS cc_start: 0.8316 (tppt) cc_final: 0.7814 (ttmt) REVERT: G 105 LYS cc_start: 0.8456 (mmmm) cc_final: 0.8137 (mptt) REVERT: G 125 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7637 (tm-30) REVERT: G 129 LYS cc_start: 0.8422 (mtmt) cc_final: 0.8125 (mtpt) REVERT: G 130 GLN cc_start: 0.8201 (tp-100) cc_final: 0.7942 (tp-100) REVERT: G 133 SER cc_start: 0.8508 (m) cc_final: 0.8179 (m) REVERT: G 163 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.8064 (mp0) REVERT: G 203 ASP cc_start: 0.8763 (m-30) cc_final: 0.8440 (m-30) REVERT: G 212 MET cc_start: 0.6797 (tpt) cc_final: 0.6170 (mmm) REVERT: G 254 GLN cc_start: 0.9042 (tp40) cc_final: 0.8671 (tp-100) REVERT: G 260 MET cc_start: 0.8055 (mpp) cc_final: 0.7542 (mmt) REVERT: H 20 MET cc_start: 0.8783 (mmt) cc_final: 0.8420 (mpm) REVERT: H 183 LEU cc_start: 0.5802 (OUTLIER) cc_final: 0.5135 (tt) REVERT: H 315 LYS cc_start: 0.8315 (tppt) cc_final: 0.7813 (ttmt) outliers start: 85 outliers final: 39 residues processed: 447 average time/residue: 0.5522 time to fit residues: 278.3703 Evaluate side-chains 414 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 364 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 407 SER Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 138 ASP Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 407 SER Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 163 GLU Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain H residue 393 LEU Chi-restraints excluded: chain H residue 407 SER Chi-restraints excluded: chain H residue 444 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 233 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 169 optimal weight: 0.9980 chunk 95 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 177 optimal weight: 0.0010 chunk 131 optimal weight: 10.0000 chunk 243 optimal weight: 7.9990 chunk 236 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 155 optimal weight: 7.9990 overall best weight: 2.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN A 264 GLN C 97 GLN E 97 GLN G 97 GLN G 130 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.151599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.100144 restraints weight = 31530.657| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.68 r_work: 0.3151 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 20744 Z= 0.217 Angle : 0.740 14.626 28028 Z= 0.361 Chirality : 0.045 0.261 3068 Planarity : 0.005 0.056 3576 Dihedral : 4.828 32.607 2772 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 4.12 % Allowed : 22.83 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 0.17 (0.17), residues: 2476 helix: 0.80 (0.13), residues: 1676 sheet: None (None), residues: 0 loop : -1.26 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 261 TYR 0.019 0.002 TYR H 186 PHE 0.022 0.002 PHE G 136 TRP 0.007 0.001 TRP H 54 HIS 0.005 0.001 HIS D 477 Details of bonding type rmsd covalent geometry : bond 0.00524 (20744) covalent geometry : angle 0.73998 (28028) hydrogen bonds : bond 0.04914 ( 1174) hydrogen bonds : angle 4.25679 ( 3366) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 376 time to evaluate : 0.732 Fit side-chains REVERT: A 125 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7689 (tm-30) REVERT: A 133 SER cc_start: 0.8510 (m) cc_final: 0.8205 (m) REVERT: A 163 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8126 (mp0) REVERT: A 245 THR cc_start: 0.8158 (t) cc_final: 0.7831 (t) REVERT: A 254 GLN cc_start: 0.9018 (tp40) cc_final: 0.8679 (tp-100) REVERT: A 264 GLN cc_start: 0.8470 (pt0) cc_final: 0.8219 (mm-40) REVERT: B 20 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.8337 (mpm) REVERT: B 171 ARG cc_start: 0.7686 (OUTLIER) cc_final: 0.7460 (tmm-80) REVERT: B 183 LEU cc_start: 0.5810 (OUTLIER) cc_final: 0.5094 (tt) REVERT: B 187 TYR cc_start: 0.7783 (m-10) cc_final: 0.7553 (m-10) REVERT: B 276 MET cc_start: 0.6383 (mpt) cc_final: 0.6141 (mmm) REVERT: B 299 LYS cc_start: 0.9266 (mttt) cc_final: 0.9053 (mtpm) REVERT: B 315 LYS cc_start: 0.8323 (tppt) cc_final: 0.7778 (ttmt) REVERT: C 125 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7703 (tm-30) REVERT: C 133 SER cc_start: 0.8513 (m) cc_final: 0.8238 (m) REVERT: C 163 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.8107 (mp0) REVERT: C 212 MET cc_start: 0.6925 (tpt) cc_final: 0.6468 (mmm) REVERT: C 254 GLN cc_start: 0.9028 (tp40) cc_final: 0.8720 (tp-100) REVERT: C 260 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.7311 (mmt) REVERT: C 264 GLN cc_start: 0.8515 (pt0) cc_final: 0.8285 (mm-40) REVERT: D 276 MET cc_start: 0.6832 (mmm) cc_final: 0.6597 (mmt) REVERT: D 315 LYS cc_start: 0.8327 (tppt) cc_final: 0.7772 (ttmt) REVERT: E 125 GLU cc_start: 0.8090 (tm-30) cc_final: 0.7774 (tm-30) REVERT: E 133 SER cc_start: 0.8564 (m) cc_final: 0.8296 (m) REVERT: E 163 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.8121 (mp0) REVERT: E 226 ARG cc_start: 0.8239 (mmm-85) cc_final: 0.7975 (mmm-85) REVERT: E 236 MET cc_start: 0.7159 (pp-130) cc_final: 0.6956 (pp-130) REVERT: E 254 GLN cc_start: 0.8989 (tp40) cc_final: 0.8677 (tp-100) REVERT: E 260 MET cc_start: 0.8192 (tpp) cc_final: 0.7481 (mpp) REVERT: E 264 GLN cc_start: 0.8528 (pt0) cc_final: 0.8299 (mm-40) REVERT: F 171 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.7486 (tmm-80) REVERT: F 183 LEU cc_start: 0.5852 (OUTLIER) cc_final: 0.5130 (tt) REVERT: F 187 TYR cc_start: 0.7828 (m-10) cc_final: 0.7574 (m-10) REVERT: F 268 MET cc_start: 0.8044 (ptm) cc_final: 0.7808 (ptp) REVERT: F 315 LYS cc_start: 0.8406 (tppt) cc_final: 0.7877 (ttmt) REVERT: G 125 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7731 (tm-30) REVERT: G 130 GLN cc_start: 0.8260 (tp40) cc_final: 0.7920 (tp-100) REVERT: G 133 SER cc_start: 0.8625 (m) cc_final: 0.8334 (m) REVERT: G 203 ASP cc_start: 0.8720 (m-30) cc_final: 0.8473 (m-30) REVERT: G 212 MET cc_start: 0.6756 (tpt) cc_final: 0.6281 (mmm) REVERT: G 245 THR cc_start: 0.8148 (t) cc_final: 0.7840 (t) REVERT: G 260 MET cc_start: 0.8034 (mpp) cc_final: 0.7519 (mmt) REVERT: H 20 MET cc_start: 0.8741 (mmt) cc_final: 0.8397 (mpm) REVERT: H 27 MET cc_start: 0.7638 (tmt) cc_final: 0.7211 (tmm) REVERT: H 77 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8296 (mp0) REVERT: H 183 LEU cc_start: 0.5838 (OUTLIER) cc_final: 0.5119 (tt) REVERT: H 187 TYR cc_start: 0.7860 (m-10) cc_final: 0.7617 (m-10) REVERT: H 315 LYS cc_start: 0.8386 (tppt) cc_final: 0.7864 (ttmt) outliers start: 91 outliers final: 43 residues processed: 439 average time/residue: 0.5545 time to fit residues: 274.7985 Evaluate side-chains 420 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 366 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 156 HIS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 171 ARG Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 156 HIS Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 407 SER Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 171 ARG Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain F residue 286 PHE Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 407 SER Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 77 GLU Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain H residue 286 PHE Chi-restraints excluded: chain H residue 393 LEU Chi-restraints excluded: chain H residue 407 SER Chi-restraints excluded: chain H residue 444 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 34 optimal weight: 4.9990 chunk 92 optimal weight: 10.0000 chunk 198 optimal weight: 0.0970 chunk 64 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 181 optimal weight: 2.9990 chunk 180 optimal weight: 6.9990 chunk 151 optimal weight: 0.9990 chunk 215 optimal weight: 6.9990 chunk 170 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN B 443 HIS C 97 GLN D 443 HIS E 97 GLN F 443 HIS G 97 GLN H 443 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.153464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.102473 restraints weight = 31492.048| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.68 r_work: 0.3186 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20744 Z= 0.149 Angle : 0.737 18.867 28028 Z= 0.355 Chirality : 0.043 0.267 3068 Planarity : 0.005 0.050 3576 Dihedral : 4.724 31.776 2772 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.31 % Allowed : 24.32 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 0.36 (0.17), residues: 2476 helix: 0.91 (0.13), residues: 1684 sheet: None (None), residues: 0 loop : -1.13 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 415 TYR 0.016 0.001 TYR D 186 PHE 0.024 0.001 PHE A 136 TRP 0.007 0.001 TRP H 54 HIS 0.006 0.001 HIS D 477 Details of bonding type rmsd covalent geometry : bond 0.00350 (20744) covalent geometry : angle 0.73706 (28028) hydrogen bonds : bond 0.04373 ( 1174) hydrogen bonds : angle 4.14473 ( 3366) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 389 time to evaluate : 0.694 Fit side-chains REVERT: A 133 SER cc_start: 0.8521 (m) cc_final: 0.8239 (m) REVERT: A 195 CYS cc_start: 0.7595 (p) cc_final: 0.7341 (p) REVERT: A 254 GLN cc_start: 0.9001 (tp40) cc_final: 0.8677 (tp-100) REVERT: A 260 MET cc_start: 0.8021 (OUTLIER) cc_final: 0.7582 (mmt) REVERT: B 20 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.8264 (mpm) REVERT: B 183 LEU cc_start: 0.5792 (OUTLIER) cc_final: 0.5098 (tt) REVERT: B 187 TYR cc_start: 0.7757 (m-10) cc_final: 0.7534 (m-10) REVERT: B 238 THR cc_start: 0.8926 (OUTLIER) cc_final: 0.8663 (p) REVERT: B 263 ASP cc_start: 0.8163 (m-30) cc_final: 0.7909 (m-30) REVERT: B 299 LYS cc_start: 0.9252 (mttt) cc_final: 0.9042 (mtpm) REVERT: B 315 LYS cc_start: 0.8296 (tppt) cc_final: 0.7760 (ttmt) REVERT: C 125 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7708 (tm-30) REVERT: C 133 SER cc_start: 0.8542 (m) cc_final: 0.8269 (m) REVERT: C 138 GLN cc_start: 0.6572 (OUTLIER) cc_final: 0.5912 (pm20) REVERT: C 195 CYS cc_start: 0.7721 (p) cc_final: 0.7449 (p) REVERT: C 212 MET cc_start: 0.6873 (tpt) cc_final: 0.6245 (mmm) REVERT: C 217 TYR cc_start: 0.4711 (OUTLIER) cc_final: 0.2725 (m-80) REVERT: C 254 GLN cc_start: 0.8984 (tp40) cc_final: 0.8660 (tp-100) REVERT: C 260 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7423 (mmt) REVERT: C 262 SER cc_start: 0.9164 (t) cc_final: 0.8926 (p) REVERT: C 264 GLN cc_start: 0.8436 (pt0) cc_final: 0.8228 (mm-40) REVERT: D 20 MET cc_start: 0.8677 (mmt) cc_final: 0.8366 (mpm) REVERT: D 238 THR cc_start: 0.8949 (OUTLIER) cc_final: 0.8693 (p) REVERT: D 315 LYS cc_start: 0.8331 (tppt) cc_final: 0.7778 (ttmt) REVERT: E 125 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7680 (tm-30) REVERT: E 133 SER cc_start: 0.8568 (m) cc_final: 0.8351 (m) REVERT: E 212 MET cc_start: 0.6732 (mmm) cc_final: 0.6437 (mmm) REVERT: E 217 TYR cc_start: 0.4679 (OUTLIER) cc_final: 0.2685 (m-80) REVERT: E 260 MET cc_start: 0.8104 (tpp) cc_final: 0.7468 (mpp) REVERT: E 264 GLN cc_start: 0.8480 (pt0) cc_final: 0.8222 (mm-40) REVERT: F 20 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.8425 (mpm) REVERT: F 171 ARG cc_start: 0.7694 (tmm-80) cc_final: 0.7372 (ttp-110) REVERT: F 183 LEU cc_start: 0.5799 (OUTLIER) cc_final: 0.5090 (tt) REVERT: F 187 TYR cc_start: 0.7799 (m-10) cc_final: 0.7541 (m-10) REVERT: F 238 THR cc_start: 0.8951 (OUTLIER) cc_final: 0.8690 (p) REVERT: F 268 MET cc_start: 0.7946 (ptm) cc_final: 0.7701 (ptp) REVERT: F 276 MET cc_start: 0.6926 (mmt) cc_final: 0.6640 (mmm) REVERT: F 315 LYS cc_start: 0.8384 (tppt) cc_final: 0.7844 (ttmt) REVERT: G 125 GLU cc_start: 0.8136 (tm-30) cc_final: 0.7766 (tm-30) REVERT: G 130 GLN cc_start: 0.8307 (tp40) cc_final: 0.8050 (tp-100) REVERT: G 133 SER cc_start: 0.8588 (m) cc_final: 0.8302 (m) REVERT: G 138 GLN cc_start: 0.6524 (OUTLIER) cc_final: 0.5932 (pm20) REVERT: G 195 CYS cc_start: 0.7600 (p) cc_final: 0.7360 (p) REVERT: G 212 MET cc_start: 0.6865 (tpt) cc_final: 0.6229 (mmm) REVERT: G 260 MET cc_start: 0.8099 (mpp) cc_final: 0.7626 (mmt) REVERT: H 20 MET cc_start: 0.8705 (mmt) cc_final: 0.8356 (mpm) REVERT: H 183 LEU cc_start: 0.5788 (OUTLIER) cc_final: 0.5067 (tt) REVERT: H 187 TYR cc_start: 0.7849 (m-10) cc_final: 0.7640 (m-10) REVERT: H 315 LYS cc_start: 0.8373 (tppt) cc_final: 0.7846 (ttmt) outliers start: 73 outliers final: 39 residues processed: 438 average time/residue: 0.5567 time to fit residues: 275.7699 Evaluate side-chains 418 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 365 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 156 HIS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 407 SER Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 407 SER Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 138 GLN Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain H residue 393 LEU Chi-restraints excluded: chain H residue 407 SER Chi-restraints excluded: chain H residue 444 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 137 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 135 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 178 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 210 optimal weight: 2.9990 chunk 98 optimal weight: 7.9990 chunk 77 optimal weight: 9.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN A 264 GLN ** B 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 GLN ** D 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 GLN G 97 GLN ** H 481 HIS ** 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 = 0.4023 r_free = 0.4023 target = 0.152993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.102753 restraints weight = 31216.753| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.83 r_work: 0.3162 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20744 Z= 0.161 Angle : 0.774 17.084 28028 Z= 0.372 Chirality : 0.044 0.228 3068 Planarity : 0.005 0.058 3576 Dihedral : 4.653 30.649 2772 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.85 % Allowed : 25.68 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.17), residues: 2476 helix: 0.88 (0.13), residues: 1688 sheet: None (None), residues: 0 loop : -1.19 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG G 261 TYR 0.018 0.001 TYR D 186 PHE 0.020 0.001 PHE E 136 TRP 0.007 0.001 TRP H 54 HIS 0.006 0.001 HIS H 477 Details of bonding type rmsd covalent geometry : bond 0.00383 (20744) covalent geometry : angle 0.77385 (28028) hydrogen bonds : bond 0.04399 ( 1174) hydrogen bonds : angle 4.15142 ( 3366) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 381 time to evaluate : 0.784 Fit side-chains REVERT: A 133 SER cc_start: 0.8445 (m) cc_final: 0.8142 (m) REVERT: A 195 CYS cc_start: 0.7545 (p) cc_final: 0.7285 (p) REVERT: A 212 MET cc_start: 0.6696 (mmm) cc_final: 0.6438 (mmm) REVERT: A 254 GLN cc_start: 0.8993 (tp40) cc_final: 0.8698 (tp-100) REVERT: A 260 MET cc_start: 0.8084 (OUTLIER) cc_final: 0.7372 (mmt) REVERT: A 264 GLN cc_start: 0.8420 (pt0) cc_final: 0.8180 (mm-40) REVERT: B 20 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.8246 (mpm) REVERT: B 183 LEU cc_start: 0.5830 (OUTLIER) cc_final: 0.5121 (tt) REVERT: B 187 TYR cc_start: 0.7750 (m-10) cc_final: 0.7511 (m-10) REVERT: B 299 LYS cc_start: 0.9210 (mttt) cc_final: 0.8999 (mtpm) REVERT: B 315 LYS cc_start: 0.8246 (tppt) cc_final: 0.7746 (ttmt) REVERT: C 125 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7541 (tm-30) REVERT: C 133 SER cc_start: 0.8525 (m) cc_final: 0.8313 (m) REVERT: C 138 GLN cc_start: 0.6610 (OUTLIER) cc_final: 0.5952 (pm20) REVERT: C 195 CYS cc_start: 0.7485 (p) cc_final: 0.7208 (p) REVERT: C 212 MET cc_start: 0.6677 (tpt) cc_final: 0.5956 (mmm) REVERT: C 217 TYR cc_start: 0.4604 (OUTLIER) cc_final: 0.2621 (m-80) REVERT: C 254 GLN cc_start: 0.8979 (tp40) cc_final: 0.8640 (tp-100) REVERT: C 260 MET cc_start: 0.8171 (OUTLIER) cc_final: 0.7710 (mmm) REVERT: C 262 SER cc_start: 0.9134 (t) cc_final: 0.8907 (p) REVERT: C 264 GLN cc_start: 0.8442 (pt0) cc_final: 0.8207 (mm-40) REVERT: D 20 MET cc_start: 0.8654 (mmt) cc_final: 0.8319 (mpm) REVERT: D 238 THR cc_start: 0.8896 (OUTLIER) cc_final: 0.8648 (p) REVERT: D 315 LYS cc_start: 0.8268 (tppt) cc_final: 0.7285 (mttt) REVERT: E 125 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7527 (tm-30) REVERT: E 133 SER cc_start: 0.8515 (m) cc_final: 0.8271 (m) REVERT: E 217 TYR cc_start: 0.4587 (OUTLIER) cc_final: 0.2596 (m-80) REVERT: E 260 MET cc_start: 0.8262 (tpp) cc_final: 0.7631 (mpp) REVERT: E 262 SER cc_start: 0.9147 (t) cc_final: 0.8890 (p) REVERT: E 264 GLN cc_start: 0.8449 (pt0) cc_final: 0.8217 (mm-40) REVERT: F 20 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.8280 (mpm) REVERT: F 171 ARG cc_start: 0.7612 (tmm-80) cc_final: 0.7291 (ttp-110) REVERT: F 183 LEU cc_start: 0.5832 (OUTLIER) cc_final: 0.5117 (tt) REVERT: F 187 TYR cc_start: 0.7777 (m-10) cc_final: 0.7515 (m-10) REVERT: F 268 MET cc_start: 0.7776 (ptm) cc_final: 0.7512 (ptp) REVERT: F 276 MET cc_start: 0.6908 (mmt) cc_final: 0.6586 (mmm) REVERT: F 315 LYS cc_start: 0.8302 (tppt) cc_final: 0.7816 (ttmt) REVERT: G 125 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7556 (tm-30) REVERT: G 130 GLN cc_start: 0.8209 (tp40) cc_final: 0.7920 (tp-100) REVERT: G 133 SER cc_start: 0.8544 (m) cc_final: 0.8271 (m) REVERT: G 138 GLN cc_start: 0.6519 (OUTLIER) cc_final: 0.5973 (pm20) REVERT: G 195 CYS cc_start: 0.7534 (p) cc_final: 0.7312 (p) REVERT: G 212 MET cc_start: 0.6787 (tpt) cc_final: 0.6239 (mmm) REVERT: G 260 MET cc_start: 0.8083 (mpp) cc_final: 0.7445 (mmt) REVERT: G 261 ARG cc_start: 0.8527 (mmm160) cc_final: 0.8203 (tmt170) REVERT: H 20 MET cc_start: 0.8691 (mmt) cc_final: 0.8309 (mpm) REVERT: H 27 MET cc_start: 0.7464 (tmt) cc_final: 0.7031 (tmm) REVERT: H 183 LEU cc_start: 0.5800 (OUTLIER) cc_final: 0.5073 (tt) REVERT: H 187 TYR cc_start: 0.7789 (m-10) cc_final: 0.7555 (m-10) REVERT: H 315 LYS cc_start: 0.8312 (tppt) cc_final: 0.7832 (ttmt) outliers start: 63 outliers final: 37 residues processed: 421 average time/residue: 0.5652 time to fit residues: 268.8705 Evaluate side-chains 420 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 371 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 407 SER Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 138 ASP Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 407 SER Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 138 GLN Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 138 ASP Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain H residue 393 LEU Chi-restraints excluded: chain H residue 407 SER Chi-restraints excluded: chain H residue 444 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 228 optimal weight: 0.9990 chunk 166 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 153 optimal weight: 4.9990 chunk 205 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 238 optimal weight: 0.9980 chunk 75 optimal weight: 9.9990 chunk 101 optimal weight: 9.9990 chunk 100 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN ** B 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 HIS ** B 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 GLN ** D 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 481 HIS E 97 GLN G 97 GLN H 478 HIS ** H 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.153751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.102702 restraints weight = 31580.561| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.67 r_work: 0.3202 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20744 Z= 0.147 Angle : 0.764 14.922 28028 Z= 0.369 Chirality : 0.043 0.224 3068 Planarity : 0.005 0.055 3576 Dihedral : 4.609 30.008 2772 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.36 % Allowed : 26.49 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.17), residues: 2476 helix: 0.96 (0.13), residues: 1680 sheet: None (None), residues: 0 loop : -1.11 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 261 TYR 0.017 0.001 TYR D 186 PHE 0.017 0.001 PHE C 136 TRP 0.007 0.001 TRP H 54 HIS 0.015 0.001 HIS B 478 Details of bonding type rmsd covalent geometry : bond 0.00341 (20744) covalent geometry : angle 0.76384 (28028) hydrogen bonds : bond 0.04195 ( 1174) hydrogen bonds : angle 4.10382 ( 3366) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 377 time to evaluate : 0.768 Fit side-chains REVERT: A 133 SER cc_start: 0.8539 (m) cc_final: 0.8305 (m) REVERT: A 195 CYS cc_start: 0.7644 (p) cc_final: 0.7400 (p) REVERT: A 212 MET cc_start: 0.6783 (mmm) cc_final: 0.6500 (mmm) REVERT: A 254 GLN cc_start: 0.8984 (tp40) cc_final: 0.8673 (tp-100) REVERT: A 260 MET cc_start: 0.8084 (OUTLIER) cc_final: 0.7371 (mmt) REVERT: A 264 GLN cc_start: 0.8425 (pt0) cc_final: 0.8183 (mm-40) REVERT: B 20 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8337 (mpm) REVERT: B 183 LEU cc_start: 0.5826 (OUTLIER) cc_final: 0.5159 (tt) REVERT: B 238 THR cc_start: 0.8906 (OUTLIER) cc_final: 0.8652 (p) REVERT: B 299 LYS cc_start: 0.9259 (mttt) cc_final: 0.9044 (mtpm) REVERT: B 315 LYS cc_start: 0.8257 (tppt) cc_final: 0.7763 (ttmt) REVERT: C 133 SER cc_start: 0.8561 (m) cc_final: 0.8345 (m) REVERT: C 195 CYS cc_start: 0.7604 (p) cc_final: 0.7333 (p) REVERT: C 212 MET cc_start: 0.6651 (tpt) cc_final: 0.6073 (mmm) REVERT: C 217 TYR cc_start: 0.4672 (OUTLIER) cc_final: 0.2530 (m-80) REVERT: C 254 GLN cc_start: 0.8980 (tp40) cc_final: 0.8622 (tp-100) REVERT: C 260 MET cc_start: 0.8158 (OUTLIER) cc_final: 0.7757 (mmm) REVERT: C 262 SER cc_start: 0.9138 (t) cc_final: 0.8936 (p) REVERT: C 264 GLN cc_start: 0.8445 (pt0) cc_final: 0.8223 (mm-40) REVERT: D 20 MET cc_start: 0.8692 (mmt) cc_final: 0.8381 (mpm) REVERT: D 238 THR cc_start: 0.8921 (OUTLIER) cc_final: 0.8680 (p) REVERT: D 276 MET cc_start: 0.7022 (mmt) cc_final: 0.6789 (mmm) REVERT: D 315 LYS cc_start: 0.8273 (tppt) cc_final: 0.7768 (ttmt) REVERT: E 125 GLU cc_start: 0.8013 (tm-30) cc_final: 0.7680 (tm-30) REVERT: E 133 SER cc_start: 0.8533 (m) cc_final: 0.8318 (m) REVERT: E 195 CYS cc_start: 0.7679 (p) cc_final: 0.7474 (p) REVERT: E 217 TYR cc_start: 0.4765 (OUTLIER) cc_final: 0.2674 (m-80) REVERT: E 260 MET cc_start: 0.8333 (tpp) cc_final: 0.7711 (mpp) REVERT: E 262 SER cc_start: 0.9170 (t) cc_final: 0.8911 (p) REVERT: E 264 GLN cc_start: 0.8454 (pt0) cc_final: 0.8205 (mm-40) REVERT: F 20 MET cc_start: 0.8771 (OUTLIER) cc_final: 0.8322 (mpm) REVERT: F 77 GLU cc_start: 0.8351 (mp0) cc_final: 0.8023 (mp0) REVERT: F 171 ARG cc_start: 0.7614 (OUTLIER) cc_final: 0.7300 (ttp-110) REVERT: F 183 LEU cc_start: 0.5858 (OUTLIER) cc_final: 0.5203 (tt) REVERT: F 238 THR cc_start: 0.8925 (OUTLIER) cc_final: 0.8689 (p) REVERT: F 268 MET cc_start: 0.7803 (ptm) cc_final: 0.7558 (ptp) REVERT: F 276 MET cc_start: 0.6835 (mmt) cc_final: 0.6488 (mmm) REVERT: F 315 LYS cc_start: 0.8292 (tppt) cc_final: 0.7811 (ttmt) REVERT: G 133 SER cc_start: 0.8565 (m) cc_final: 0.8270 (m) REVERT: G 195 CYS cc_start: 0.7629 (p) cc_final: 0.7394 (p) REVERT: G 212 MET cc_start: 0.6678 (tpt) cc_final: 0.6166 (mmm) REVERT: G 260 MET cc_start: 0.8099 (mpp) cc_final: 0.7608 (mmt) REVERT: G 261 ARG cc_start: 0.8474 (mmm160) cc_final: 0.8249 (tmt170) REVERT: H 20 MET cc_start: 0.8704 (mmt) cc_final: 0.8310 (mpm) REVERT: H 27 MET cc_start: 0.7495 (tmt) cc_final: 0.7197 (tmm) REVERT: H 183 LEU cc_start: 0.5814 (OUTLIER) cc_final: 0.5130 (tt) REVERT: H 315 LYS cc_start: 0.8349 (tppt) cc_final: 0.7851 (ttmt) outliers start: 52 outliers final: 34 residues processed: 407 average time/residue: 0.5317 time to fit residues: 245.6898 Evaluate side-chains 416 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 369 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 478 HIS Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 407 SER Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 171 ARG Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 138 ASP Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain H residue 393 LEU Chi-restraints excluded: chain H residue 407 SER Chi-restraints excluded: chain H residue 478 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 132 optimal weight: 20.0000 chunk 21 optimal weight: 0.6980 chunk 186 optimal weight: 3.9990 chunk 184 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 70 optimal weight: 9.9990 chunk 235 optimal weight: 2.9990 chunk 224 optimal weight: 0.8980 chunk 175 optimal weight: 0.9990 chunk 204 optimal weight: 0.6980 chunk 104 optimal weight: 7.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN ** B 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 GLN ** D 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 HIS E 97 GLN G 97 GLN ** H 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 481 HIS ** 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 = 0.4019 r_free = 0.4019 target = 0.152871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.101630 restraints weight = 31388.675| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.66 r_work: 0.3193 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20744 Z= 0.155 Angle : 0.766 16.032 28028 Z= 0.369 Chirality : 0.043 0.225 3068 Planarity : 0.005 0.057 3576 Dihedral : 4.574 29.187 2772 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.81 % Allowed : 26.22 % Favored : 70.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.17), residues: 2476 helix: 0.92 (0.13), residues: 1688 sheet: None (None), residues: 0 loop : -1.08 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 139 TYR 0.020 0.001 TYR B 186 PHE 0.015 0.001 PHE A 165 TRP 0.007 0.001 TRP H 54 HIS 0.020 0.001 HIS B 478 Details of bonding type rmsd covalent geometry : bond 0.00366 (20744) covalent geometry : angle 0.76608 (28028) hydrogen bonds : bond 0.04232 ( 1174) hydrogen bonds : angle 4.11279 ( 3366) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10518.94 seconds wall clock time: 178 minutes 55.57 seconds (10735.57 seconds total)