Starting phenix.real_space_refine on Sat Sep 28 19:35:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w6s_32334/09_2024/7w6s_32334.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w6s_32334/09_2024/7w6s_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w6s_32334/09_2024/7w6s_32334.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w6s_32334/09_2024/7w6s_32334.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w6s_32334/09_2024/7w6s_32334.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w6s_32334/09_2024/7w6s_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 11.17, per 1000 atoms: 0.55 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: 4.86 Conformation dependent library (CDL) restraints added in 2.4 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: 1.78 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: 5.71 Time building geometry restraints manager: 5.71 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: 0.00 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: 1.210 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: 0.020 Extract box with map and model: 0.740 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 41.980 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.210 ------------------------------------------------------------------------------- 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= 0.346 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 *********************** 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 fitting. rotamer outliers: 4 poor density : 539 time to evaluate : 2.211 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: 1.3462 time to fit residues: 819.1023 Evaluate side-chains 373 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 373 time to evaluate : 2.419 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 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= 0.222 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 *********************** 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 fitting. rotamer outliers: 68 poor density : 437 time to evaluate : 2.317 Fit side-chains REVERT: A 125 GLU cc_start: 0.7432 (tm-30) cc_final: 0.7127 (tm-30) REVERT: A 129 LYS cc_start: 0.8292 (mtmt) cc_final: 0.7979 (mtpt) REVERT: A 133 SER cc_start: 0.8610 (m) cc_final: 0.8292 (m) REVERT: A 134 GLN cc_start: 0.8205 (mm110) cc_final: 0.8004 (mm110) REVERT: A 232 PHE cc_start: 0.8109 (t80) cc_final: 0.7843 (t80) REVERT: A 254 GLN cc_start: 0.8832 (tp40) cc_final: 0.8595 (tp40) REVERT: B 187 TYR cc_start: 0.8020 (m-10) cc_final: 0.7802 (m-10) REVERT: B 292 PHE cc_start: 0.8702 (m-80) cc_final: 0.8488 (m-80) REVERT: B 315 LYS cc_start: 0.8305 (tppt) cc_final: 0.8001 (ttmt) REVERT: C 125 GLU cc_start: 0.7457 (tm-30) cc_final: 0.7224 (tm-30) REVERT: C 129 LYS cc_start: 0.8303 (mtmt) cc_final: 0.7997 (mtpt) REVERT: C 133 SER cc_start: 0.8621 (m) cc_final: 0.8306 (m) REVERT: C 212 MET cc_start: 0.6870 (tpt) cc_final: 0.6205 (mmm) REVERT: C 226 ARG cc_start: 0.8339 (mmm-85) cc_final: 0.8051 (mmm-85) REVERT: C 254 GLN cc_start: 0.8820 (tp40) cc_final: 0.8574 (tp40) REVERT: C 263 MET cc_start: 0.8323 (ttm) cc_final: 0.7863 (tpp) REVERT: D 146 ARG cc_start: 0.7917 (ttm170) cc_final: 0.7702 (ttp-170) REVERT: D 170 TRP cc_start: 0.7518 (t-100) cc_final: 0.7296 (t-100) REVERT: D 315 LYS cc_start: 0.8316 (tppt) cc_final: 0.7999 (ttmt) REVERT: E 125 GLU cc_start: 0.7390 (tm-30) cc_final: 0.7181 (tm-30) REVERT: E 129 LYS cc_start: 0.8328 (mtmt) cc_final: 0.8005 (mtpt) REVERT: E 133 SER cc_start: 0.8564 (m) cc_final: 0.8234 (m) REVERT: E 134 GLN cc_start: 0.8113 (mm110) cc_final: 0.7885 (mm110) REVERT: E 236 MET cc_start: 0.7470 (mtt) cc_final: 0.7127 (pp-130) REVERT: E 254 GLN cc_start: 0.8883 (tp40) cc_final: 0.8549 (tp-100) REVERT: E 263 MET cc_start: 0.8378 (ttm) cc_final: 0.8166 (tpp) REVERT: F 315 LYS cc_start: 0.8291 (tppt) cc_final: 0.7957 (ttmt) REVERT: G 125 GLU cc_start: 0.7398 (tm-30) cc_final: 0.7124 (tm-30) REVERT: G 129 LYS cc_start: 0.8274 (mtmt) cc_final: 0.7956 (mtpt) REVERT: G 133 SER cc_start: 0.8602 (m) cc_final: 0.8282 (m) REVERT: G 134 GLN cc_start: 0.8184 (mm110) cc_final: 0.7972 (mm110) REVERT: G 236 MET cc_start: 0.7665 (mtt) cc_final: 0.6899 (pp-130) REVERT: G 254 GLN cc_start: 0.8844 (tp40) cc_final: 0.8607 (tp40) REVERT: G 263 MET cc_start: 0.8397 (ttm) cc_final: 0.8169 (tpp) REVERT: H 187 TYR cc_start: 0.8090 (m-10) cc_final: 0.7843 (m-10) REVERT: H 315 LYS cc_start: 0.8289 (tppt) cc_final: 0.7993 (ttmt) outliers start: 68 outliers final: 31 residues processed: 484 average time/residue: 1.2063 time to fit residues: 661.7580 Evaluate side-chains 417 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 386 time to evaluate : 2.107 ------------------------------------------------------------------------------- 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 123 optimal weight: 0.5980 chunk 68 optimal weight: 0.8980 chunk 184 optimal weight: 0.6980 chunk 150 optimal weight: 0.7980 chunk 61 optimal weight: 0.0670 chunk 221 optimal weight: 0.9990 chunk 239 optimal weight: 0.6980 chunk 197 optimal weight: 10.0000 chunk 220 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 chunk 178 optimal weight: 5.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20744 Z= 0.182 Angle : 0.648 13.491 28028 Z= 0.323 Chirality : 0.041 0.142 3068 Planarity : 0.005 0.059 3576 Dihedral : 4.805 32.243 2772 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.58 % Allowed : 18.30 % Favored : 79.12 % 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: -0.24 (0.17), residues: 2476 helix: 0.55 (0.13), residues: 1684 sheet: None (None), residues: 0 loop : -1.64 (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 0.024 0.001 PHE E 232 TYR 0.017 0.001 TYR D 186 ARG 0.006 0.000 ARG B 415 *********************** 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 491 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 434 time to evaluate : 2.255 Fit side-chains revert: symmetry clash REVERT: A 125 GLU cc_start: 0.7372 (tm-30) cc_final: 0.7111 (tm-30) REVERT: A 129 LYS cc_start: 0.8361 (mtmt) cc_final: 0.7991 (mtpt) REVERT: A 133 SER cc_start: 0.8509 (m) cc_final: 0.8234 (m) REVERT: A 203 ASP cc_start: 0.8731 (m-30) cc_final: 0.8525 (m-30) REVERT: A 212 MET cc_start: 0.6893 (mmm) cc_final: 0.6624 (mmm) REVERT: A 254 GLN cc_start: 0.8914 (tp40) cc_final: 0.8594 (tp-100) REVERT: B 276 MET cc_start: 0.6949 (mmm) cc_final: 0.6746 (mmt) REVERT: B 292 PHE cc_start: 0.8698 (m-80) cc_final: 0.8493 (m-80) REVERT: B 315 LYS cc_start: 0.8185 (tppt) cc_final: 0.7897 (ttmt) REVERT: C 129 LYS cc_start: 0.8322 (mtmt) cc_final: 0.7971 (mtpt) REVERT: C 133 SER cc_start: 0.8498 (m) cc_final: 0.8244 (m) REVERT: C 212 MET cc_start: 0.6784 (tpt) cc_final: 0.6193 (mmm) REVERT: C 226 ARG cc_start: 0.8390 (mmm-85) cc_final: 0.8052 (mmm-85) REVERT: C 254 GLN cc_start: 0.8856 (tp40) cc_final: 0.8555 (tp-100) REVERT: C 263 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.7883 (tpp) REVERT: D 146 ARG cc_start: 0.8058 (ttm170) cc_final: 0.7751 (ttp-170) REVERT: D 276 MET cc_start: 0.6926 (mmm) cc_final: 0.6705 (mmt) REVERT: D 315 LYS cc_start: 0.8222 (tppt) cc_final: 0.7930 (ttmt) REVERT: E 129 LYS cc_start: 0.8312 (mtmt) cc_final: 0.8007 (mtpt) REVERT: E 133 SER cc_start: 0.8499 (m) cc_final: 0.8213 (m) REVERT: E 163 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7309 (pm20) REVERT: E 254 GLN cc_start: 0.8847 (tp40) cc_final: 0.8553 (tp-100) REVERT: E 263 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.7887 (tpp) REVERT: F 146 ARG cc_start: 0.8041 (ttm170) cc_final: 0.7786 (ttp-170) REVERT: F 171 ARG cc_start: 0.7691 (tmm-80) cc_final: 0.7478 (tmm-80) REVERT: F 268 MET cc_start: 0.7709 (ptm) cc_final: 0.7403 (ptp) REVERT: F 315 LYS cc_start: 0.8241 (tppt) cc_final: 0.7980 (ttmt) REVERT: G 129 LYS cc_start: 0.8328 (mtmt) cc_final: 0.8026 (mtpt) REVERT: G 133 SER cc_start: 0.8457 (m) cc_final: 0.8123 (m) REVERT: G 134 GLN cc_start: 0.8131 (mm110) cc_final: 0.7886 (mm110) REVERT: G 212 MET cc_start: 0.6540 (tpt) cc_final: 0.6054 (mmm) REVERT: G 226 ARG cc_start: 0.8268 (mmm-85) cc_final: 0.8034 (mmm-85) REVERT: G 254 GLN cc_start: 0.8849 (tp40) cc_final: 0.8538 (tp-100) REVERT: H 171 ARG cc_start: 0.7670 (tmm-80) cc_final: 0.7453 (tmm-80) REVERT: H 268 MET cc_start: 0.7687 (ptm) cc_final: 0.7379 (ptp) REVERT: H 315 LYS cc_start: 0.8231 (tppt) cc_final: 0.7983 (ttmt) outliers start: 57 outliers final: 13 residues processed: 480 average time/residue: 1.1820 time to fit residues: 645.8765 Evaluate side-chains 396 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 380 time to evaluate : 2.231 ------------------------------------------------------------------------------- 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 444 SER 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 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 E residue 263 MET 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 444 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 0.0030 chunk 166 optimal weight: 0.0980 chunk 115 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 222 optimal weight: 8.9990 chunk 235 optimal weight: 3.9990 chunk 116 optimal weight: 0.0980 chunk 211 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.4392 ------------------------------------------------------------------------------- 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 C 264 GLN D 177 HIS D 443 HIS E 97 GLN F 443 HIS F 478 HIS G 97 GLN H 443 HIS H 478 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20744 Z= 0.162 Angle : 0.634 12.467 28028 Z= 0.313 Chirality : 0.041 0.164 3068 Planarity : 0.004 0.050 3576 Dihedral : 4.614 29.744 2772 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.63 % Allowed : 20.79 % Favored : 76.59 % 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: 0.21 (0.17), residues: 2476 helix: 0.91 (0.13), residues: 1648 sheet: None (None), residues: 0 loop : -1.40 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 54 HIS 0.013 0.001 HIS F 478 PHE 0.012 0.001 PHE A 136 TYR 0.015 0.001 TYR H 186 ARG 0.009 0.000 ARG F 415 *********************** 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 476 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 418 time to evaluate : 2.405 Fit side-chains revert: symmetry clash REVERT: A 105 LYS cc_start: 0.8126 (mmmm) cc_final: 0.7863 (mmtm) REVERT: A 129 LYS cc_start: 0.8358 (mtmt) cc_final: 0.7981 (mtpt) REVERT: A 133 SER cc_start: 0.8456 (m) cc_final: 0.8158 (m) REVERT: A 241 ASP cc_start: 0.7387 (OUTLIER) cc_final: 0.7087 (p0) REVERT: A 254 GLN cc_start: 0.8850 (tp40) cc_final: 0.8592 (tp-100) REVERT: B 146 ARG cc_start: 0.8034 (ttm170) cc_final: 0.7668 (ttp-170) REVERT: B 268 MET cc_start: 0.7970 (ptp) cc_final: 0.7714 (ptm) REVERT: B 315 LYS cc_start: 0.8187 (tppt) cc_final: 0.7912 (ttmt) REVERT: C 105 LYS cc_start: 0.8074 (mmmm) cc_final: 0.7793 (mmtp) REVERT: C 129 LYS cc_start: 0.8282 (mtmt) cc_final: 0.8019 (mtpt) REVERT: C 133 SER cc_start: 0.8490 (m) cc_final: 0.8189 (m) REVERT: C 163 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7237 (pm20) REVERT: C 212 MET cc_start: 0.6721 (tpt) cc_final: 0.6325 (mmm) REVERT: C 226 ARG cc_start: 0.8330 (mmm-85) cc_final: 0.7991 (mmm-85) REVERT: C 254 GLN cc_start: 0.8826 (tp40) cc_final: 0.8534 (tp-100) REVERT: D 20 MET cc_start: 0.8870 (mmt) cc_final: 0.8551 (mpm) REVERT: D 146 ARG cc_start: 0.8047 (ttm170) cc_final: 0.7734 (ttp-170) REVERT: D 268 MET cc_start: 0.7986 (ptp) cc_final: 0.7738 (ptm) REVERT: D 276 MET cc_start: 0.6849 (mmm) cc_final: 0.6610 (mmt) REVERT: D 315 LYS cc_start: 0.8148 (tppt) cc_final: 0.7896 (ttmt) REVERT: E 129 LYS cc_start: 0.8278 (mtmt) cc_final: 0.8052 (mtpt) REVERT: E 133 SER cc_start: 0.8431 (m) cc_final: 0.8181 (m) REVERT: E 254 GLN cc_start: 0.8851 (tp40) cc_final: 0.8522 (tp-100) REVERT: E 262 SER cc_start: 0.9196 (t) cc_final: 0.8973 (p) REVERT: F 20 MET cc_start: 0.8920 (mmt) cc_final: 0.8590 (mpm) REVERT: F 146 ARG cc_start: 0.8114 (ttm170) cc_final: 0.7812 (ttp-170) REVERT: F 259 MET cc_start: 0.7845 (mtt) cc_final: 0.7415 (mtt) REVERT: F 268 MET cc_start: 0.7650 (ptm) cc_final: 0.7332 (ptp) REVERT: F 315 LYS cc_start: 0.8177 (tppt) cc_final: 0.7919 (ttmt) REVERT: G 129 LYS cc_start: 0.8260 (mtmt) cc_final: 0.7974 (mtpt) REVERT: G 133 SER cc_start: 0.8409 (m) cc_final: 0.8110 (m) REVERT: G 163 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7261 (pm20) REVERT: G 212 MET cc_start: 0.6670 (tpt) cc_final: 0.5999 (mmm) REVERT: G 226 ARG cc_start: 0.8342 (mmm-85) cc_final: 0.8120 (mmm-85) REVERT: G 254 GLN cc_start: 0.8843 (tp40) cc_final: 0.8586 (tp-100) REVERT: H 20 MET cc_start: 0.9025 (mmt) cc_final: 0.8657 (mpm) REVERT: H 171 ARG cc_start: 0.7757 (tmm-80) cc_final: 0.7552 (tmm-80) REVERT: H 268 MET cc_start: 0.7643 (ptm) cc_final: 0.7321 (ptp) REVERT: H 315 LYS cc_start: 0.8172 (tppt) cc_final: 0.7928 (ttmt) outliers start: 58 outliers final: 19 residues processed: 465 average time/residue: 1.2593 time to fit residues: 662.1035 Evaluate side-chains 407 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 385 time to evaluate : 2.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain C residue 122 ILE 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 29 LEU Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 407 SER Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain G residue 163 GLU Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 393 LEU Chi-restraints excluded: chain H residue 407 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 0.6980 chunk 133 optimal weight: 9.9990 chunk 3 optimal weight: 5.9990 chunk 175 optimal weight: 3.9990 chunk 97 optimal weight: 0.2980 chunk 201 optimal weight: 0.0470 chunk 163 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 120 optimal weight: 4.9990 chunk 211 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 overall best weight: 1.4082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN ** B 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 GLN D 478 HIS ** D 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 GLN ** F 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN ** H 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 20744 Z= 0.225 Angle : 0.664 13.330 28028 Z= 0.329 Chirality : 0.042 0.166 3068 Planarity : 0.005 0.049 3576 Dihedral : 4.614 29.214 2772 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.35 % Allowed : 20.70 % Favored : 75.95 % 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: 0.30 (0.17), residues: 2476 helix: 0.95 (0.13), residues: 1672 sheet: None (None), residues: 0 loop : -1.33 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 54 HIS 0.012 0.001 HIS D 478 PHE 0.019 0.001 PHE A 136 TYR 0.017 0.001 TYR H 186 ARG 0.009 0.000 ARG D 415 *********************** 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 494 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 420 time to evaluate : 2.524 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 LYS cc_start: 0.8175 (mmmm) cc_final: 0.7918 (mmtm) REVERT: A 133 SER cc_start: 0.8603 (m) cc_final: 0.8281 (m) REVERT: A 254 GLN cc_start: 0.8852 (tp40) cc_final: 0.8642 (tp-100) REVERT: A 260 MET cc_start: 0.8237 (mpp) cc_final: 0.7739 (mpp) REVERT: B 315 LYS cc_start: 0.8213 (tppt) cc_final: 0.7940 (ttmt) REVERT: B 415 ARG cc_start: 0.7893 (mtm110) cc_final: 0.7651 (ptp-110) REVERT: C 133 SER cc_start: 0.8595 (m) cc_final: 0.8263 (m) REVERT: C 212 MET cc_start: 0.6744 (tpt) cc_final: 0.6378 (mmm) REVERT: C 226 ARG cc_start: 0.8340 (mmm-85) cc_final: 0.8012 (mmm-85) REVERT: C 254 GLN cc_start: 0.8860 (tp40) cc_final: 0.8568 (tp-100) REVERT: D 20 MET cc_start: 0.8840 (mmt) cc_final: 0.8543 (mpm) REVERT: D 146 ARG cc_start: 0.8067 (ttm170) cc_final: 0.7704 (ttp-170) REVERT: D 238 THR cc_start: 0.8966 (OUTLIER) cc_final: 0.8752 (p) REVERT: D 315 LYS cc_start: 0.8249 (tppt) cc_final: 0.7957 (ttmt) REVERT: E 105 LYS cc_start: 0.8171 (mmmm) cc_final: 0.7869 (mmtm) REVERT: E 129 LYS cc_start: 0.8270 (mtmt) cc_final: 0.8033 (mtpt) REVERT: E 133 SER cc_start: 0.8579 (m) cc_final: 0.8262 (m) REVERT: E 254 GLN cc_start: 0.8864 (tp40) cc_final: 0.8555 (tp-100) REVERT: F 20 MET cc_start: 0.8944 (mmt) cc_final: 0.8672 (mpm) REVERT: F 146 ARG cc_start: 0.8108 (ttm170) cc_final: 0.7785 (ttp-170) REVERT: F 268 MET cc_start: 0.7668 (ptm) cc_final: 0.7365 (ptp) REVERT: F 315 LYS cc_start: 0.8193 (tppt) cc_final: 0.7940 (ttmt) REVERT: G 133 SER cc_start: 0.8588 (m) cc_final: 0.8263 (m) REVERT: G 212 MET cc_start: 0.6662 (tpt) cc_final: 0.6035 (mmm) REVERT: G 226 ARG cc_start: 0.8316 (mmm-85) cc_final: 0.8043 (mmm-85) REVERT: G 254 GLN cc_start: 0.8875 (tp40) cc_final: 0.8633 (tp-100) REVERT: H 20 MET cc_start: 0.8881 (mmt) cc_final: 0.8540 (mpm) REVERT: H 259 MET cc_start: 0.7824 (OUTLIER) cc_final: 0.7460 (mtt) REVERT: H 268 MET cc_start: 0.7682 (ptm) cc_final: 0.7382 (ptp) REVERT: H 315 LYS cc_start: 0.8186 (tppt) cc_final: 0.7922 (ttmt) outliers start: 74 outliers final: 39 residues processed: 464 average time/residue: 1.2839 time to fit residues: 675.6550 Evaluate side-chains 428 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 387 time to evaluate : 2.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 156 HIS Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain 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 D residue 478 HIS Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 156 HIS Chi-restraints excluded: chain E residue 160 VAL 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 G residue 122 ILE Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 259 MET 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 79 optimal weight: 3.9990 chunk 212 optimal weight: 0.7980 chunk 46 optimal weight: 6.9990 chunk 138 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 236 optimal weight: 0.9980 chunk 195 optimal weight: 0.3980 chunk 109 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 123 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN ** B 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 481 HIS C 97 GLN E 97 GLN F 481 HIS G 97 GLN H 481 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3079 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= 0.184 Angle : 0.679 15.246 28028 Z= 0.331 Chirality : 0.041 0.173 3068 Planarity : 0.005 0.049 3576 Dihedral : 4.536 29.047 2772 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.67 % Allowed : 22.60 % Favored : 73.73 % 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: 0.41 (0.17), residues: 2476 helix: 1.01 (0.13), residues: 1684 sheet: None (None), residues: 0 loop : -1.27 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 54 HIS 0.020 0.001 HIS D 478 PHE 0.020 0.001 PHE C 136 TYR 0.018 0.001 TYR H 186 ARG 0.011 0.001 ARG F 415 *********************** 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 488 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 407 time to evaluate : 2.358 Fit side-chains revert: symmetry clash REVERT: A 133 SER cc_start: 0.8634 (m) cc_final: 0.8305 (m) REVERT: A 203 ASP cc_start: 0.8621 (m-30) cc_final: 0.8330 (m-30) REVERT: A 254 GLN cc_start: 0.8822 (tp40) cc_final: 0.8542 (tp-100) REVERT: A 260 MET cc_start: 0.8195 (mpp) cc_final: 0.7799 (mmt) REVERT: A 261 ARG cc_start: 0.8364 (mmm160) cc_final: 0.8163 (tmt170) REVERT: B 238 THR cc_start: 0.8937 (OUTLIER) cc_final: 0.8732 (p) REVERT: B 315 LYS cc_start: 0.8220 (tppt) cc_final: 0.7952 (ttmt) REVERT: C 133 SER cc_start: 0.8624 (m) cc_final: 0.8306 (m) REVERT: C 195 CYS cc_start: 0.6993 (p) cc_final: 0.6704 (p) REVERT: C 212 MET cc_start: 0.6771 (tpt) cc_final: 0.6414 (mmm) REVERT: C 226 ARG cc_start: 0.8197 (mmm-85) cc_final: 0.7996 (mmm-85) REVERT: C 254 GLN cc_start: 0.8798 (tp40) cc_final: 0.8523 (tp-100) REVERT: D 20 MET cc_start: 0.8813 (mmt) cc_final: 0.8491 (mpm) REVERT: D 238 THR cc_start: 0.8952 (OUTLIER) cc_final: 0.8744 (p) REVERT: D 315 LYS cc_start: 0.8214 (tppt) cc_final: 0.7943 (ttmt) REVERT: D 415 ARG cc_start: 0.7912 (mtm110) cc_final: 0.7670 (ptp-110) REVERT: E 105 LYS cc_start: 0.8172 (mmmm) cc_final: 0.7873 (mmtm) REVERT: E 129 LYS cc_start: 0.8226 (mtmt) cc_final: 0.8024 (mtpt) REVERT: E 133 SER cc_start: 0.8596 (m) cc_final: 0.8289 (m) REVERT: E 195 CYS cc_start: 0.6868 (p) cc_final: 0.6599 (p) REVERT: E 254 GLN cc_start: 0.8841 (tp40) cc_final: 0.8534 (tp-100) REVERT: E 260 MET cc_start: 0.8234 (mpp) cc_final: 0.7688 (mmt) REVERT: F 20 MET cc_start: 0.8959 (mmt) cc_final: 0.8678 (mpm) REVERT: F 183 LEU cc_start: 0.6457 (OUTLIER) cc_final: 0.5556 (tt) REVERT: F 238 THR cc_start: 0.8921 (OUTLIER) cc_final: 0.8720 (p) REVERT: F 268 MET cc_start: 0.7520 (ptm) cc_final: 0.7238 (ptp) REVERT: F 315 LYS cc_start: 0.8266 (tppt) cc_final: 0.7995 (ttmt) REVERT: G 133 SER cc_start: 0.8643 (m) cc_final: 0.8314 (m) REVERT: G 212 MET cc_start: 0.6769 (tpt) cc_final: 0.6166 (mmm) REVERT: G 226 ARG cc_start: 0.8321 (mmm-85) cc_final: 0.8043 (mmm-85) REVERT: G 254 GLN cc_start: 0.8834 (tp40) cc_final: 0.8543 (tp-100) REVERT: G 260 MET cc_start: 0.8202 (mpp) cc_final: 0.7739 (mmt) REVERT: H 20 MET cc_start: 0.8853 (mmt) cc_final: 0.8493 (mpm) REVERT: H 268 MET cc_start: 0.7514 (ptm) cc_final: 0.7232 (ptp) REVERT: H 315 LYS cc_start: 0.8224 (tppt) cc_final: 0.7953 (ttmt) REVERT: H 415 ARG cc_start: 0.7848 (mtm110) cc_final: 0.7611 (ptp-110) outliers start: 81 outliers final: 35 residues processed: 459 average time/residue: 1.2323 time to fit residues: 640.5880 Evaluate side-chains 418 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 379 time to evaluate : 2.277 ------------------------------------------------------------------------------- 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 143 THR Chi-restraints excluded: chain A residue 251 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 274 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 160 VAL 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 E residue 122 ILE Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 393 LEU Chi-restraints excluded: chain H residue 407 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 227 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 134 optimal weight: 6.9990 chunk 172 optimal weight: 0.0970 chunk 133 optimal weight: 0.8980 chunk 198 optimal weight: 3.9990 chunk 131 optimal weight: 10.0000 chunk 235 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 GLN C 264 GLN ** D 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 481 HIS E 97 GLN G 97 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20744 Z= 0.221 Angle : 0.728 17.927 28028 Z= 0.349 Chirality : 0.043 0.231 3068 Planarity : 0.005 0.062 3576 Dihedral : 4.492 28.355 2772 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.31 % Allowed : 23.64 % Favored : 73.05 % 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: 0.54 (0.17), residues: 2476 helix: 1.08 (0.13), residues: 1684 sheet: None (None), residues: 0 loop : -1.17 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 54 HIS 0.004 0.001 HIS B 477 PHE 0.022 0.001 PHE A 136 TYR 0.018 0.001 TYR B 186 ARG 0.013 0.001 ARG G 261 *********************** 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 468 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 395 time to evaluate : 2.454 Fit side-chains REVERT: A 133 SER cc_start: 0.8618 (m) cc_final: 0.8314 (m) REVERT: A 195 CYS cc_start: 0.6934 (p) cc_final: 0.6636 (p) REVERT: A 203 ASP cc_start: 0.8584 (m-30) cc_final: 0.8342 (m-30) REVERT: A 254 GLN cc_start: 0.8806 (tp40) cc_final: 0.8563 (tp-100) REVERT: A 260 MET cc_start: 0.8248 (mpp) cc_final: 0.7652 (mmt) REVERT: B 238 THR cc_start: 0.8916 (OUTLIER) cc_final: 0.8699 (p) REVERT: C 133 SER cc_start: 0.8594 (m) cc_final: 0.8324 (m) REVERT: C 195 CYS cc_start: 0.6978 (p) cc_final: 0.6671 (p) REVERT: C 203 ASP cc_start: 0.8525 (m-30) cc_final: 0.8316 (m-30) REVERT: C 212 MET cc_start: 0.6891 (tpt) cc_final: 0.6345 (mmm) REVERT: C 217 TYR cc_start: 0.4531 (OUTLIER) cc_final: 0.2259 (m-80) REVERT: C 254 GLN cc_start: 0.8784 (tp40) cc_final: 0.8519 (tp-100) REVERT: C 260 MET cc_start: 0.8338 (mpp) cc_final: 0.7864 (mmt) REVERT: D 238 THR cc_start: 0.8960 (OUTLIER) cc_final: 0.8740 (p) REVERT: D 315 LYS cc_start: 0.8244 (tppt) cc_final: 0.7963 (ttmt) REVERT: E 133 SER cc_start: 0.8616 (m) cc_final: 0.8316 (m) REVERT: E 195 CYS cc_start: 0.6616 (p) cc_final: 0.6381 (p) REVERT: E 254 GLN cc_start: 0.8823 (tp40) cc_final: 0.8544 (tp-100) REVERT: F 20 MET cc_start: 0.8950 (mmt) cc_final: 0.8587 (mpm) REVERT: F 183 LEU cc_start: 0.6467 (OUTLIER) cc_final: 0.5568 (tt) REVERT: F 238 THR cc_start: 0.8948 (OUTLIER) cc_final: 0.8738 (p) REVERT: F 268 MET cc_start: 0.7511 (ptm) cc_final: 0.7224 (ptp) REVERT: F 315 LYS cc_start: 0.8276 (tppt) cc_final: 0.7998 (ttmt) REVERT: G 133 SER cc_start: 0.8657 (m) cc_final: 0.8377 (m) REVERT: G 203 ASP cc_start: 0.8441 (m-30) cc_final: 0.8224 (m-30) REVERT: G 212 MET cc_start: 0.6846 (tpt) cc_final: 0.6244 (mmm) REVERT: G 254 GLN cc_start: 0.8791 (tp40) cc_final: 0.8541 (tp-100) REVERT: G 260 MET cc_start: 0.8199 (mpp) cc_final: 0.7661 (mmt) REVERT: H 20 MET cc_start: 0.8803 (mmt) cc_final: 0.8436 (mpm) REVERT: H 259 MET cc_start: 0.7892 (OUTLIER) cc_final: 0.7486 (mtt) REVERT: H 268 MET cc_start: 0.7421 (ptm) cc_final: 0.7138 (ptp) REVERT: H 315 LYS cc_start: 0.8275 (tppt) cc_final: 0.7982 (ttmt) outliers start: 73 outliers final: 38 residues processed: 438 average time/residue: 1.1714 time to fit residues: 584.2272 Evaluate side-chains 419 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 375 time to evaluate : 2.120 ------------------------------------------------------------------------------- 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 138 ASP Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 160 VAL 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 E residue 122 ILE Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 160 VAL 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 274 LEU Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 138 ASP Chi-restraints excluded: chain H residue 259 MET Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 393 LEU Chi-restraints excluded: chain H residue 407 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 145 optimal weight: 0.9990 chunk 93 optimal weight: 8.9990 chunk 140 optimal weight: 0.0070 chunk 70 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 chunk 160 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 184 optimal weight: 3.9990 overall best weight: 0.7800 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3317 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= 0.202 Angle : 0.732 16.867 28028 Z= 0.352 Chirality : 0.043 0.243 3068 Planarity : 0.005 0.055 3576 Dihedral : 4.496 28.205 2772 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.03 % Allowed : 24.37 % Favored : 72.60 % 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: 0.65 (0.17), residues: 2476 helix: 1.16 (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 0.004 0.001 HIS H 477 PHE 0.016 0.001 PHE C 249 TYR 0.017 0.001 TYR F 186 ARG 0.011 0.000 ARG D 415 *********************** 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 445 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 378 time to evaluate : 2.391 Fit side-chains REVERT: A 133 SER cc_start: 0.8557 (m) cc_final: 0.8241 (m) REVERT: A 156 HIS cc_start: 0.7461 (m-70) cc_final: 0.7247 (m90) REVERT: A 195 CYS cc_start: 0.6760 (p) cc_final: 0.6436 (p) REVERT: A 254 GLN cc_start: 0.8803 (tp40) cc_final: 0.8532 (tp-100) REVERT: A 260 MET cc_start: 0.8197 (mpp) cc_final: 0.7828 (mmt) REVERT: C 133 SER cc_start: 0.8580 (m) cc_final: 0.8301 (m) REVERT: C 195 CYS cc_start: 0.6936 (p) cc_final: 0.6631 (p) REVERT: C 212 MET cc_start: 0.6826 (tpt) cc_final: 0.6415 (mmm) REVERT: C 254 GLN cc_start: 0.8771 (tp40) cc_final: 0.8529 (tp-100) REVERT: C 260 MET cc_start: 0.8281 (mpp) cc_final: 0.7878 (mmt) REVERT: C 263 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.7677 (tpp) REVERT: D 238 THR cc_start: 0.8956 (OUTLIER) cc_final: 0.8745 (p) REVERT: D 315 LYS cc_start: 0.8243 (tppt) cc_final: 0.7977 (ttmt) REVERT: E 133 SER cc_start: 0.8585 (m) cc_final: 0.8320 (m) REVERT: E 195 CYS cc_start: 0.6571 (p) cc_final: 0.6325 (p) REVERT: E 254 GLN cc_start: 0.8796 (tp40) cc_final: 0.8518 (tp-100) REVERT: E 260 MET cc_start: 0.8334 (mpp) cc_final: 0.7825 (mmt) REVERT: F 20 MET cc_start: 0.8974 (mmt) cc_final: 0.8558 (mpm) REVERT: F 183 LEU cc_start: 0.6477 (OUTLIER) cc_final: 0.5526 (tt) REVERT: F 238 THR cc_start: 0.8945 (OUTLIER) cc_final: 0.8742 (p) REVERT: F 268 MET cc_start: 0.7379 (ptm) cc_final: 0.7098 (ptp) REVERT: F 315 LYS cc_start: 0.8261 (tppt) cc_final: 0.7961 (ttmt) REVERT: G 133 SER cc_start: 0.8666 (m) cc_final: 0.8400 (m) REVERT: G 195 CYS cc_start: 0.7011 (p) cc_final: 0.6739 (p) REVERT: G 212 MET cc_start: 0.6843 (tpt) cc_final: 0.6278 (mmm) REVERT: G 260 MET cc_start: 0.8292 (mpp) cc_final: 0.7633 (mmt) REVERT: H 20 MET cc_start: 0.8812 (mmt) cc_final: 0.8498 (mpm) REVERT: H 238 THR cc_start: 0.8949 (OUTLIER) cc_final: 0.8726 (p) REVERT: H 259 MET cc_start: 0.7881 (OUTLIER) cc_final: 0.7384 (mtt) REVERT: H 268 MET cc_start: 0.7391 (ptm) cc_final: 0.7103 (ptp) outliers start: 67 outliers final: 35 residues processed: 419 average time/residue: 1.1801 time to fit residues: 565.8095 Evaluate side-chains 410 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 369 time to evaluate : 2.133 ------------------------------------------------------------------------------- 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 143 THR 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 258 VAL Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 263 MET 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 274 LEU Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 407 SER Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain 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 274 LEU Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 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 259 MET Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 393 LEU Chi-restraints excluded: chain H residue 407 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 213 optimal weight: 6.9990 chunk 225 optimal weight: 4.9990 chunk 205 optimal weight: 0.8980 chunk 219 optimal weight: 10.0000 chunk 131 optimal weight: 7.9990 chunk 95 optimal weight: 1.9990 chunk 172 optimal weight: 0.8980 chunk 67 optimal weight: 6.9990 chunk 198 optimal weight: 0.0170 chunk 207 optimal weight: 2.9990 chunk 218 optimal weight: 2.9990 overall best weight: 1.3622 ------------------------------------------------------------------------------- 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 C 264 GLN E 97 GLN G 97 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 20744 Z= 0.236 Angle : 0.764 16.972 28028 Z= 0.368 Chirality : 0.043 0.242 3068 Planarity : 0.005 0.058 3576 Dihedral : 4.469 27.836 2772 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.08 % Allowed : 24.91 % Favored : 72.01 % 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: 0.66 (0.17), residues: 2476 helix: 1.13 (0.13), residues: 1680 sheet: None (None), residues: 0 loop : -1.00 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 54 HIS 0.007 0.001 HIS D 477 PHE 0.017 0.001 PHE E 136 TYR 0.018 0.001 TYR B 186 ARG 0.013 0.001 ARG G 261 *********************** 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 439 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 371 time to evaluate : 2.257 Fit side-chains revert: symmetry clash REVERT: A 133 SER cc_start: 0.8565 (m) cc_final: 0.8300 (m) REVERT: A 195 CYS cc_start: 0.6767 (p) cc_final: 0.6447 (p) REVERT: A 254 GLN cc_start: 0.8803 (tp40) cc_final: 0.8535 (tp-100) REVERT: A 260 MET cc_start: 0.8213 (mpp) cc_final: 0.7680 (mmt) REVERT: B 183 LEU cc_start: 0.6391 (OUTLIER) cc_final: 0.5552 (tt) REVERT: B 280 GLU cc_start: 0.4082 (OUTLIER) cc_final: 0.3712 (pm20) REVERT: C 133 SER cc_start: 0.8598 (m) cc_final: 0.8341 (m) REVERT: C 195 CYS cc_start: 0.6535 (p) cc_final: 0.6252 (p) REVERT: C 212 MET cc_start: 0.6843 (tpt) cc_final: 0.6360 (mmm) REVERT: C 217 TYR cc_start: 0.4549 (OUTLIER) cc_final: 0.2394 (m-80) REVERT: C 254 GLN cc_start: 0.8756 (tp40) cc_final: 0.8525 (tp-100) REVERT: C 260 MET cc_start: 0.8291 (mpp) cc_final: 0.7702 (mmt) REVERT: D 238 THR cc_start: 0.8963 (OUTLIER) cc_final: 0.8740 (p) REVERT: D 315 LYS cc_start: 0.8237 (tppt) cc_final: 0.7954 (ttmt) REVERT: E 133 SER cc_start: 0.8583 (m) cc_final: 0.8329 (m) REVERT: E 195 CYS cc_start: 0.6738 (p) cc_final: 0.6452 (p) REVERT: E 217 TYR cc_start: 0.4517 (OUTLIER) cc_final: 0.2202 (m-80) REVERT: E 254 GLN cc_start: 0.8769 (tp40) cc_final: 0.8550 (tp-100) REVERT: E 260 MET cc_start: 0.8381 (mpp) cc_final: 0.7835 (mmt) REVERT: F 20 MET cc_start: 0.8912 (mmt) cc_final: 0.8508 (mpm) REVERT: F 183 LEU cc_start: 0.6481 (OUTLIER) cc_final: 0.5576 (tt) REVERT: F 238 THR cc_start: 0.8956 (OUTLIER) cc_final: 0.8739 (p) REVERT: F 268 MET cc_start: 0.7415 (ptm) cc_final: 0.7125 (ptp) REVERT: F 315 LYS cc_start: 0.8289 (tppt) cc_final: 0.7972 (ttmt) REVERT: G 133 SER cc_start: 0.8658 (m) cc_final: 0.8393 (m) REVERT: G 195 CYS cc_start: 0.7063 (p) cc_final: 0.6770 (p) REVERT: G 212 MET cc_start: 0.6826 (tpt) cc_final: 0.6353 (mmm) REVERT: G 260 MET cc_start: 0.8309 (mpp) cc_final: 0.7639 (mmt) REVERT: G 261 ARG cc_start: 0.8180 (mmm160) cc_final: 0.7748 (tmt170) REVERT: H 20 MET cc_start: 0.8803 (mmt) cc_final: 0.8427 (mpm) REVERT: H 183 LEU cc_start: 0.6344 (OUTLIER) cc_final: 0.5548 (tt) REVERT: H 259 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.7384 (mtt) REVERT: H 268 MET cc_start: 0.7396 (ptm) cc_final: 0.7104 (ptp) REVERT: H 315 LYS cc_start: 0.8266 (tppt) cc_final: 0.7974 (ttmt) outliers start: 68 outliers final: 38 residues processed: 412 average time/residue: 1.1409 time to fit residues: 537.5851 Evaluate side-chains 409 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 362 time to evaluate : 2.229 ------------------------------------------------------------------------------- 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 A residue 209 TYR 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 183 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 143 THR 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 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 209 TYR 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 274 LEU Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 138 ASP Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain H residue 259 MET Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 393 LEU Chi-restraints excluded: chain H residue 407 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 143 optimal weight: 0.0870 chunk 231 optimal weight: 0.8980 chunk 141 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 161 optimal weight: 4.9990 chunk 243 optimal weight: 3.9990 chunk 223 optimal weight: 8.9990 chunk 193 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 149 optimal weight: 0.6980 chunk 118 optimal weight: 9.9990 overall best weight: 1.1362 ------------------------------------------------------------------------------- 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 ** B 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 GLN E 97 GLN G 97 GLN G 254 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20744 Z= 0.227 Angle : 0.779 16.656 28028 Z= 0.372 Chirality : 0.043 0.220 3068 Planarity : 0.005 0.056 3576 Dihedral : 4.487 28.025 2772 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.49 % Allowed : 25.36 % Favored : 72.15 % 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: 0.70 (0.17), residues: 2476 helix: 1.14 (0.13), residues: 1680 sheet: None (None), residues: 0 loop : -0.94 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 19 HIS 0.005 0.001 HIS H 477 PHE 0.019 0.001 PHE E 136 TYR 0.017 0.001 TYR B 186 ARG 0.013 0.001 ARG G 261 ********************** 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 427 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 372 time to evaluate : 2.253 Fit side-chains revert: symmetry clash REVERT: A 133 SER cc_start: 0.8550 (m) cc_final: 0.8280 (m) REVERT: A 195 CYS cc_start: 0.6855 (p) cc_final: 0.6543 (p) REVERT: A 254 GLN cc_start: 0.8786 (tp40) cc_final: 0.8527 (tp-100) REVERT: A 260 MET cc_start: 0.8228 (mpp) cc_final: 0.7817 (mmt) REVERT: B 315 LYS cc_start: 0.8216 (tppt) cc_final: 0.7941 (ttmt) REVERT: B 431 ARG cc_start: 0.7881 (tpp80) cc_final: 0.7541 (tmm-80) REVERT: C 133 SER cc_start: 0.8584 (m) cc_final: 0.8350 (m) REVERT: C 195 CYS cc_start: 0.6689 (p) cc_final: 0.6385 (p) REVERT: C 212 MET cc_start: 0.6830 (tpt) cc_final: 0.6359 (mmm) REVERT: C 217 TYR cc_start: 0.4488 (OUTLIER) cc_final: 0.2316 (m-80) REVERT: C 254 GLN cc_start: 0.8716 (tp40) cc_final: 0.8492 (tp-100) REVERT: C 260 MET cc_start: 0.8251 (mpp) cc_final: 0.7888 (mmt) REVERT: C 261 ARG cc_start: 0.8185 (mmm160) cc_final: 0.7936 (tmt170) REVERT: D 238 THR cc_start: 0.8962 (OUTLIER) cc_final: 0.8743 (p) REVERT: D 315 LYS cc_start: 0.8258 (tppt) cc_final: 0.7991 (ttmt) REVERT: D 431 ARG cc_start: 0.7928 (tpp80) cc_final: 0.7505 (tmm-80) REVERT: E 133 SER cc_start: 0.8576 (m) cc_final: 0.8327 (m) REVERT: E 195 CYS cc_start: 0.6780 (p) cc_final: 0.6490 (p) REVERT: E 212 MET cc_start: 0.6828 (mmm) cc_final: 0.6457 (mmm) REVERT: E 254 GLN cc_start: 0.8759 (tp40) cc_final: 0.8514 (tp-100) REVERT: E 260 MET cc_start: 0.8298 (mpp) cc_final: 0.7753 (mmt) REVERT: F 20 MET cc_start: 0.8883 (mmt) cc_final: 0.8479 (mpm) REVERT: F 238 THR cc_start: 0.8952 (OUTLIER) cc_final: 0.8740 (p) REVERT: F 268 MET cc_start: 0.7399 (ptm) cc_final: 0.7106 (ptp) REVERT: F 315 LYS cc_start: 0.8277 (tppt) cc_final: 0.7969 (ttmt) REVERT: G 133 SER cc_start: 0.8593 (m) cc_final: 0.8321 (m) REVERT: G 195 CYS cc_start: 0.7023 (p) cc_final: 0.6719 (p) REVERT: G 212 MET cc_start: 0.6659 (tpt) cc_final: 0.6193 (mmm) REVERT: G 260 MET cc_start: 0.8242 (mpp) cc_final: 0.7536 (mmt) REVERT: G 261 ARG cc_start: 0.8117 (mmm160) cc_final: 0.7697 (tmt170) REVERT: H 20 MET cc_start: 0.8800 (mmt) cc_final: 0.8455 (mpm) REVERT: H 238 THR cc_start: 0.8947 (OUTLIER) cc_final: 0.8709 (p) REVERT: H 259 MET cc_start: 0.7875 (OUTLIER) cc_final: 0.7374 (mtt) REVERT: H 268 MET cc_start: 0.7386 (ptm) cc_final: 0.7095 (ptp) REVERT: H 315 LYS cc_start: 0.8265 (tppt) cc_final: 0.7975 (ttmt) outliers start: 55 outliers final: 37 residues processed: 403 average time/residue: 1.1465 time to fit residues: 529.8542 Evaluate side-chains 405 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 363 time to evaluate : 2.121 ------------------------------------------------------------------------------- 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 138 ASP 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 C residue 97 GLN Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 143 THR 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 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 209 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 238 THR Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain G residue 97 GLN Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 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 259 MET Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 393 LEU Chi-restraints excluded: chain H residue 407 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 153 optimal weight: 7.9990 chunk 206 optimal weight: 0.4980 chunk 59 optimal weight: 5.9990 chunk 178 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 193 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 199 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN B 167 GLN B 443 HIS C 97 GLN E 97 GLN G 97 GLN G 254 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.155412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.104475 restraints weight = 31345.756| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.70 r_work: 0.3224 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3424 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= 0.223 Angle : 0.762 13.457 28028 Z= 0.368 Chirality : 0.043 0.218 3068 Planarity : 0.005 0.051 3576 Dihedral : 4.460 27.164 2772 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.54 % Allowed : 25.18 % Favored : 72.28 % 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: 0.72 (0.17), residues: 2476 helix: 1.15 (0.13), residues: 1680 sheet: None (None), residues: 0 loop : -0.89 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 19 HIS 0.004 0.001 HIS F 477 PHE 0.019 0.001 PHE C 249 TYR 0.017 0.001 TYR B 186 ARG 0.012 0.001 ARG G 261 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9727.27 seconds wall clock time: 169 minutes 32.84 seconds (10172.84 seconds total)