Starting phenix.real_space_refine on Tue Jun 17 18:27:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w6s_32334/06_2025/7w6s_32334.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w6s_32334/06_2025/7w6s_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7w6s_32334/06_2025/7w6s_32334.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w6s_32334/06_2025/7w6s_32334.map" model { file = "/net/cci-nas-00/data/ceres_data/7w6s_32334/06_2025/7w6s_32334.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w6s_32334/06_2025/7w6s_32334.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.52s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 14.21, per 1000 atoms: 0.70 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: 6.61 Conformation dependent library (CDL) restraints added in 2.8 seconds 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: 2.18 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: 8.16 Time building geometry restraints manager: 7.02 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: 0.02 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 121.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.800 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 53.500 Find NCS groups from input model: 1.610 Set up NCS constraints: 0.200 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: 0.020 Load rotamer database and sin/cos tables:78.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 256.270 ------------------------------------------------------------------------------- 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 : 9.61 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.009 0.002 TRP F 359 HIS 0.005 0.001 HIS B 477 PHE 0.021 0.002 PHE A 165 TYR 0.024 0.002 TYR C 132 ARG 0.022 0.001 ARG A 112 Details of bonding type rmsd hydrogen bonds : bond 0.14994 ( 1174) hydrogen bonds : angle 5.69490 ( 3366) covalent geometry : bond 0.00536 (20744) covalent geometry : angle 0.67515 (28028) *********************** 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 : 6.247 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: 0.7294 (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: G 232 PHE cc_start: 0.8284 (t80) cc_final: 0.7961 (t80) 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: 1.5535 time to fit residues: 949.6893 Evaluate side-chains 373 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 373 time to evaluate : 2.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 0.8980 chunk 184 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 191 optimal weight: 0.2980 chunk 74 optimal weight: 10.0000 chunk 116 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 221 optimal weight: 4.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 = 0.4017 r_free = 0.4017 target = 0.152671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.101676 restraints weight = 31344.875| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.63 r_work: 0.3190 rms_B_bonded: 3.03 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: 0.8103 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20744 Z= 0.155 Angle : 0.660 12.486 28028 Z= 0.337 Chirality : 0.043 0.166 3068 Planarity : 0.005 0.054 3576 Dihedral : 5.115 35.121 2772 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.08 % Allowed : 15.17 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.17), residues: 2476 helix: 0.07 (0.13), residues: 1664 sheet: None (None), residues: 0 loop : -1.88 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 54 HIS 0.009 0.001 HIS B 443 PHE 0.017 0.001 PHE E 165 TYR 0.021 0.001 TYR H 186 ARG 0.006 0.001 ARG F 415 Details of bonding type rmsd hydrogen bonds : bond 0.04996 ( 1174) hydrogen bonds : angle 4.30665 ( 3366) covalent geometry : bond 0.00345 (20744) covalent geometry : angle 0.65978 (28028) *********************** 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: 68 poor density : 437 time to evaluate : 2.286 Fit side-chains REVERT: A 125 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7519 (tm-30) REVERT: A 129 LYS cc_start: 0.8299 (mtmt) cc_final: 0.8006 (mtpt) REVERT: A 133 SER cc_start: 0.8577 (m) cc_final: 0.8260 (m) REVERT: A 134 GLN cc_start: 0.8598 (mm110) cc_final: 0.8345 (mm110) REVERT: A 212 MET cc_start: 0.6836 (tpt) cc_final: 0.6635 (mmm) REVERT: A 232 PHE cc_start: 0.8102 (t80) cc_final: 0.7793 (t80) REVERT: A 254 GLN cc_start: 0.8982 (tp40) cc_final: 0.8717 (tp40) REVERT: A 261 ARG cc_start: 0.8402 (tmt170) cc_final: 0.8181 (tpt90) REVERT: B 29 LEU cc_start: 0.7910 (mm) cc_final: 0.7656 (tp) REVERT: B 130 ASP cc_start: 0.8349 (m-30) cc_final: 0.8138 (m-30) REVERT: B 187 TYR cc_start: 0.7962 (m-10) cc_final: 0.7724 (m-10) REVERT: B 292 PHE cc_start: 0.8755 (m-80) cc_final: 0.8536 (m-80) REVERT: B 299 LYS cc_start: 0.9213 (mttt) cc_final: 0.8961 (mtpt) REVERT: B 315 LYS cc_start: 0.8284 (tppt) cc_final: 0.7794 (ttmt) REVERT: C 125 GLU cc_start: 0.8045 (tm-30) cc_final: 0.7580 (tm-30) REVERT: C 129 LYS cc_start: 0.8332 (mtmt) cc_final: 0.8039 (mtpt) REVERT: C 133 SER cc_start: 0.8587 (m) cc_final: 0.8268 (m) REVERT: C 134 GLN cc_start: 0.8581 (mm110) cc_final: 0.8327 (mm110) REVERT: C 212 MET cc_start: 0.6932 (tpt) cc_final: 0.6249 (mmm) REVERT: C 226 ARG cc_start: 0.8275 (mmm-85) cc_final: 0.7949 (mmm-85) REVERT: C 254 GLN cc_start: 0.8994 (tp40) cc_final: 0.8707 (tp40) REVERT: C 262 SER cc_start: 0.9143 (t) cc_final: 0.8845 (p) REVERT: C 263 MET cc_start: 0.8320 (ttm) cc_final: 0.7853 (tpp) REVERT: D 29 LEU cc_start: 0.7887 (mm) cc_final: 0.7651 (tp) REVERT: D 130 ASP cc_start: 0.8422 (m-30) cc_final: 0.8217 (m-30) REVERT: D 142 GLU cc_start: 0.7741 (tm-30) cc_final: 0.7510 (tm-30) REVERT: D 146 ARG cc_start: 0.8061 (ttm170) cc_final: 0.7750 (ttp-170) REVERT: D 170 TRP cc_start: 0.7290 (t-100) cc_final: 0.7000 (t-100) REVERT: D 315 LYS cc_start: 0.8298 (tppt) cc_final: 0.7787 (ttmt) REVERT: E 125 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7518 (tm-30) REVERT: E 129 LYS cc_start: 0.8349 (mtmt) cc_final: 0.8043 (mtpt) REVERT: E 133 SER cc_start: 0.8524 (m) cc_final: 0.8189 (m) REVERT: E 134 GLN cc_start: 0.8532 (mm110) cc_final: 0.8254 (mm110) REVERT: E 236 MET cc_start: 0.7843 (mtt) cc_final: 0.7128 (pp-130) REVERT: E 254 GLN cc_start: 0.9053 (tp40) cc_final: 0.8677 (tp-100) REVERT: E 260 MET cc_start: 0.8010 (tpp) cc_final: 0.7801 (mpp) REVERT: F 29 LEU cc_start: 0.7912 (mm) cc_final: 0.7644 (tp) REVERT: F 315 LYS cc_start: 0.8270 (tppt) cc_final: 0.7747 (ttmt) REVERT: G 125 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7533 (tm-30) REVERT: G 129 LYS cc_start: 0.8291 (mtmt) cc_final: 0.7997 (mtpt) REVERT: G 133 SER cc_start: 0.8571 (m) cc_final: 0.8251 (m) REVERT: G 134 GLN cc_start: 0.8568 (mm110) cc_final: 0.8302 (mm110) REVERT: G 236 MET cc_start: 0.7908 (mtt) cc_final: 0.6922 (pp-130) REVERT: G 254 GLN cc_start: 0.9000 (tp40) cc_final: 0.8734 (tp40) REVERT: G 262 SER cc_start: 0.9187 (t) cc_final: 0.8870 (p) REVERT: G 263 MET cc_start: 0.8385 (ttm) cc_final: 0.8158 (tpp) REVERT: H 29 LEU cc_start: 0.7897 (mm) cc_final: 0.7628 (tp) REVERT: H 187 TYR cc_start: 0.8033 (m-10) cc_final: 0.7776 (m-10) REVERT: H 315 LYS cc_start: 0.8264 (tppt) cc_final: 0.7779 (ttmt) outliers start: 68 outliers final: 31 residues processed: 484 average time/residue: 1.2654 time to fit residues: 694.0172 Evaluate side-chains 421 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 390 time to evaluate : 2.506 ------------------------------------------------------------------------------- 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 274 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 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 39 optimal weight: 0.9990 chunk 201 optimal weight: 5.9990 chunk 170 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 136 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 134 optimal weight: 0.0370 chunk 172 optimal weight: 3.9990 overall best weight: 0.8064 ------------------------------------------------------------------------------- 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 = 0.4031 r_free = 0.4031 target = 0.153938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.102784 restraints weight = 31278.356| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.68 r_work: 0.3205 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20744 Z= 0.136 Angle : 0.645 13.509 28028 Z= 0.322 Chirality : 0.041 0.156 3068 Planarity : 0.005 0.059 3576 Dihedral : 4.805 32.211 2772 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.72 % Allowed : 18.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.17), residues: 2476 helix: 0.57 (0.13), residues: 1684 sheet: None (None), residues: 0 loop : -1.63 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 54 HIS 0.005 0.001 HIS B 477 PHE 0.025 0.001 PHE E 232 TYR 0.017 0.001 TYR D 186 ARG 0.007 0.000 ARG F 415 Details of bonding type rmsd hydrogen bonds : bond 0.04474 ( 1174) hydrogen bonds : angle 4.16947 ( 3366) covalent geometry : bond 0.00303 (20744) covalent geometry : angle 0.64526 (28028) *********************** 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 497 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 437 time to evaluate : 2.278 Fit side-chains revert: symmetry clash REVERT: A 125 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7478 (tm-30) REVERT: A 129 LYS cc_start: 0.8411 (mtmt) cc_final: 0.8073 (mtpt) REVERT: A 133 SER cc_start: 0.8494 (m) cc_final: 0.8228 (m) REVERT: A 203 ASP cc_start: 0.8923 (m-30) cc_final: 0.8702 (m-30) REVERT: A 212 MET cc_start: 0.6897 (tpt) cc_final: 0.6260 (mmm) REVERT: A 226 ARG cc_start: 0.8145 (mmm-85) cc_final: 0.7856 (mmm-85) REVERT: A 254 GLN cc_start: 0.9016 (tp40) cc_final: 0.8667 (tp-100) REVERT: B 27 MET cc_start: 0.7570 (tmt) cc_final: 0.7135 (tmt) REVERT: B 29 LEU cc_start: 0.7885 (mm) cc_final: 0.7526 (tp) REVERT: B 130 ASP cc_start: 0.8405 (m-30) cc_final: 0.8170 (m-30) REVERT: B 142 GLU cc_start: 0.7680 (tm-30) cc_final: 0.7470 (tm-30) REVERT: B 146 ARG cc_start: 0.8157 (ttm170) cc_final: 0.7753 (ttp-170) REVERT: B 276 MET cc_start: 0.7009 (mmm) cc_final: 0.6798 (mmt) REVERT: B 292 PHE cc_start: 0.8774 (m-80) cc_final: 0.8564 (m-80) REVERT: B 299 LYS cc_start: 0.9238 (mttt) cc_final: 0.8968 (mtpt) REVERT: B 315 LYS cc_start: 0.8110 (tppt) cc_final: 0.7646 (ttmt) REVERT: C 125 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7619 (tm-30) REVERT: C 129 LYS cc_start: 0.8394 (mtmt) cc_final: 0.8062 (mtpt) REVERT: C 133 SER cc_start: 0.8485 (m) cc_final: 0.8212 (m) REVERT: C 212 MET cc_start: 0.6899 (tpt) cc_final: 0.6314 (mmm) REVERT: C 226 ARG cc_start: 0.8315 (mmm-85) cc_final: 0.7943 (mmm-85) REVERT: C 236 MET cc_start: 0.7339 (pp-130) cc_final: 0.7112 (pp-130) REVERT: C 254 GLN cc_start: 0.9072 (tp40) cc_final: 0.8842 (tp40) REVERT: C 262 SER cc_start: 0.9167 (t) cc_final: 0.8863 (p) REVERT: C 263 MET cc_start: 0.8116 (OUTLIER) cc_final: 0.7824 (tpp) REVERT: D 29 LEU cc_start: 0.7906 (mm) cc_final: 0.7620 (tp) REVERT: D 130 ASP cc_start: 0.8422 (m-30) cc_final: 0.8201 (m-30) REVERT: D 142 GLU cc_start: 0.7828 (tm-30) cc_final: 0.7574 (tm-30) REVERT: D 146 ARG cc_start: 0.8206 (ttm170) cc_final: 0.7775 (ttp-170) REVERT: D 276 MET cc_start: 0.6959 (mmm) cc_final: 0.6649 (mmt) REVERT: D 315 LYS cc_start: 0.8185 (tppt) cc_final: 0.7709 (ttmt) REVERT: E 125 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7612 (tm-30) REVERT: E 129 LYS cc_start: 0.8369 (mtmt) cc_final: 0.8040 (mtpt) REVERT: E 130 GLN cc_start: 0.8071 (tp-100) cc_final: 0.7854 (tp-100) REVERT: E 133 SER cc_start: 0.8457 (m) cc_final: 0.8170 (m) REVERT: E 163 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8067 (pm20) REVERT: E 212 MET cc_start: 0.6825 (tpt) cc_final: 0.6154 (mmm) REVERT: E 254 GLN cc_start: 0.9052 (tp40) cc_final: 0.8702 (tp-100) REVERT: E 260 MET cc_start: 0.7863 (tpp) cc_final: 0.7534 (mpp) REVERT: F 29 LEU cc_start: 0.7921 (mm) cc_final: 0.7626 (tp) REVERT: F 142 GLU cc_start: 0.7747 (tm-30) cc_final: 0.7501 (tm-30) REVERT: F 146 ARG cc_start: 0.8148 (ttm170) cc_final: 0.7781 (ttp-170) REVERT: F 171 ARG cc_start: 0.7587 (tmm-80) cc_final: 0.7349 (tmm-80) REVERT: F 315 LYS cc_start: 0.8199 (tppt) cc_final: 0.7761 (ttmt) REVERT: G 125 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7660 (tm-30) REVERT: G 129 LYS cc_start: 0.8346 (mtmt) cc_final: 0.8090 (mtpt) REVERT: G 130 GLN cc_start: 0.8132 (tp-100) cc_final: 0.7917 (tp-100) REVERT: G 133 SER cc_start: 0.8463 (m) cc_final: 0.8188 (m) REVERT: G 212 MET cc_start: 0.6616 (tpt) cc_final: 0.6107 (mmm) REVERT: G 226 ARG cc_start: 0.8219 (mmm-85) cc_final: 0.7938 (mmm-85) REVERT: G 254 GLN cc_start: 0.9029 (tp40) cc_final: 0.8689 (tp-100) REVERT: G 262 SER cc_start: 0.9180 (t) cc_final: 0.8928 (p) REVERT: H 29 LEU cc_start: 0.7883 (mm) cc_final: 0.7540 (tp) REVERT: H 171 ARG cc_start: 0.7550 (tmm-80) cc_final: 0.7307 (tmm-80) REVERT: H 315 LYS cc_start: 0.8200 (tppt) cc_final: 0.7769 (ttmt) outliers start: 60 outliers final: 19 residues processed: 486 average time/residue: 1.2302 time to fit residues: 680.5493 Evaluate side-chains 406 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 385 time to evaluate : 2.248 ------------------------------------------------------------------------------- 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 274 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 163 GLU Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 263 MET 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 163 GLU Chi-restraints excluded: chain F residue 393 LEU 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 64 optimal weight: 0.8980 chunk 92 optimal weight: 6.9990 chunk 114 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 184 optimal weight: 2.9990 chunk 162 optimal weight: 7.9990 chunk 196 optimal weight: 6.9990 chunk 177 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 126 optimal weight: 0.7980 overall best weight: 1.9184 ------------------------------------------------------------------------------- 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 C 264 GLN D 177 HIS D 443 HIS E 97 GLN F 177 HIS F 443 HIS G 97 GLN H 443 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.151889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.100223 restraints weight = 31544.037| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.66 r_work: 0.3161 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 20744 Z= 0.175 Angle : 0.660 11.493 28028 Z= 0.328 Chirality : 0.043 0.148 3068 Planarity : 0.005 0.053 3576 Dihedral : 4.819 31.943 2772 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.12 % Allowed : 20.70 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.17), residues: 2476 helix: 0.69 (0.13), residues: 1680 sheet: None (None), residues: 0 loop : -1.52 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 54 HIS 0.004 0.001 HIS F 477 PHE 0.017 0.002 PHE E 136 TYR 0.019 0.001 TYR H 186 ARG 0.007 0.000 ARG H 415 Details of bonding type rmsd hydrogen bonds : bond 0.04738 ( 1174) hydrogen bonds : angle 4.16190 ( 3366) covalent geometry : bond 0.00413 (20744) covalent geometry : angle 0.66032 (28028) *********************** 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 474 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 405 time to evaluate : 2.497 Fit side-chains REVERT: A 125 GLU cc_start: 0.8014 (tm-30) cc_final: 0.7583 (tm-30) REVERT: A 129 LYS cc_start: 0.8348 (mtmt) cc_final: 0.8048 (mtpt) REVERT: A 133 SER cc_start: 0.8543 (m) cc_final: 0.8178 (m) REVERT: A 134 GLN cc_start: 0.8749 (mm-40) cc_final: 0.8426 (mm110) REVERT: A 163 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8066 (pm20) REVERT: A 212 MET cc_start: 0.6821 (tpt) cc_final: 0.6470 (mmm) REVERT: A 226 ARG cc_start: 0.8216 (mmm-85) cc_final: 0.7879 (mmm-85) REVERT: A 254 GLN cc_start: 0.9048 (tp40) cc_final: 0.8730 (tp-100) REVERT: B 29 LEU cc_start: 0.7884 (mm) cc_final: 0.7582 (tp) REVERT: B 142 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7597 (tm-30) REVERT: B 146 ARG cc_start: 0.8173 (ttm170) cc_final: 0.7702 (ttp-170) REVERT: B 268 MET cc_start: 0.8385 (ptp) cc_final: 0.8143 (ptm) REVERT: B 276 MET cc_start: 0.6923 (mmm) cc_final: 0.6663 (mmt) REVERT: B 299 LYS cc_start: 0.9251 (mttt) cc_final: 0.8983 (mtpt) REVERT: B 315 LYS cc_start: 0.8276 (tppt) cc_final: 0.7775 (ttmt) REVERT: C 125 GLU cc_start: 0.8090 (tm-30) cc_final: 0.7632 (tm-30) REVERT: C 129 LYS cc_start: 0.8319 (mtmt) cc_final: 0.7967 (mtpt) REVERT: C 133 SER cc_start: 0.8519 (m) cc_final: 0.8158 (m) REVERT: C 163 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7986 (pm20) REVERT: C 212 MET cc_start: 0.6799 (tpt) cc_final: 0.6264 (mmm) REVERT: C 226 ARG cc_start: 0.8298 (mmm-85) cc_final: 0.7894 (mmm-85) REVERT: C 254 GLN cc_start: 0.9065 (tp40) cc_final: 0.8783 (tp-100) REVERT: C 262 SER cc_start: 0.9185 (t) cc_final: 0.8898 (p) REVERT: D 29 LEU cc_start: 0.7878 (mm) cc_final: 0.7542 (tp) REVERT: D 142 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7576 (tm-30) REVERT: D 146 ARG cc_start: 0.8199 (ttm170) cc_final: 0.7720 (ttp-170) REVERT: D 268 MET cc_start: 0.8404 (ptp) cc_final: 0.8173 (ptm) REVERT: D 276 MET cc_start: 0.6966 (mmm) cc_final: 0.6662 (mmt) REVERT: D 315 LYS cc_start: 0.8297 (tppt) cc_final: 0.7782 (ttmt) REVERT: D 415 ARG cc_start: 0.7832 (mtm110) cc_final: 0.7629 (ptp-110) REVERT: E 125 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7592 (tm-30) REVERT: E 129 LYS cc_start: 0.8367 (mtmt) cc_final: 0.8045 (mtpt) REVERT: E 130 GLN cc_start: 0.8185 (tp-100) cc_final: 0.7884 (tp-100) REVERT: E 133 SER cc_start: 0.8506 (m) cc_final: 0.8253 (m) REVERT: E 163 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.8072 (mp0) REVERT: E 212 MET cc_start: 0.6811 (tpt) cc_final: 0.6183 (mmm) REVERT: E 236 MET cc_start: 0.7439 (pp-130) cc_final: 0.7174 (pp-130) REVERT: E 254 GLN cc_start: 0.9043 (tp40) cc_final: 0.8691 (tp-100) REVERT: E 260 MET cc_start: 0.8021 (tpp) cc_final: 0.7534 (mpp) REVERT: E 264 GLN cc_start: 0.8517 (pt0) cc_final: 0.8301 (mm-40) REVERT: F 29 LEU cc_start: 0.7886 (mm) cc_final: 0.7548 (tp) REVERT: F 142 GLU cc_start: 0.7818 (tm-30) cc_final: 0.7527 (tm-30) REVERT: F 146 ARG cc_start: 0.8205 (ttm170) cc_final: 0.7800 (ttp-170) REVERT: F 171 ARG cc_start: 0.7588 (tmm-80) cc_final: 0.7334 (tmm-80) REVERT: F 315 LYS cc_start: 0.8305 (tppt) cc_final: 0.7820 (ttmt) REVERT: G 125 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7684 (tm-30) REVERT: G 129 LYS cc_start: 0.8425 (mtmt) cc_final: 0.8167 (mtpt) REVERT: G 130 GLN cc_start: 0.8197 (tp-100) cc_final: 0.7849 (tp-100) REVERT: G 133 SER cc_start: 0.8493 (m) cc_final: 0.8113 (m) REVERT: G 134 GLN cc_start: 0.8636 (mm110) cc_final: 0.8340 (mm110) REVERT: G 212 MET cc_start: 0.6601 (tpt) cc_final: 0.6209 (mmm) REVERT: G 226 ARG cc_start: 0.8267 (mmm-85) cc_final: 0.8024 (mmm-85) REVERT: G 236 MET cc_start: 0.7302 (pp-130) cc_final: 0.7063 (pp-130) REVERT: G 254 GLN cc_start: 0.9062 (tp40) cc_final: 0.8741 (tp-100) REVERT: H 20 MET cc_start: 0.8870 (mmt) cc_final: 0.8527 (mpm) REVERT: H 29 LEU cc_start: 0.7928 (mm) cc_final: 0.7550 (tp) REVERT: H 171 ARG cc_start: 0.7537 (tmm-80) cc_final: 0.7290 (tmm-80) REVERT: H 315 LYS cc_start: 0.8236 (tppt) cc_final: 0.7773 (ttmt) REVERT: H 415 ARG cc_start: 0.7799 (mtm110) cc_final: 0.7586 (ptp-110) outliers start: 69 outliers final: 34 residues processed: 458 average time/residue: 1.2878 time to fit residues: 666.7207 Evaluate side-chains 414 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 377 time to evaluate : 2.302 ------------------------------------------------------------------------------- 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 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 444 SER Chi-restraints excluded: chain C residue 122 ILE 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 25 CYS 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 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 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 258 VAL 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 137 optimal weight: 7.9990 chunk 154 optimal weight: 1.9990 chunk 209 optimal weight: 1.9990 chunk 231 optimal weight: 0.6980 chunk 242 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 140 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 228 optimal weight: 1.9990 chunk 236 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.4038 r_free = 0.4038 target = 0.154164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.103005 restraints weight = 31559.768| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.70 r_work: 0.3184 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20744 Z= 0.138 Angle : 0.649 13.825 28028 Z= 0.320 Chirality : 0.041 0.171 3068 Planarity : 0.004 0.048 3576 Dihedral : 4.664 30.675 2772 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.12 % Allowed : 21.51 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.17), residues: 2476 helix: 0.90 (0.13), residues: 1672 sheet: None (None), residues: 0 loop : -1.37 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 54 HIS 0.004 0.001 HIS B 477 PHE 0.020 0.001 PHE A 136 TYR 0.016 0.001 TYR H 186 ARG 0.008 0.000 ARG B 415 Details of bonding type rmsd hydrogen bonds : bond 0.04310 ( 1174) hydrogen bonds : angle 4.02890 ( 3366) covalent geometry : bond 0.00315 (20744) covalent geometry : angle 0.64853 (28028) *********************** 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 479 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 410 time to evaluate : 2.136 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 LYS cc_start: 0.8436 (mmmm) cc_final: 0.8086 (mmtm) REVERT: A 125 GLU cc_start: 0.8092 (tm-30) cc_final: 0.7621 (tm-30) REVERT: A 129 LYS cc_start: 0.8326 (mtmt) cc_final: 0.8025 (mtpt) REVERT: A 130 GLN cc_start: 0.8165 (tp-100) cc_final: 0.7946 (tp-100) REVERT: A 133 SER cc_start: 0.8543 (m) cc_final: 0.8205 (m) REVERT: A 163 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8130 (mp0) REVERT: A 212 MET cc_start: 0.6778 (tpt) cc_final: 0.6216 (mmm) REVERT: A 226 ARG cc_start: 0.8231 (mmm-85) cc_final: 0.7969 (mmm-85) REVERT: A 254 GLN cc_start: 0.9064 (tp40) cc_final: 0.8749 (tp-100) REVERT: B 276 MET cc_start: 0.6703 (mmm) cc_final: 0.6447 (mmt) REVERT: B 299 LYS cc_start: 0.9245 (mttt) cc_final: 0.9021 (mtpm) REVERT: C 105 LYS cc_start: 0.8372 (mmmm) cc_final: 0.8058 (mmtp) REVERT: C 125 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7639 (tm-30) REVERT: C 129 LYS cc_start: 0.8308 (mtmt) cc_final: 0.7975 (mtpt) REVERT: C 133 SER cc_start: 0.8554 (m) cc_final: 0.8238 (m) REVERT: C 138 GLN cc_start: 0.6618 (OUTLIER) cc_final: 0.5929 (pm20) REVERT: C 163 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.8070 (mp0) REVERT: C 212 MET cc_start: 0.6781 (tpt) cc_final: 0.6128 (mmm) REVERT: C 226 ARG cc_start: 0.8290 (mmm-85) cc_final: 0.7907 (mmm-85) REVERT: C 236 MET cc_start: 0.6820 (pp-130) cc_final: 0.6601 (pp-130) REVERT: C 254 GLN cc_start: 0.9057 (tp40) cc_final: 0.8736 (tp-100) REVERT: D 20 MET cc_start: 0.8762 (mmt) cc_final: 0.8455 (mpm) REVERT: D 142 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7577 (tm-30) REVERT: D 146 ARG cc_start: 0.8193 (ttm170) cc_final: 0.7695 (ttp-170) REVERT: D 238 THR cc_start: 0.8940 (OUTLIER) cc_final: 0.8696 (p) REVERT: D 276 MET cc_start: 0.6825 (mmm) cc_final: 0.6517 (mmt) REVERT: D 315 LYS cc_start: 0.8254 (tppt) cc_final: 0.7746 (ttmt) REVERT: E 125 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7660 (tm-30) REVERT: E 129 LYS cc_start: 0.8427 (mtmt) cc_final: 0.8112 (mtpt) REVERT: E 130 GLN cc_start: 0.8373 (tp-100) cc_final: 0.8055 (tp-100) REVERT: E 133 SER cc_start: 0.8552 (m) cc_final: 0.8262 (m) REVERT: E 163 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.8083 (mp0) REVERT: E 212 MET cc_start: 0.6712 (tpt) cc_final: 0.6168 (mmm) REVERT: E 236 MET cc_start: 0.7371 (pp-130) cc_final: 0.7166 (pp-130) REVERT: E 254 GLN cc_start: 0.9038 (tp40) cc_final: 0.8714 (tp-100) REVERT: E 260 MET cc_start: 0.8139 (tpp) cc_final: 0.7508 (mpp) REVERT: E 264 GLN cc_start: 0.8434 (pt0) cc_final: 0.8214 (mm-40) REVERT: F 142 GLU cc_start: 0.7817 (tm-30) cc_final: 0.7503 (tm-30) REVERT: F 146 ARG cc_start: 0.8209 (ttm170) cc_final: 0.7729 (ttp-170) REVERT: F 171 ARG cc_start: 0.7586 (tmm-80) cc_final: 0.7340 (tmm-80) REVERT: F 187 TYR cc_start: 0.7822 (m-10) cc_final: 0.7620 (m-10) REVERT: F 268 MET cc_start: 0.7884 (ptm) cc_final: 0.7626 (ptp) REVERT: F 315 LYS cc_start: 0.8254 (tppt) cc_final: 0.7750 (ttmt) REVERT: G 125 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7651 (tm-30) REVERT: G 129 LYS cc_start: 0.8359 (mtmt) cc_final: 0.8069 (mtpt) REVERT: G 130 GLN cc_start: 0.8394 (tp-100) cc_final: 0.8092 (tp-100) REVERT: G 133 SER cc_start: 0.8561 (m) cc_final: 0.8212 (m) REVERT: G 163 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.8024 (mp0) REVERT: G 212 MET cc_start: 0.6643 (tpt) cc_final: 0.6174 (mmm) REVERT: G 226 ARG cc_start: 0.8214 (mmm-85) cc_final: 0.7913 (mmm-85) REVERT: G 254 GLN cc_start: 0.9046 (tp40) cc_final: 0.8721 (tp-100) REVERT: H 20 MET cc_start: 0.8780 (mmt) cc_final: 0.8414 (mpm) REVERT: H 171 ARG cc_start: 0.7632 (tmm-80) cc_final: 0.7420 (tmm-80) REVERT: H 315 LYS cc_start: 0.8262 (tppt) cc_final: 0.7784 (ttmt) outliers start: 69 outliers final: 38 residues processed: 461 average time/residue: 1.2888 time to fit residues: 669.7420 Evaluate side-chains 418 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 374 time to evaluate : 2.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 197 THR Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 39 ASP 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 138 GLN Chi-restraints excluded: chain C residue 143 THR 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 25 CYS 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 163 GLU Chi-restraints excluded: chain F residue 9 LEU 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 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 138 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 33 optimal weight: 5.9990 chunk 189 optimal weight: 6.9990 chunk 69 optimal weight: 9.9990 chunk 171 optimal weight: 5.9990 chunk 205 optimal weight: 2.9990 chunk 162 optimal weight: 9.9990 chunk 226 optimal weight: 8.9990 chunk 82 optimal weight: 0.5980 chunk 218 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 65 optimal weight: 9.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- 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 H 177 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.151169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.099740 restraints weight = 31441.817| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.67 r_work: 0.3148 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 20744 Z= 0.225 Angle : 0.701 11.417 28028 Z= 0.350 Chirality : 0.044 0.210 3068 Planarity : 0.005 0.054 3576 Dihedral : 4.808 32.184 2772 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 4.03 % Allowed : 22.06 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.17), residues: 2476 helix: 0.76 (0.13), residues: 1684 sheet: None (None), residues: 0 loop : -1.35 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 54 HIS 0.006 0.001 HIS B 477 PHE 0.023 0.002 PHE C 136 TYR 0.020 0.002 TYR H 186 ARG 0.011 0.001 ARG G 261 Details of bonding type rmsd hydrogen bonds : bond 0.04949 ( 1174) hydrogen bonds : angle 4.21680 ( 3366) covalent geometry : bond 0.00541 (20744) covalent geometry : angle 0.70101 (28028) *********************** 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: 89 poor density : 384 time to evaluate : 2.298 Fit side-chains REVERT: A 125 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7686 (tm-30) REVERT: A 130 GLN cc_start: 0.8213 (tp-100) cc_final: 0.7968 (tp-100) REVERT: A 133 SER cc_start: 0.8556 (m) cc_final: 0.8260 (m) REVERT: A 163 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8130 (mp0) REVERT: A 203 ASP cc_start: 0.8771 (m-30) cc_final: 0.8499 (m-30) REVERT: A 254 GLN cc_start: 0.9012 (tp40) cc_final: 0.8668 (tp-100) REVERT: A 260 MET cc_start: 0.8044 (mpp) cc_final: 0.7381 (mmt) REVERT: A 264 GLN cc_start: 0.8501 (pt0) cc_final: 0.8240 (mm-40) REVERT: B 259 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.7744 (mtt) REVERT: B 268 MET cc_start: 0.8305 (ptp) cc_final: 0.8065 (ptm) REVERT: B 276 MET cc_start: 0.6788 (mmm) cc_final: 0.6532 (mmt) REVERT: B 299 LYS cc_start: 0.9265 (mttt) cc_final: 0.9048 (mtpm) REVERT: B 315 LYS cc_start: 0.8329 (tppt) cc_final: 0.7788 (ttmt) REVERT: C 105 LYS cc_start: 0.8429 (mmmm) cc_final: 0.8074 (mmtm) REVERT: C 125 GLU cc_start: 0.8068 (tm-30) cc_final: 0.7655 (tm-30) REVERT: C 129 LYS cc_start: 0.8436 (mtmt) cc_final: 0.8199 (mtpt) REVERT: C 133 SER cc_start: 0.8534 (m) cc_final: 0.8259 (m) REVERT: C 163 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.8056 (mp0) REVERT: C 212 MET cc_start: 0.6870 (tpt) cc_final: 0.6414 (mmm) REVERT: C 226 ARG cc_start: 0.8312 (mmm-85) cc_final: 0.7907 (mmm-85) REVERT: C 254 GLN cc_start: 0.9038 (tp40) cc_final: 0.8718 (tp-100) REVERT: D 20 MET cc_start: 0.8737 (mmt) cc_final: 0.8416 (mpm) REVERT: D 142 GLU cc_start: 0.7963 (tm-30) cc_final: 0.7680 (tm-30) REVERT: D 146 ARG cc_start: 0.8223 (ttm170) cc_final: 0.7744 (ttp-170) REVERT: D 259 MET cc_start: 0.8164 (OUTLIER) cc_final: 0.7736 (mtt) REVERT: D 276 MET cc_start: 0.6821 (mmm) cc_final: 0.6500 (mmt) REVERT: D 315 LYS cc_start: 0.8319 (tppt) cc_final: 0.7775 (ttmt) REVERT: E 125 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7782 (tm-30) REVERT: E 130 GLN cc_start: 0.8465 (tp-100) cc_final: 0.8095 (tp-100) REVERT: E 133 SER cc_start: 0.8688 (m) cc_final: 0.8371 (m) REVERT: E 163 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8077 (mp0) REVERT: E 212 MET cc_start: 0.6860 (tpt) cc_final: 0.6626 (mmm) REVERT: E 236 MET cc_start: 0.7363 (pp-130) cc_final: 0.7162 (pp-130) REVERT: E 260 MET cc_start: 0.8208 (tpp) cc_final: 0.7548 (mpp) REVERT: E 264 GLN cc_start: 0.8530 (pt0) cc_final: 0.8277 (mm-40) REVERT: F 142 GLU cc_start: 0.7906 (tm-30) cc_final: 0.7611 (tm-30) REVERT: F 146 ARG cc_start: 0.8190 (ttm170) cc_final: 0.7743 (ttp-170) REVERT: F 171 ARG cc_start: 0.7660 (tmm-80) cc_final: 0.7422 (tmm-80) REVERT: F 315 LYS cc_start: 0.8412 (tppt) cc_final: 0.7890 (ttmt) REVERT: G 105 LYS cc_start: 0.8454 (mmmm) cc_final: 0.8126 (mptt) REVERT: G 125 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7637 (tm-30) REVERT: G 129 LYS cc_start: 0.8453 (mtmt) cc_final: 0.8210 (mtpt) REVERT: G 130 GLN cc_start: 0.8459 (tp-100) cc_final: 0.8104 (tp-100) REVERT: G 133 SER cc_start: 0.8662 (m) cc_final: 0.8366 (m) REVERT: G 163 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.8068 (mp0) REVERT: G 203 ASP cc_start: 0.8758 (m-30) cc_final: 0.8362 (m-30) REVERT: G 226 ARG cc_start: 0.8244 (mmm-85) cc_final: 0.7905 (mmm-85) REVERT: G 236 MET cc_start: 0.6825 (pp-130) cc_final: 0.6617 (pp-130) REVERT: G 254 GLN cc_start: 0.9037 (tp40) cc_final: 0.8658 (tp-100) REVERT: G 260 MET cc_start: 0.8071 (mpp) cc_final: 0.7634 (mmt) REVERT: H 20 MET cc_start: 0.8782 (mmt) cc_final: 0.8382 (mpm) REVERT: H 171 ARG cc_start: 0.7693 (tmm-80) cc_final: 0.7461 (tmm-80) REVERT: H 315 LYS cc_start: 0.8377 (tppt) cc_final: 0.7862 (ttmt) outliers start: 89 outliers final: 41 residues processed: 447 average time/residue: 1.3296 time to fit residues: 685.1071 Evaluate side-chains 408 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 361 time to evaluate : 2.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE 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 238 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 259 MET 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 163 GLU Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 259 MET 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 238 THR Chi-restraints excluded: chain F residue 258 VAL 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 238 THR Chi-restraints excluded: chain H residue 258 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 28 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 chunk 145 optimal weight: 0.6980 chunk 201 optimal weight: 0.4980 chunk 108 optimal weight: 2.9990 chunk 220 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN C 97 GLN E 97 GLN G 97 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.152762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.101647 restraints weight = 31205.482| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.68 r_work: 0.3178 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20744 Z= 0.165 Angle : 0.714 15.002 28028 Z= 0.347 Chirality : 0.043 0.285 3068 Planarity : 0.005 0.050 3576 Dihedral : 4.729 31.897 2772 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 4.21 % Allowed : 22.78 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.17), residues: 2476 helix: 0.86 (0.13), residues: 1684 sheet: None (None), residues: 0 loop : -1.26 (0.20), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 54 HIS 0.005 0.001 HIS D 477 PHE 0.022 0.001 PHE A 136 TYR 0.018 0.001 TYR H 186 ARG 0.011 0.000 ARG G 261 Details of bonding type rmsd hydrogen bonds : bond 0.04532 ( 1174) hydrogen bonds : angle 4.13799 ( 3366) covalent geometry : bond 0.00392 (20744) covalent geometry : angle 0.71359 (28028) *********************** 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 478 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 385 time to evaluate : 2.138 Fit side-chains revert: symmetry clash REVERT: A 125 GLU cc_start: 0.8125 (tm-30) cc_final: 0.7707 (tm-30) REVERT: A 130 GLN cc_start: 0.8307 (tp-100) cc_final: 0.8020 (tp-100) REVERT: A 133 SER cc_start: 0.8587 (m) cc_final: 0.8313 (m) REVERT: A 163 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8159 (mp0) REVERT: A 212 MET cc_start: 0.6661 (mmm) cc_final: 0.6393 (mmm) REVERT: A 254 GLN cc_start: 0.9009 (tp40) cc_final: 0.8664 (tp-100) REVERT: A 260 MET cc_start: 0.8013 (mpp) cc_final: 0.7404 (mmt) REVERT: A 264 GLN cc_start: 0.8461 (pt0) cc_final: 0.8192 (mm-40) REVERT: B 183 LEU cc_start: 0.5764 (OUTLIER) cc_final: 0.5142 (tt) REVERT: B 268 MET cc_start: 0.8263 (ptp) cc_final: 0.8038 (ptm) REVERT: B 276 MET cc_start: 0.6670 (mmm) cc_final: 0.6458 (mmt) REVERT: B 299 LYS cc_start: 0.9246 (mttt) cc_final: 0.9034 (mtpm) REVERT: B 315 LYS cc_start: 0.8324 (tppt) cc_final: 0.7787 (ttmt) REVERT: C 125 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7727 (tm-30) REVERT: C 133 SER cc_start: 0.8503 (m) cc_final: 0.8249 (m) REVERT: C 163 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.8114 (mp0) REVERT: C 203 ASP cc_start: 0.8900 (m-30) cc_final: 0.8547 (m-30) REVERT: C 212 MET cc_start: 0.6788 (tpt) cc_final: 0.6350 (mmm) REVERT: C 226 ARG cc_start: 0.8257 (mmm-85) cc_final: 0.7872 (mmm-85) REVERT: C 236 MET cc_start: 0.6856 (pp-130) cc_final: 0.6631 (pp-130) REVERT: C 254 GLN cc_start: 0.9053 (tp40) cc_final: 0.8745 (tp-100) REVERT: C 260 MET cc_start: 0.8118 (mpp) cc_final: 0.7621 (mmt) REVERT: D 20 MET cc_start: 0.8696 (mmt) cc_final: 0.8316 (mpm) REVERT: D 142 GLU cc_start: 0.7879 (tm-30) cc_final: 0.7601 (tm-30) REVERT: D 238 THR cc_start: 0.8944 (OUTLIER) cc_final: 0.8683 (p) REVERT: D 276 MET cc_start: 0.6794 (mmm) cc_final: 0.6554 (mmt) REVERT: D 315 LYS cc_start: 0.8332 (tppt) cc_final: 0.7785 (ttmt) REVERT: E 125 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7716 (tm-30) REVERT: E 130 GLN cc_start: 0.8463 (tp-100) cc_final: 0.8105 (tp-100) REVERT: E 133 SER cc_start: 0.8662 (m) cc_final: 0.8405 (m) REVERT: E 163 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8136 (mp0) REVERT: E 212 MET cc_start: 0.6822 (tpt) cc_final: 0.6300 (mmm) REVERT: E 217 TYR cc_start: 0.4649 (OUTLIER) cc_final: 0.2668 (m-80) REVERT: E 236 MET cc_start: 0.7312 (pp-130) cc_final: 0.7102 (pp-130) REVERT: E 260 MET cc_start: 0.8047 (tpp) cc_final: 0.7503 (mpp) REVERT: E 262 SER cc_start: 0.9147 (t) cc_final: 0.8903 (p) REVERT: E 264 GLN cc_start: 0.8497 (pt0) cc_final: 0.8240 (mm-40) REVERT: F 20 MET cc_start: 0.8726 (mmt) cc_final: 0.8397 (mpm) REVERT: F 171 ARG cc_start: 0.7688 (tmm-80) cc_final: 0.7343 (ttp-110) REVERT: F 183 LEU cc_start: 0.5846 (OUTLIER) cc_final: 0.5194 (tt) REVERT: F 259 MET cc_start: 0.8108 (OUTLIER) cc_final: 0.7751 (mtt) REVERT: F 315 LYS cc_start: 0.8410 (tppt) cc_final: 0.7862 (ttmt) REVERT: G 125 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7695 (tm-30) REVERT: G 130 GLN cc_start: 0.8448 (tp-100) cc_final: 0.8105 (tp-100) REVERT: G 133 SER cc_start: 0.8658 (m) cc_final: 0.8380 (m) REVERT: G 163 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.8109 (mp0) REVERT: G 203 ASP cc_start: 0.8623 (m-30) cc_final: 0.8416 (m-30) REVERT: G 212 MET cc_start: 0.6728 (mmm) cc_final: 0.6321 (mmm) REVERT: G 260 MET cc_start: 0.7988 (mpp) cc_final: 0.7417 (mmt) REVERT: G 261 ARG cc_start: 0.8518 (mmm160) cc_final: 0.8276 (tmt170) REVERT: H 20 MET cc_start: 0.8738 (mmt) cc_final: 0.8353 (mpm) REVERT: H 171 ARG cc_start: 0.7706 (OUTLIER) cc_final: 0.7502 (tmm-80) REVERT: H 183 LEU cc_start: 0.5776 (OUTLIER) cc_final: 0.5135 (tt) REVERT: H 315 LYS cc_start: 0.8336 (tppt) cc_final: 0.7809 (ttmt) outliers start: 93 outliers final: 48 residues processed: 453 average time/residue: 1.2013 time to fit residues: 619.1246 Evaluate side-chains 429 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 370 time to evaluate : 2.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE 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 39 ASP Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 258 VAL 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 138 GLN 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 D residue 9 LEU Chi-restraints excluded: chain D residue 25 CYS 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 435 THR Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 138 GLN Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain F residue 9 LEU 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 258 VAL Chi-restraints excluded: chain F residue 259 MET 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 122 ILE Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 156 HIS 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 138 ASP Chi-restraints excluded: chain H residue 171 ARG Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain H residue 258 VAL 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 200 optimal weight: 0.0060 chunk 102 optimal weight: 0.9990 chunk 223 optimal weight: 0.6980 chunk 209 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 128 optimal weight: 6.9990 chunk 116 optimal weight: 3.9990 chunk 185 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 213 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 overall best weight: 1.5402 ------------------------------------------------------------------------------- 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 = 0.4025 r_free = 0.4025 target = 0.152649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.101565 restraints weight = 31531.524| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.68 r_work: 0.3168 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20744 Z= 0.164 Angle : 0.736 17.809 28028 Z= 0.352 Chirality : 0.044 0.271 3068 Planarity : 0.005 0.058 3576 Dihedral : 4.713 31.429 2772 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.76 % Allowed : 23.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.17), residues: 2476 helix: 0.95 (0.13), residues: 1672 sheet: None (None), residues: 0 loop : -1.20 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 54 HIS 0.004 0.001 HIS D 477 PHE 0.022 0.002 PHE G 136 TYR 0.019 0.001 TYR H 186 ARG 0.012 0.001 ARG C 261 Details of bonding type rmsd hydrogen bonds : bond 0.04479 ( 1174) hydrogen bonds : angle 4.14845 ( 3366) covalent geometry : bond 0.00387 (20744) covalent geometry : angle 0.73647 (28028) *********************** 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 460 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 377 time to evaluate : 2.443 Fit side-chains REVERT: A 130 GLN cc_start: 0.8304 (tp-100) cc_final: 0.7998 (tp-100) REVERT: A 133 SER cc_start: 0.8590 (m) cc_final: 0.8335 (m) REVERT: A 163 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8131 (mp0) REVERT: A 195 CYS cc_start: 0.7614 (p) cc_final: 0.7324 (p) REVERT: A 212 MET cc_start: 0.6631 (mmm) cc_final: 0.6352 (mmm) REVERT: A 254 GLN cc_start: 0.9009 (tp40) cc_final: 0.8672 (tp-100) REVERT: A 260 MET cc_start: 0.8016 (mpp) cc_final: 0.7373 (mmt) REVERT: A 264 GLN cc_start: 0.8425 (pt0) cc_final: 0.8195 (mm-40) REVERT: B 171 ARG cc_start: 0.7612 (tmm-80) cc_final: 0.7404 (tmm-80) REVERT: B 259 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.7703 (mtt) REVERT: B 268 MET cc_start: 0.8219 (ptp) cc_final: 0.8005 (ptm) REVERT: B 276 MET cc_start: 0.6658 (mmm) cc_final: 0.6444 (mmt) REVERT: B 299 LYS cc_start: 0.9253 (mttt) cc_final: 0.9043 (mtpm) REVERT: B 315 LYS cc_start: 0.8320 (tppt) cc_final: 0.7784 (ttmt) REVERT: C 125 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7742 (tm-30) REVERT: C 133 SER cc_start: 0.8474 (m) cc_final: 0.8206 (m) REVERT: C 138 GLN cc_start: 0.6656 (OUTLIER) cc_final: 0.5973 (pm20) REVERT: C 163 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8111 (mp0) REVERT: C 212 MET cc_start: 0.6771 (tpt) cc_final: 0.6444 (mmm) REVERT: C 217 TYR cc_start: 0.4696 (OUTLIER) cc_final: 0.2700 (m-80) REVERT: C 226 ARG cc_start: 0.8123 (mmm-85) cc_final: 0.7882 (mmm-85) REVERT: C 236 MET cc_start: 0.6811 (pp-130) cc_final: 0.6608 (pp-130) REVERT: C 254 GLN cc_start: 0.9044 (tp40) cc_final: 0.8748 (tp-100) REVERT: C 260 MET cc_start: 0.8064 (mpp) cc_final: 0.7533 (mmt) REVERT: C 261 ARG cc_start: 0.8579 (mmm160) cc_final: 0.8339 (tmt170) REVERT: D 20 MET cc_start: 0.8718 (mmt) cc_final: 0.8337 (mpm) REVERT: D 27 MET cc_start: 0.7554 (tmt) cc_final: 0.7102 (tmm) REVERT: D 238 THR cc_start: 0.8937 (OUTLIER) cc_final: 0.8675 (p) REVERT: D 315 LYS cc_start: 0.8320 (tppt) cc_final: 0.7781 (ttmt) REVERT: E 125 GLU cc_start: 0.8139 (tm-30) cc_final: 0.7733 (tm-30) REVERT: E 130 GLN cc_start: 0.8501 (tp-100) cc_final: 0.8295 (tp-100) REVERT: E 133 SER cc_start: 0.8687 (m) cc_final: 0.8442 (m) REVERT: E 138 GLN cc_start: 0.6666 (OUTLIER) cc_final: 0.5983 (pm20) REVERT: E 163 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8153 (mp0) REVERT: E 212 MET cc_start: 0.6595 (tpt) cc_final: 0.6233 (mmm) REVERT: E 217 TYR cc_start: 0.4653 (OUTLIER) cc_final: 0.2630 (m-80) REVERT: E 236 MET cc_start: 0.7330 (pp-130) cc_final: 0.7127 (pp-130) REVERT: E 260 MET cc_start: 0.8081 (tpp) cc_final: 0.7510 (mpp) REVERT: E 262 SER cc_start: 0.9154 (t) cc_final: 0.8920 (p) REVERT: E 264 GLN cc_start: 0.8490 (pt0) cc_final: 0.8242 (mm-40) REVERT: F 20 MET cc_start: 0.8709 (mmt) cc_final: 0.8384 (mpm) REVERT: F 27 MET cc_start: 0.7472 (tmt) cc_final: 0.7028 (tmm) REVERT: F 171 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.7360 (ttp-110) REVERT: F 259 MET cc_start: 0.8110 (OUTLIER) cc_final: 0.7385 (mtt) REVERT: F 276 MET cc_start: 0.6580 (mmt) cc_final: 0.6317 (mmm) REVERT: F 315 LYS cc_start: 0.8402 (tppt) cc_final: 0.7857 (ttmt) REVERT: G 125 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7772 (tm-30) REVERT: G 130 GLN cc_start: 0.8465 (tp-100) cc_final: 0.8091 (tp-100) REVERT: G 133 SER cc_start: 0.8655 (m) cc_final: 0.8397 (m) REVERT: G 163 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.8102 (mp0) REVERT: G 212 MET cc_start: 0.6640 (mmm) cc_final: 0.6224 (mmm) REVERT: G 260 MET cc_start: 0.8023 (mpp) cc_final: 0.7544 (mmt) REVERT: H 20 MET cc_start: 0.8700 (mmt) cc_final: 0.8357 (mpm) REVERT: H 171 ARG cc_start: 0.7594 (tmm-80) cc_final: 0.7275 (ttp-110) REVERT: H 276 MET cc_start: 0.6693 (mmt) cc_final: 0.6430 (mmm) REVERT: H 315 LYS cc_start: 0.8375 (tppt) cc_final: 0.7842 (ttmt) outliers start: 83 outliers final: 42 residues processed: 433 average time/residue: 1.2765 time to fit residues: 626.0687 Evaluate side-chains 416 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 362 time to evaluate : 2.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE 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 39 ASP Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 259 MET 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 160 VAL Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 25 CYS 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 435 THR Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 138 GLN Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 138 ASP Chi-restraints excluded: chain F residue 171 ARG Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain F residue 258 VAL Chi-restraints excluded: chain F residue 259 MET 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 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 138 ASP Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain H residue 258 VAL 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 143 optimal weight: 0.6980 chunk 84 optimal weight: 0.9980 chunk 37 optimal weight: 7.9990 chunk 155 optimal weight: 7.9990 chunk 109 optimal weight: 1.9990 chunk 129 optimal weight: 0.5980 chunk 218 optimal weight: 0.9980 chunk 173 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 116 optimal weight: 0.2980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN A 130 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 = 0.4027 r_free = 0.4027 target = 0.153690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.102722 restraints weight = 31347.515| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.64 r_work: 0.3205 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20744 Z= 0.140 Angle : 0.751 16.741 28028 Z= 0.360 Chirality : 0.042 0.259 3068 Planarity : 0.005 0.055 3576 Dihedral : 4.588 30.241 2772 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.99 % Allowed : 25.18 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.17), residues: 2476 helix: 1.06 (0.13), residues: 1668 sheet: None (None), residues: 0 loop : -1.12 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 54 HIS 0.004 0.000 HIS H 477 PHE 0.024 0.001 PHE E 136 TYR 0.017 0.001 TYR F 186 ARG 0.013 0.000 ARG H 415 Details of bonding type rmsd hydrogen bonds : bond 0.04173 ( 1174) hydrogen bonds : angle 4.07427 ( 3366) covalent geometry : bond 0.00320 (20744) covalent geometry : angle 0.75118 (28028) *********************** 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 447 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 381 time to evaluate : 2.723 Fit side-chains REVERT: A 133 SER cc_start: 0.8665 (m) cc_final: 0.8398 (m) REVERT: A 195 CYS cc_start: 0.7631 (p) cc_final: 0.7366 (p) REVERT: A 236 MET cc_start: 0.6739 (pp-130) cc_final: 0.6506 (ppp) REVERT: A 254 GLN cc_start: 0.8990 (tp40) cc_final: 0.8740 (tp-100) REVERT: A 260 MET cc_start: 0.8059 (mpp) cc_final: 0.7578 (mmt) REVERT: B 27 MET cc_start: 0.7376 (tmt) cc_final: 0.7084 (tmm) REVERT: B 171 ARG cc_start: 0.7668 (tmm-80) cc_final: 0.7463 (tmm-80) REVERT: B 183 LEU cc_start: 0.5763 (OUTLIER) cc_final: 0.5108 (tt) REVERT: B 238 THR cc_start: 0.8914 (OUTLIER) cc_final: 0.8659 (p) REVERT: B 259 MET cc_start: 0.8154 (OUTLIER) cc_final: 0.7703 (mtt) REVERT: B 299 LYS cc_start: 0.9249 (mttt) cc_final: 0.9036 (mtpm) REVERT: B 315 LYS cc_start: 0.8266 (tppt) cc_final: 0.7770 (ttmt) REVERT: C 125 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7649 (tm-30) REVERT: C 133 SER cc_start: 0.8455 (m) cc_final: 0.8246 (m) REVERT: C 163 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8064 (mp0) REVERT: C 195 CYS cc_start: 0.7538 (p) cc_final: 0.7260 (p) REVERT: C 212 MET cc_start: 0.6823 (tpt) cc_final: 0.5998 (mmm) REVERT: C 217 TYR cc_start: 0.4709 (OUTLIER) cc_final: 0.2590 (m-80) REVERT: C 226 ARG cc_start: 0.8169 (mmm-85) cc_final: 0.7957 (mmm-85) REVERT: C 236 MET cc_start: 0.6692 (pp-130) cc_final: 0.6466 (pp-130) REVERT: C 254 GLN cc_start: 0.9015 (tp40) cc_final: 0.8725 (tp-100) REVERT: C 260 MET cc_start: 0.8133 (mpp) cc_final: 0.7760 (mmt) REVERT: D 20 MET cc_start: 0.8693 (mmt) cc_final: 0.8299 (mpm) REVERT: D 27 MET cc_start: 0.7526 (tmt) cc_final: 0.7201 (tmm) REVERT: D 238 THR cc_start: 0.8928 (OUTLIER) cc_final: 0.8685 (p) REVERT: D 315 LYS cc_start: 0.8233 (tppt) cc_final: 0.7745 (ttmt) REVERT: E 125 GLU cc_start: 0.8021 (tm-30) cc_final: 0.7672 (tm-30) REVERT: E 130 GLN cc_start: 0.8620 (tp-100) cc_final: 0.8351 (tp-100) REVERT: E 133 SER cc_start: 0.8694 (m) cc_final: 0.8461 (m) REVERT: E 163 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.8088 (mp0) REVERT: E 195 CYS cc_start: 0.7610 (p) cc_final: 0.7403 (p) REVERT: E 212 MET cc_start: 0.6651 (tpt) cc_final: 0.6415 (mmm) REVERT: E 217 TYR cc_start: 0.4684 (OUTLIER) cc_final: 0.2603 (m-80) REVERT: E 260 MET cc_start: 0.8155 (tpp) cc_final: 0.7527 (mpp) REVERT: E 261 ARG cc_start: 0.8519 (mmm160) cc_final: 0.8296 (tmt170) REVERT: E 262 SER cc_start: 0.9197 (t) cc_final: 0.8981 (p) REVERT: E 264 GLN cc_start: 0.8460 (pt0) cc_final: 0.8246 (mm-40) REVERT: F 20 MET cc_start: 0.8671 (mmt) cc_final: 0.8323 (mpm) REVERT: F 27 MET cc_start: 0.7436 (tmt) cc_final: 0.7201 (tmm) REVERT: F 171 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.7287 (ttp-110) REVERT: F 183 LEU cc_start: 0.5787 (OUTLIER) cc_final: 0.5114 (tt) REVERT: F 187 TYR cc_start: 0.7755 (m-10) cc_final: 0.7554 (m-10) REVERT: F 238 THR cc_start: 0.8931 (OUTLIER) cc_final: 0.8697 (p) REVERT: F 276 MET cc_start: 0.6590 (mmt) cc_final: 0.6329 (mmm) REVERT: F 315 LYS cc_start: 0.8300 (tppt) cc_final: 0.7796 (ttmt) REVERT: G 130 GLN cc_start: 0.8619 (tp-100) cc_final: 0.8406 (tp-100) REVERT: G 133 SER cc_start: 0.8690 (m) cc_final: 0.8439 (m) REVERT: G 163 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.8058 (mp0) REVERT: G 195 CYS cc_start: 0.7589 (p) cc_final: 0.7356 (p) REVERT: G 212 MET cc_start: 0.6797 (mmm) cc_final: 0.6564 (mmm) REVERT: G 260 MET cc_start: 0.8109 (mpp) cc_final: 0.7499 (mmt) REVERT: G 261 ARG cc_start: 0.8509 (mmm160) cc_final: 0.8207 (tmt170) REVERT: H 20 MET cc_start: 0.8754 (mmt) cc_final: 0.8367 (mpm) REVERT: H 27 MET cc_start: 0.7472 (tmt) cc_final: 0.7202 (tmm) REVERT: H 139 ARG cc_start: 0.8659 (tpp-160) cc_final: 0.8340 (tpp80) REVERT: H 171 ARG cc_start: 0.7615 (OUTLIER) cc_final: 0.7321 (ttp-110) REVERT: H 276 MET cc_start: 0.6726 (mmt) cc_final: 0.6410 (mmm) REVERT: H 315 LYS cc_start: 0.8320 (tppt) cc_final: 0.7796 (ttmt) outliers start: 66 outliers final: 31 residues processed: 424 average time/residue: 1.5538 time to fit residues: 751.4522 Evaluate side-chains 406 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 362 time to evaluate : 3.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain B residue 9 LEU 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 258 VAL Chi-restraints excluded: chain B residue 259 MET Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain D residue 9 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 444 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 163 GLU Chi-restraints excluded: chain E residue 209 TYR Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain F residue 9 LEU 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 F residue 444 SER Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 163 GLU 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 171 ARG Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain H residue 393 LEU 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 164 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 171 optimal weight: 4.9990 chunk 203 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 212 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 142 optimal weight: 0.9980 chunk 214 optimal weight: 0.0770 chunk 206 optimal weight: 0.9980 overall best weight: 0.9940 ------------------------------------------------------------------------------- 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** C 97 GLN C 264 GLN ** D 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.153529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.102206 restraints weight = 31529.870| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.67 r_work: 0.3199 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20744 Z= 0.145 Angle : 0.741 14.342 28028 Z= 0.360 Chirality : 0.043 0.310 3068 Planarity : 0.005 0.059 3576 Dihedral : 4.543 29.197 2772 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.17 % Allowed : 26.90 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.17), residues: 2476 helix: 1.04 (0.13), residues: 1680 sheet: None (None), residues: 0 loop : -1.08 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 54 HIS 0.007 0.001 HIS B 477 PHE 0.020 0.001 PHE C 249 TYR 0.016 0.001 TYR F 186 ARG 0.012 0.000 ARG G 261 Details of bonding type rmsd hydrogen bonds : bond 0.04116 ( 1174) hydrogen bonds : angle 4.07547 ( 3366) covalent geometry : bond 0.00339 (20744) covalent geometry : angle 0.74114 (28028) ********************** 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 431 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 383 time to evaluate : 2.191 Fit side-chains REVERT: A 133 SER cc_start: 0.8570 (m) cc_final: 0.8340 (m) REVERT: A 195 CYS cc_start: 0.7549 (p) cc_final: 0.7280 (p) REVERT: A 254 GLN cc_start: 0.8965 (tp40) cc_final: 0.8694 (tp-100) REVERT: A 260 MET cc_start: 0.8085 (mpp) cc_final: 0.7545 (mmt) REVERT: B 27 MET cc_start: 0.7608 (tmt) cc_final: 0.7224 (tmm) REVERT: B 183 LEU cc_start: 0.5761 (OUTLIER) cc_final: 0.5089 (tt) REVERT: B 238 THR cc_start: 0.8921 (OUTLIER) cc_final: 0.8658 (p) REVERT: B 299 LYS cc_start: 0.9257 (mttt) cc_final: 0.9040 (mtpm) REVERT: B 315 LYS cc_start: 0.8260 (tppt) cc_final: 0.7774 (ttmt) REVERT: C 163 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8086 (mp0) REVERT: C 195 CYS cc_start: 0.7542 (p) cc_final: 0.7286 (p) REVERT: C 212 MET cc_start: 0.6784 (tpt) cc_final: 0.6542 (mmm) REVERT: C 217 TYR cc_start: 0.4620 (OUTLIER) cc_final: 0.2397 (m-80) REVERT: C 226 ARG cc_start: 0.8193 (mmm-85) cc_final: 0.7983 (mmm-85) REVERT: C 236 MET cc_start: 0.6665 (pp-130) cc_final: 0.6420 (pp-130) REVERT: C 260 MET cc_start: 0.8150 (mpp) cc_final: 0.7373 (mmt) REVERT: D 20 MET cc_start: 0.8712 (mmt) cc_final: 0.8365 (mpm) REVERT: D 27 MET cc_start: 0.7658 (tmt) cc_final: 0.7178 (tmm) REVERT: D 238 THR cc_start: 0.8922 (OUTLIER) cc_final: 0.8674 (p) REVERT: D 276 MET cc_start: 0.7080 (mmt) cc_final: 0.6807 (mmm) REVERT: D 315 LYS cc_start: 0.8269 (tppt) cc_final: 0.7772 (ttmt) REVERT: E 130 GLN cc_start: 0.8633 (tp-100) cc_final: 0.8307 (tp-100) REVERT: E 133 SER cc_start: 0.8705 (m) cc_final: 0.8485 (m) REVERT: E 163 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.8142 (mp0) REVERT: E 195 CYS cc_start: 0.7604 (p) cc_final: 0.7383 (p) REVERT: E 212 MET cc_start: 0.6775 (tpt) cc_final: 0.6247 (mmm) REVERT: E 217 TYR cc_start: 0.4699 (OUTLIER) cc_final: 0.2583 (m-80) REVERT: E 260 MET cc_start: 0.8204 (tpp) cc_final: 0.7642 (mpp) REVERT: F 20 MET cc_start: 0.8653 (mmt) cc_final: 0.8333 (mpm) REVERT: F 27 MET cc_start: 0.7620 (tmt) cc_final: 0.7219 (tmm) REVERT: F 171 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.7294 (ttp-110) REVERT: F 183 LEU cc_start: 0.5746 (OUTLIER) cc_final: 0.5066 (tt) REVERT: F 187 TYR cc_start: 0.7734 (m-10) cc_final: 0.7516 (m-10) REVERT: F 238 THR cc_start: 0.8986 (OUTLIER) cc_final: 0.8741 (p) REVERT: F 276 MET cc_start: 0.6532 (mmt) cc_final: 0.6257 (mmm) REVERT: F 315 LYS cc_start: 0.8322 (tppt) cc_final: 0.7804 (ttmt) REVERT: G 130 GLN cc_start: 0.8727 (tp-100) cc_final: 0.8489 (tp-100) REVERT: G 133 SER cc_start: 0.8653 (m) cc_final: 0.8417 (m) REVERT: G 195 CYS cc_start: 0.7512 (p) cc_final: 0.7278 (p) REVERT: G 260 MET cc_start: 0.8094 (mpp) cc_final: 0.7486 (mmt) REVERT: G 261 ARG cc_start: 0.8482 (mmm160) cc_final: 0.8202 (tmt170) REVERT: H 20 MET cc_start: 0.8767 (mmt) cc_final: 0.8407 (mpm) REVERT: H 27 MET cc_start: 0.7590 (tmt) cc_final: 0.7177 (tmm) REVERT: H 171 ARG cc_start: 0.7644 (OUTLIER) cc_final: 0.7383 (ttp-110) REVERT: H 183 LEU cc_start: 0.5751 (OUTLIER) cc_final: 0.5069 (tt) REVERT: H 276 MET cc_start: 0.6619 (mmt) cc_final: 0.6314 (mmm) REVERT: H 315 LYS cc_start: 0.8313 (tppt) cc_final: 0.7804 (ttmt) outliers start: 48 outliers final: 31 residues processed: 415 average time/residue: 1.2249 time to fit residues: 578.2260 Evaluate side-chains 410 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 367 time to evaluate : 2.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain B residue 9 LEU 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 258 VAL Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 217 TYR 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 E residue 97 GLN Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 209 TYR Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 29 LEU 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 143 THR Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 138 ASP Chi-restraints excluded: chain H residue 171 ARG Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain H residue 258 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 96 optimal weight: 2.9990 chunk 211 optimal weight: 0.5980 chunk 194 optimal weight: 1.9990 chunk 177 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 213 optimal weight: 1.9990 chunk 203 optimal weight: 4.9990 chunk 212 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 8 optimal weight: 6.9990 chunk 155 optimal weight: 10.0000 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 GLN ** D 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 GLN ** F 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN ** H 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 478 HIS ** 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 = 0.4027 r_free = 0.4027 target = 0.153516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.102857 restraints weight = 31559.594| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.62 r_work: 0.3191 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20744 Z= 0.157 Angle : 0.771 16.558 28028 Z= 0.373 Chirality : 0.044 0.336 3068 Planarity : 0.005 0.054 3576 Dihedral : 4.539 28.885 2772 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.26 % Allowed : 26.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.17), residues: 2476 helix: 1.01 (0.13), residues: 1680 sheet: None (None), residues: 0 loop : -1.01 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 54 HIS 0.016 0.001 HIS H 478 PHE 0.019 0.001 PHE C 249 TYR 0.016 0.001 TYR F 186 ARG 0.012 0.001 ARG B 415 Details of bonding type rmsd hydrogen bonds : bond 0.04208 ( 1174) hydrogen bonds : angle 4.11547 ( 3366) covalent geometry : bond 0.00369 (20744) covalent geometry : angle 0.77114 (28028) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23311.61 seconds wall clock time: 398 minutes 46.03 seconds (23926.03 seconds total)