Starting phenix.real_space_refine on Thu Feb 5 00:34:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pkw_71705/02_2026/9pkw_71705.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pkw_71705/02_2026/9pkw_71705.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9pkw_71705/02_2026/9pkw_71705.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pkw_71705/02_2026/9pkw_71705.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pkw_71705/02_2026/9pkw_71705.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pkw_71705/02_2026/9pkw_71705.map" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 89 5.16 5 C 9025 2.51 5 N 2216 2.21 5 O 2461 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13791 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2713 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 15, 'TRANS': 319} Chain breaks: 1 Chain: "D" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2738 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 15, 'TRANS': 322} Chain breaks: 1 Chain: "C" Number of atoms: 2713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2713 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 15, 'TRANS': 319} Chain breaks: 1 Chain: "B" Number of atoms: 2741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2741 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 15, 'TRANS': 322} Chain breaks: 1 Chain: "E" Number of atoms: 2691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2691 Classifications: {'peptide': 331} Link IDs: {'PTRANS': 16, 'TRANS': 314} Chain breaks: 1 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Unusual residues: {'NAG': 1, 'SY9': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'NAG': 1, 'SY9': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'NAG': 1, 'SY9': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'NAG': 1, 'SY9': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.44, per 1000 atoms: 0.25 Number of scatterers: 13791 At special positions: 0 Unit cell: (93.24, 94.08, 133.56, 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 89 16.00 O 2461 8.00 N 2216 7.00 C 9025 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS E 182 " - pdb=" SG CYS E 196 " distance=2.04 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 Links applied NAG-ASN " NAG A 502 " - " ASN A 62 " " NAG B 502 " - " ASN B 62 " " NAG C 502 " - " ASN C 62 " " NAG D 501 " - " ASN D 62 " " NAG E 602 " - " ASN E 241 " Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 619.5 milliseconds 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3218 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 24 sheets defined 40.0% alpha, 42.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 33 through 43 removed outlier: 3.656A pdb=" N ASP A 39 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LYS A 40 " --> pdb=" O GLU A 36 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU A 41 " --> pdb=" O PHE A 37 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N MET A 42 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 98 removed outlier: 3.514A pdb=" N ALA A 98 " --> pdb=" O PRO A 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 95 through 98' Processing helix chain 'A' and resid 113 through 117 Processing helix chain 'A' and resid 244 through 252 removed outlier: 3.510A pdb=" N ILE A 249 " --> pdb=" O GLY A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 263 removed outlier: 3.790A pdb=" N VAL A 259 " --> pdb=" O SER A 255 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE A 260 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TRP A 263 " --> pdb=" O VAL A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 268 Processing helix chain 'A' and resid 272 through 295 removed outlier: 3.504A pdb=" N THR A 282 " --> pdb=" O GLY A 278 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 298 No H-bonds generated for 'chain 'A' and resid 296 through 298' Processing helix chain 'A' and resid 305 through 334 removed outlier: 3.941A pdb=" N TYR A 325 " --> pdb=" O ALA A 321 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA A 326 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA A 327 " --> pdb=" O LEU A 323 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN A 334 " --> pdb=" O PHE A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 433 removed outlier: 3.778A pdb=" N ASP A 411 " --> pdb=" O ALA A 407 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N VAL A 416 " --> pdb=" O THR A 412 " (cutoff:3.500A) Proline residue: A 419 - end of helix removed outlier: 3.575A pdb=" N TYR A 433 " --> pdb=" O TYR A 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 42 removed outlier: 4.037A pdb=" N LEU D 41 " --> pdb=" O PHE D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 98 removed outlier: 3.702A pdb=" N ALA D 98 " --> pdb=" O PRO D 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 95 through 98' Processing helix chain 'D' and resid 113 through 117 Processing helix chain 'D' and resid 244 through 251 removed outlier: 3.557A pdb=" N ILE D 249 " --> pdb=" O GLY D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 263 removed outlier: 3.596A pdb=" N VAL D 259 " --> pdb=" O SER D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 268 Processing helix chain 'D' and resid 272 through 294 Processing helix chain 'D' and resid 295 through 298 removed outlier: 3.802A pdb=" N LEU D 298 " --> pdb=" O ARG D 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 295 through 298' Processing helix chain 'D' and resid 305 through 334 removed outlier: 3.515A pdb=" N ILE D 309 " --> pdb=" O LYS D 305 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU D 322 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N TYR D 325 " --> pdb=" O ALA D 321 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA D 326 " --> pdb=" O LEU D 322 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA D 327 " --> pdb=" O LEU D 323 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG D 333 " --> pdb=" O ASN D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 436 removed outlier: 4.066A pdb=" N VAL D 416 " --> pdb=" O THR D 412 " (cutoff:3.500A) Proline residue: D 419 - end of helix removed outlier: 3.630A pdb=" N TYR D 433 " --> pdb=" O TYR D 429 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N LYS D 434 " --> pdb=" O TRP D 430 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE D 436 " --> pdb=" O THR D 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 43 removed outlier: 3.903A pdb=" N LEU C 38 " --> pdb=" O PRO C 34 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ASP C 39 " --> pdb=" O SER C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 98 removed outlier: 3.595A pdb=" N ALA C 98 " --> pdb=" O PRO C 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 95 through 98' Processing helix chain 'C' and resid 110 through 117 removed outlier: 3.684A pdb=" N LEU C 114 " --> pdb=" O PRO C 111 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ASP C 115 " --> pdb=" O SER C 112 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE C 117 " --> pdb=" O LEU C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 171 Processing helix chain 'C' and resid 244 through 251 removed outlier: 3.509A pdb=" N LEU C 248 " --> pdb=" O MET C 244 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE C 249 " --> pdb=" O GLY C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 263 removed outlier: 3.596A pdb=" N VAL C 259 " --> pdb=" O SER C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 268 Processing helix chain 'C' and resid 272 through 294 Processing helix chain 'C' and resid 295 through 297 No H-bonds generated for 'chain 'C' and resid 295 through 297' Processing helix chain 'C' and resid 305 through 334 removed outlier: 3.653A pdb=" N ILE C 309 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL C 318 " --> pdb=" O CYS C 314 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU C 322 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR C 325 " --> pdb=" O ALA C 321 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA C 327 " --> pdb=" O LEU C 323 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLN C 334 " --> pdb=" O PHE C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 415 removed outlier: 3.576A pdb=" N ASP C 411 " --> pdb=" O ALA C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 435 removed outlier: 3.682A pdb=" N PHE C 422 " --> pdb=" O PHE C 418 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE C 431 " --> pdb=" O ILE C 427 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR C 432 " --> pdb=" O PHE C 428 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR C 433 " --> pdb=" O TYR C 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 43 removed outlier: 3.790A pdb=" N LEU B 38 " --> pdb=" O PRO B 34 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASP B 39 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS B 40 " --> pdb=" O GLU B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 98 removed outlier: 3.760A pdb=" N ALA B 98 " --> pdb=" O PRO B 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 95 through 98' Processing helix chain 'B' and resid 113 through 117 Processing helix chain 'B' and resid 244 through 251 removed outlier: 3.665A pdb=" N ILE B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 263 removed outlier: 3.527A pdb=" N TRP B 263 " --> pdb=" O VAL B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 267 Processing helix chain 'B' and resid 272 through 294 Processing helix chain 'B' and resid 305 through 334 removed outlier: 3.501A pdb=" N VAL B 318 " --> pdb=" O CYS B 314 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU B 322 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU B 323 " --> pdb=" O PHE B 319 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N TYR B 325 " --> pdb=" O ALA B 321 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN B 334 " --> pdb=" O PHE B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 435 removed outlier: 3.697A pdb=" N SER B 405 " --> pdb=" O LYS B 401 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE B 410 " --> pdb=" O ARG B 406 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP B 411 " --> pdb=" O ALA B 407 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL B 416 " --> pdb=" O THR B 412 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE B 418 " --> pdb=" O SER B 414 " (cutoff:3.500A) Proline residue: B 419 - end of helix removed outlier: 3.854A pdb=" N THR B 432 " --> pdb=" O PHE B 428 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR B 433 " --> pdb=" O TYR B 429 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 64 removed outlier: 3.725A pdb=" N ASN E 61 " --> pdb=" O SER E 57 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS E 62 " --> pdb=" O ASN E 58 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU E 63 " --> pdb=" O ILE E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 137 removed outlier: 4.029A pdb=" N PHE E 134 " --> pdb=" O PRO E 131 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LYS E 135 " --> pdb=" O LYS E 132 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N CYS E 136 " --> pdb=" O MET E 133 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU E 137 " --> pdb=" O PHE E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 191 Processing helix chain 'E' and resid 265 through 272 removed outlier: 3.569A pdb=" N MET E 270 " --> pdb=" O GLY E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 284 removed outlier: 3.529A pdb=" N ILE E 279 " --> pdb=" O PRO E 275 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL E 280 " --> pdb=" O THR E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 289 Processing helix chain 'E' and resid 293 through 319 removed outlier: 3.754A pdb=" N VAL E 298 " --> pdb=" O SER E 294 " (cutoff:3.500A) Proline residue: E 299 - end of helix removed outlier: 3.674A pdb=" N ALA E 316 " --> pdb=" O CYS E 312 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N SER E 317 " --> pdb=" O THR E 313 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLU E 318 " --> pdb=" O SER E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 355 removed outlier: 3.634A pdb=" N ILE E 330 " --> pdb=" O LYS E 326 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU E 343 " --> pdb=" O GLY E 339 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TYR E 346 " --> pdb=" O SER E 342 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN E 350 " --> pdb=" O TYR E 346 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL E 351 " --> pdb=" O ALA E 347 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N MET E 352 " --> pdb=" O VAL E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 468 through 476 removed outlier: 3.959A pdb=" N LEU E 472 " --> pdb=" O LYS E 468 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA E 476 " --> pdb=" O LEU E 472 " (cutoff:3.500A) Processing helix chain 'E' and resid 477 through 494 removed outlier: 3.580A pdb=" N LEU E 494 " --> pdb=" O TRP E 490 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 106 through 108 removed outlier: 4.629A pdb=" N ASN A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ASP A 81 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N SER A 74 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ARG A 83 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N PHE A 72 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ASN A 85 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ASN A 93 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ASN A 62 " --> pdb=" O ASN A 93 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N VAL A 61 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N GLU A 193 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL A 63 " --> pdb=" O GLU A 193 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 127 through 132 removed outlier: 6.561A pdb=" N VAL A 159 " --> pdb=" O LYS A 128 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ALA A 130 " --> pdb=" O THR A 157 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N THR A 157 " --> pdb=" O ALA A 130 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N PHE A 132 " --> pdb=" O ARG A 155 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N ARG A 155 " --> pdb=" O PHE A 132 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ASP A 81 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N SER A 74 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ARG A 83 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N PHE A 72 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ASN A 85 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ASN A 93 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ASN A 62 " --> pdb=" O ASN A 93 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N GLN A 201 " --> pdb=" O CYS A 65 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ILE A 67 " --> pdb=" O GLN A 201 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 122 through 124 Processing sheet with id=AA4, first strand: chain 'A' and resid 122 through 124 Processing sheet with id=AA5, first strand: chain 'A' and resid 224 through 225 Processing sheet with id=AA6, first strand: chain 'D' and resid 106 through 108 removed outlier: 3.541A pdb=" N ILE D 144 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ASN D 149 " --> pdb=" O SER D 145 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ASP D 81 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N SER D 74 " --> pdb=" O ASP D 81 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ARG D 83 " --> pdb=" O PHE D 72 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N PHE D 72 " --> pdb=" O ARG D 83 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ASN D 85 " --> pdb=" O ASN D 70 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ASN D 93 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ASN D 62 " --> pdb=" O ASN D 93 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N VAL D 61 " --> pdb=" O ILE D 191 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N GLU D 193 " --> pdb=" O VAL D 61 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N VAL D 63 " --> pdb=" O GLU D 193 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 127 through 132 removed outlier: 6.580A pdb=" N VAL D 159 " --> pdb=" O LYS D 128 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ALA D 130 " --> pdb=" O THR D 157 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N THR D 157 " --> pdb=" O ALA D 130 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N PHE D 132 " --> pdb=" O ARG D 155 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N ARG D 155 " --> pdb=" O PHE D 132 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ASP D 81 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N SER D 74 " --> pdb=" O ASP D 81 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ARG D 83 " --> pdb=" O PHE D 72 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N PHE D 72 " --> pdb=" O ARG D 83 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ASN D 85 " --> pdb=" O ASN D 70 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ASN D 93 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ASN D 62 " --> pdb=" O ASN D 93 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 122 through 124 Processing sheet with id=AA9, first strand: chain 'D' and resid 122 through 124 removed outlier: 3.503A pdb=" N GLU D 235 " --> pdb=" O ARG D 220 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 224 through 225 Processing sheet with id=AB2, first strand: chain 'C' and resid 106 through 108 removed outlier: 4.594A pdb=" N ASN C 149 " --> pdb=" O SER C 145 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N ASP C 81 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N SER C 74 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ARG C 83 " --> pdb=" O PHE C 72 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N PHE C 72 " --> pdb=" O ARG C 83 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ASN C 85 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ASN C 93 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ASN C 62 " --> pdb=" O ASN C 93 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N VAL C 61 " --> pdb=" O ILE C 191 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N GLU C 193 " --> pdb=" O VAL C 61 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N VAL C 63 " --> pdb=" O GLU C 193 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 127 through 132 removed outlier: 6.427A pdb=" N VAL C 159 " --> pdb=" O LYS C 128 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ALA C 130 " --> pdb=" O THR C 157 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N THR C 157 " --> pdb=" O ALA C 130 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N PHE C 132 " --> pdb=" O ARG C 155 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N ARG C 155 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N ASP C 81 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N SER C 74 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ARG C 83 " --> pdb=" O PHE C 72 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N PHE C 72 " --> pdb=" O ARG C 83 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ASN C 85 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ASN C 93 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ASN C 62 " --> pdb=" O ASN C 93 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 122 through 124 removed outlier: 5.901A pdb=" N THR C 232 " --> pdb=" O SER C 182 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N GLY C 184 " --> pdb=" O LYS C 230 " (cutoff:3.500A) removed outlier: 9.412A pdb=" N LYS C 230 " --> pdb=" O GLY C 184 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 211 through 213 Processing sheet with id=AB6, first strand: chain 'B' and resid 106 through 109 removed outlier: 4.060A pdb=" N LEU B 142 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ASN B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ASP B 81 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N SER B 74 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ARG B 83 " --> pdb=" O PHE B 72 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N PHE B 72 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ASN B 85 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ASN B 93 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ASN B 62 " --> pdb=" O ASN B 93 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N VAL B 61 " --> pdb=" O ILE B 191 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N GLU B 193 " --> pdb=" O VAL B 61 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N VAL B 63 " --> pdb=" O GLU B 193 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 127 through 132 removed outlier: 6.620A pdb=" N VAL B 159 " --> pdb=" O LYS B 128 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ALA B 130 " --> pdb=" O THR B 157 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N THR B 157 " --> pdb=" O ALA B 130 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N PHE B 132 " --> pdb=" O ARG B 155 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N ARG B 155 " --> pdb=" O PHE B 132 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ASP B 81 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N SER B 74 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ARG B 83 " --> pdb=" O PHE B 72 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N PHE B 72 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ASN B 85 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ASN B 93 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ASN B 62 " --> pdb=" O ASN B 93 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 122 through 124 Processing sheet with id=AB9, first strand: chain 'B' and resid 122 through 124 Processing sheet with id=AC1, first strand: chain 'B' and resid 224 through 225 Processing sheet with id=AC2, first strand: chain 'E' and resid 126 through 128 removed outlier: 4.656A pdb=" N ASP E 169 " --> pdb=" O PHE E 165 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ASP E 100 " --> pdb=" O SER E 93 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N SER E 93 " --> pdb=" O ASP E 100 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ARG E 102 " --> pdb=" O PHE E 91 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N PHE E 91 " --> pdb=" O ARG E 102 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ASN E 104 " --> pdb=" O ASN E 89 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N ASN E 112 " --> pdb=" O GLU E 81 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLU E 81 " --> pdb=" O ASN E 112 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 147 through 149 removed outlier: 6.585A pdb=" N THR E 179 " --> pdb=" O LYS E 148 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ASP E 100 " --> pdb=" O SER E 93 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N SER E 93 " --> pdb=" O ASP E 100 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ARG E 102 " --> pdb=" O PHE E 91 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N PHE E 91 " --> pdb=" O ARG E 102 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ASN E 104 " --> pdb=" O ASN E 89 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N ASN E 112 " --> pdb=" O GLU E 81 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLU E 81 " --> pdb=" O ASN E 112 " (cutoff:3.500A) removed outlier: 8.696A pdb=" N GLN E 221 " --> pdb=" O VAL E 84 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE E 86 " --> pdb=" O GLN E 221 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 142 through 144 Processing sheet with id=AC5, first strand: chain 'E' and resid 142 through 144 removed outlier: 3.630A pdb=" N ILE E 237 " --> pdb=" O ILE E 258 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 244 through 245 746 hydrogen bonds defined for protein. 2151 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: 2.48 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2164 1.31 - 1.44: 3970 1.44 - 1.57: 7885 1.57 - 1.69: 0 1.69 - 1.82: 147 Bond restraints: 14166 Sorted by residual: bond pdb=" CA SER A 112 " pdb=" CB SER A 112 " ideal model delta sigma weight residual 1.537 1.480 0.057 1.41e-02 5.03e+03 1.64e+01 bond pdb=" N PHE A 169 " pdb=" CA PHE A 169 " ideal model delta sigma weight residual 1.462 1.493 -0.031 7.70e-03 1.69e+04 1.61e+01 bond pdb=" C PRO E 219 " pdb=" O PRO E 219 " ideal model delta sigma weight residual 1.237 1.187 0.050 1.26e-02 6.30e+03 1.59e+01 bond pdb=" N ILE D 117 " pdb=" CA ILE D 117 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.14e-02 7.69e+03 1.09e+01 bond pdb=" N ASP B 172 " pdb=" CA ASP B 172 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.15e-02 7.56e+03 9.27e+00 ... (remaining 14161 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 18542 2.09 - 4.17: 629 4.17 - 6.26: 68 6.26 - 8.35: 34 8.35 - 10.43: 2 Bond angle restraints: 19275 Sorted by residual: angle pdb=" N MET A 113 " pdb=" CA MET A 113 " pdb=" C MET A 113 " ideal model delta sigma weight residual 112.72 107.11 5.61 1.14e+00 7.69e-01 2.42e+01 angle pdb=" C PRO B 170 " pdb=" CA PRO B 170 " pdb=" CB PRO B 170 " ideal model delta sigma weight residual 110.60 115.91 -5.31 1.38e+00 5.25e-01 1.48e+01 angle pdb=" CA ASP E 192 " pdb=" CB ASP E 192 " pdb=" CG ASP E 192 " ideal model delta sigma weight residual 112.60 116.44 -3.84 1.00e+00 1.00e+00 1.47e+01 angle pdb=" CA ASN A 139 " pdb=" C ASN A 139 " pdb=" O ASN A 139 " ideal model delta sigma weight residual 122.64 117.85 4.79 1.25e+00 6.40e-01 1.47e+01 angle pdb=" CB GLU B 196 " pdb=" CG GLU B 196 " pdb=" CD GLU B 196 " ideal model delta sigma weight residual 112.60 119.09 -6.49 1.70e+00 3.46e-01 1.46e+01 ... (remaining 19270 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 7972 17.96 - 35.92: 632 35.92 - 53.88: 82 53.88 - 71.85: 20 71.85 - 89.81: 12 Dihedral angle restraints: 8718 sinusoidal: 3758 harmonic: 4960 Sorted by residual: dihedral pdb=" CA TYR C 102 " pdb=" C TYR C 102 " pdb=" N PRO C 103 " pdb=" CA PRO C 103 " ideal model delta harmonic sigma weight residual -180.00 -152.68 -27.32 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA MET D 244 " pdb=" C MET D 244 " pdb=" N GLY D 245 " pdb=" CA GLY D 245 " ideal model delta harmonic sigma weight residual 180.00 -152.73 -27.27 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA TYR D 102 " pdb=" C TYR D 102 " pdb=" N PRO D 103 " pdb=" CA PRO D 103 " ideal model delta harmonic sigma weight residual 180.00 -153.84 -26.16 0 5.00e+00 4.00e-02 2.74e+01 ... (remaining 8715 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1643 0.057 - 0.114: 432 0.114 - 0.171: 87 0.171 - 0.229: 23 0.229 - 0.286: 3 Chirality restraints: 2188 Sorted by residual: chirality pdb=" CB VAL E 265 " pdb=" CA VAL E 265 " pdb=" CG1 VAL E 265 " pdb=" CG2 VAL E 265 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CA VAL B 173 " pdb=" N VAL B 173 " pdb=" C VAL B 173 " pdb=" CB VAL B 173 " both_signs ideal model delta sigma weight residual False 2.44 2.72 -0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CA MET A 113 " pdb=" N MET A 113 " pdb=" C MET A 113 " pdb=" CB MET A 113 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 2185 not shown) Planarity restraints: 2386 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAA SY9 C 501 " 0.029 2.00e-02 2.50e+03 1.33e-01 2.65e+02 pdb=" CAI SY9 C 501 " -0.156 2.00e-02 2.50e+03 pdb=" CAK SY9 C 501 " 0.143 2.00e-02 2.50e+03 pdb=" CAL SY9 C 501 " 0.006 2.00e-02 2.50e+03 pdb=" NAH SY9 C 501 " -0.185 2.00e-02 2.50e+03 pdb=" OAJ SY9 C 501 " 0.162 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAA SY9 A 501 " -0.029 2.00e-02 2.50e+03 1.29e-01 2.48e+02 pdb=" CAI SY9 A 501 " 0.152 2.00e-02 2.50e+03 pdb=" CAK SY9 A 501 " -0.138 2.00e-02 2.50e+03 pdb=" CAL SY9 A 501 " -0.006 2.00e-02 2.50e+03 pdb=" NAH SY9 A 501 " 0.178 2.00e-02 2.50e+03 pdb=" OAJ SY9 A 501 " -0.157 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAA SY9 B 501 " -0.115 2.00e-02 2.50e+03 1.28e-01 2.45e+02 pdb=" CAI SY9 B 501 " 0.148 2.00e-02 2.50e+03 pdb=" CAK SY9 B 501 " -0.068 2.00e-02 2.50e+03 pdb=" CAL SY9 B 501 " -0.088 2.00e-02 2.50e+03 pdb=" NAH SY9 B 501 " 0.209 2.00e-02 2.50e+03 pdb=" OAJ SY9 B 501 " -0.085 2.00e-02 2.50e+03 ... (remaining 2383 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3058 2.79 - 3.32: 11604 3.32 - 3.84: 22232 3.84 - 4.37: 26483 4.37 - 4.90: 46529 Nonbonded interactions: 109906 Sorted by model distance: nonbonded pdb=" OE1 GLU C 193 " pdb=" OH TYR C 221 " model vdw 2.259 3.040 nonbonded pdb=" O ALA D 306 " pdb=" OH TYR D 429 " model vdw 2.284 3.040 nonbonded pdb=" OE1 GLU B 193 " pdb=" OH TYR B 221 " model vdw 2.305 3.040 nonbonded pdb=" O LEU B 279 " pdb=" OG1 THR B 283 " model vdw 2.313 3.040 nonbonded pdb=" O THR E 207 " pdb=" NE2 GLN E 211 " model vdw 2.324 3.120 ... (remaining 109901 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' and (resid 33 through 435 or resid 502)) selection = (chain 'B' and (resid 33 through 334 or resid 403 through 435 or resid 502)) selection = (chain 'C' and (resid 33 through 435 or resid 502)) selection = (chain 'D' and (resid 33 through 334 or resid 403 through 435 or resid 501)) } 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: 2.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 14.140 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 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 0.062 14172 Z= 0.275 Angle : 0.856 11.497 19292 Z= 0.459 Chirality : 0.056 0.286 2188 Planarity : 0.009 0.133 2381 Dihedral : 13.126 89.807 5497 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.18), residues: 1657 helix: -3.39 (0.12), residues: 513 sheet: 0.74 (0.28), residues: 407 loop : -0.93 (0.20), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 333 TYR 0.017 0.002 TYR E 473 PHE 0.026 0.001 PHE E 484 TRP 0.020 0.001 TRP E 214 HIS 0.008 0.001 HIS A 133 Details of bonding type rmsd covalent geometry : bond 0.00490 (14166) covalent geometry : angle 0.85140 (19275) SS BOND : bond 0.00439 ( 1) SS BOND : angle 0.84306 ( 2) hydrogen bonds : bond 0.28560 ( 611) hydrogen bonds : angle 8.83468 ( 2151) link_NAG-ASN : bond 0.00645 ( 5) link_NAG-ASN : angle 3.17888 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 363 time to evaluate : 0.552 Fit side-chains REVERT: A 171 MET cc_start: 0.8215 (mtm) cc_final: 0.8014 (mpp) REVERT: A 406 ARG cc_start: 0.7857 (mtp85) cc_final: 0.7639 (ttm170) REVERT: C 40 LYS cc_start: 0.8595 (ptpp) cc_final: 0.8145 (ptpt) REVERT: B 44 LYS cc_start: 0.8780 (mmtp) cc_final: 0.8495 (tptm) REVERT: B 81 ASP cc_start: 0.8701 (p0) cc_final: 0.8329 (p0) REVERT: B 110 ASP cc_start: 0.7917 (p0) cc_final: 0.7393 (p0) REVERT: B 143 ARG cc_start: 0.7668 (mtp180) cc_final: 0.7437 (mmt90) REVERT: B 244 MET cc_start: 0.7328 (ptt) cc_final: 0.7054 (ptm) REVERT: B 409 ARG cc_start: 0.7588 (ttp-110) cc_final: 0.6973 (ttp-110) REVERT: E 162 LEU cc_start: 0.8647 (tt) cc_final: 0.8395 (tp) REVERT: E 262 ARG cc_start: 0.8298 (mpt-90) cc_final: 0.8033 (mmt90) REVERT: E 473 TYR cc_start: 0.7278 (m-80) cc_final: 0.6977 (m-10) REVERT: E 480 PHE cc_start: 0.7903 (t80) cc_final: 0.7362 (t80) outliers start: 0 outliers final: 1 residues processed: 363 average time/residue: 0.7114 time to fit residues: 278.3333 Evaluate side-chains 296 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 295 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 204 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 334 GLN B 188 ASN B 225 HIS E 157 GLN E 194 GLN E 354 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.118592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.098431 restraints weight = 20650.541| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.80 r_work: 0.3034 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14172 Z= 0.142 Angle : 0.615 7.454 19292 Z= 0.311 Chirality : 0.044 0.168 2188 Planarity : 0.005 0.056 2381 Dihedral : 5.575 87.706 2250 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.45 % Allowed : 12.73 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.20), residues: 1657 helix: 0.02 (0.21), residues: 520 sheet: 0.84 (0.27), residues: 405 loop : -0.57 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 83 TYR 0.015 0.001 TYR E 473 PHE 0.012 0.001 PHE A 123 TRP 0.010 0.001 TRP D 92 HIS 0.002 0.000 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00319 (14166) covalent geometry : angle 0.61195 (19275) SS BOND : bond 0.00415 ( 1) SS BOND : angle 0.63450 ( 2) hydrogen bonds : bond 0.05488 ( 611) hydrogen bonds : angle 4.88758 ( 2151) link_NAG-ASN : bond 0.00393 ( 5) link_NAG-ASN : angle 2.19490 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 334 time to evaluate : 0.659 Fit side-chains REVERT: A 171 MET cc_start: 0.8366 (mtm) cc_final: 0.7998 (mpp) REVERT: A 300 LYS cc_start: 0.8832 (mmmt) cc_final: 0.8233 (mmtm) REVERT: A 406 ARG cc_start: 0.7371 (mtp85) cc_final: 0.6785 (mtm110) REVERT: D 108 ASP cc_start: 0.8081 (m-30) cc_final: 0.7879 (m-30) REVERT: D 121 ASP cc_start: 0.8872 (p0) cc_final: 0.8621 (p0) REVERT: D 143 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7550 (mmt90) REVERT: D 244 MET cc_start: 0.7807 (mmm) cc_final: 0.7597 (mmm) REVERT: D 250 GLN cc_start: 0.7849 (tp40) cc_final: 0.7271 (tm-30) REVERT: D 406 ARG cc_start: 0.7514 (ttt180) cc_final: 0.6849 (mtp85) REVERT: C 36 GLU cc_start: 0.7465 (pm20) cc_final: 0.6797 (pm20) REVERT: C 40 LYS cc_start: 0.8702 (ptpp) cc_final: 0.8228 (ptpt) REVERT: C 250 GLN cc_start: 0.8362 (tp-100) cc_final: 0.6724 (tp-100) REVERT: C 270 MET cc_start: 0.8775 (ptp) cc_final: 0.8512 (ptt) REVERT: B 44 LYS cc_start: 0.8953 (mmtp) cc_final: 0.8539 (tptt) REVERT: B 143 ARG cc_start: 0.8102 (mtp180) cc_final: 0.7645 (mmt90) REVERT: B 409 ARG cc_start: 0.7388 (ttp-110) cc_final: 0.6923 (ttp-110) REVERT: B 420 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8267 (mm) REVERT: E 211 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.7140 (mp10) REVERT: E 251 TYR cc_start: 0.8062 (m-80) cc_final: 0.7803 (m-80) REVERT: E 262 ARG cc_start: 0.8530 (mpt-90) cc_final: 0.8212 (mmt90) REVERT: E 473 TYR cc_start: 0.7893 (m-80) cc_final: 0.7280 (m-10) REVERT: E 480 PHE cc_start: 0.7919 (t80) cc_final: 0.7394 (t80) outliers start: 37 outliers final: 11 residues processed: 350 average time/residue: 0.7205 time to fit residues: 272.1240 Evaluate side-chains 317 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 303 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 243 GLN Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 211 GLN Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 348 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 100 optimal weight: 9.9990 chunk 102 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 156 optimal weight: 0.6980 chunk 94 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 106 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 168 ASN D 174 GLN D 210 GLN D 239 HIS D 334 GLN B 290 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.116095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.095166 restraints weight = 20686.680| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.78 r_work: 0.3001 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 14172 Z= 0.136 Angle : 0.560 6.457 19292 Z= 0.284 Chirality : 0.043 0.179 2188 Planarity : 0.004 0.056 2381 Dihedral : 4.557 47.715 2248 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.72 % Allowed : 15.85 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.20), residues: 1657 helix: 1.05 (0.22), residues: 527 sheet: 1.00 (0.28), residues: 406 loop : -0.40 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 83 TYR 0.015 0.001 TYR B 325 PHE 0.017 0.001 PHE E 122 TRP 0.009 0.001 TRP D 92 HIS 0.001 0.000 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00318 (14166) covalent geometry : angle 0.55781 (19275) SS BOND : bond 0.00301 ( 1) SS BOND : angle 0.46097 ( 2) hydrogen bonds : bond 0.04590 ( 611) hydrogen bonds : angle 4.30784 ( 2151) link_NAG-ASN : bond 0.00354 ( 5) link_NAG-ASN : angle 1.96307 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 315 time to evaluate : 0.584 Fit side-chains REVERT: A 171 MET cc_start: 0.8548 (mtm) cc_final: 0.8122 (mpp) REVERT: D 121 ASP cc_start: 0.8913 (p0) cc_final: 0.8650 (p0) REVERT: D 143 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7973 (mmm-85) REVERT: D 244 MET cc_start: 0.7735 (mmm) cc_final: 0.7294 (mmm) REVERT: D 250 GLN cc_start: 0.7903 (tp40) cc_final: 0.7305 (tm-30) REVERT: D 406 ARG cc_start: 0.7532 (ttt180) cc_final: 0.6959 (mtp85) REVERT: C 36 GLU cc_start: 0.7613 (pm20) cc_final: 0.6940 (pm20) REVERT: C 40 LYS cc_start: 0.8769 (ptpp) cc_final: 0.8362 (ptpt) REVERT: C 196 GLU cc_start: 0.8483 (mp0) cc_final: 0.8120 (mp0) REVERT: C 244 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.8375 (tpt) REVERT: C 270 MET cc_start: 0.8750 (ptp) cc_final: 0.8487 (ptt) REVERT: C 418 PHE cc_start: 0.8953 (OUTLIER) cc_final: 0.8589 (t80) REVERT: B 44 LYS cc_start: 0.8915 (mmtp) cc_final: 0.8525 (tptt) REVERT: B 409 ARG cc_start: 0.7539 (ttp-110) cc_final: 0.7031 (ttp-110) REVERT: B 420 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8480 (mm) REVERT: E 122 PHE cc_start: 0.6676 (t80) cc_final: 0.6369 (t80) REVERT: E 221 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.8154 (mm110) REVERT: E 251 TYR cc_start: 0.8124 (m-80) cc_final: 0.7863 (m-80) REVERT: E 262 ARG cc_start: 0.8576 (mpt-90) cc_final: 0.8311 (mmt90) REVERT: E 473 TYR cc_start: 0.7928 (m-80) cc_final: 0.7329 (m-10) REVERT: E 480 PHE cc_start: 0.7938 (t80) cc_final: 0.7363 (t80) outliers start: 41 outliers final: 17 residues processed: 334 average time/residue: 0.6774 time to fit residues: 244.9681 Evaluate side-chains 314 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 292 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 243 GLN Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 244 MET Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 418 PHE Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 221 GLN Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 303 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 134 optimal weight: 2.9990 chunk 46 optimal weight: 0.2980 chunk 89 optimal weight: 0.9990 chunk 153 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 118 optimal weight: 0.7980 chunk 11 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 334 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.115823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.095057 restraints weight = 20507.358| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.78 r_work: 0.2994 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14172 Z= 0.122 Angle : 0.549 7.033 19292 Z= 0.277 Chirality : 0.043 0.180 2188 Planarity : 0.004 0.054 2381 Dihedral : 4.459 47.740 2248 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 2.92 % Allowed : 17.18 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.21), residues: 1657 helix: 1.49 (0.23), residues: 526 sheet: 1.15 (0.28), residues: 401 loop : -0.32 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 83 TYR 0.015 0.001 TYR B 325 PHE 0.013 0.001 PHE E 340 TRP 0.008 0.001 TRP D 92 HIS 0.001 0.000 HIS C 133 Details of bonding type rmsd covalent geometry : bond 0.00287 (14166) covalent geometry : angle 0.54665 (19275) SS BOND : bond 0.00258 ( 1) SS BOND : angle 0.37947 ( 2) hydrogen bonds : bond 0.04047 ( 611) hydrogen bonds : angle 4.11209 ( 2151) link_NAG-ASN : bond 0.00363 ( 5) link_NAG-ASN : angle 1.80303 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 308 time to evaluate : 0.562 Fit side-chains REVERT: A 77 GLU cc_start: 0.8570 (mp0) cc_final: 0.8349 (mp0) REVERT: A 134 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7824 (tm-30) REVERT: A 171 MET cc_start: 0.8562 (mtm) cc_final: 0.8212 (mpp) REVERT: D 121 ASP cc_start: 0.8939 (p0) cc_final: 0.8705 (p0) REVERT: D 244 MET cc_start: 0.7816 (mmm) cc_final: 0.7294 (mmm) REVERT: D 250 GLN cc_start: 0.7915 (tp40) cc_final: 0.7313 (tm-30) REVERT: D 406 ARG cc_start: 0.7496 (ttt180) cc_final: 0.6988 (mtp180) REVERT: C 36 GLU cc_start: 0.7616 (pm20) cc_final: 0.7181 (pm20) REVERT: C 40 LYS cc_start: 0.8791 (ptpp) cc_final: 0.8451 (ptpt) REVERT: C 77 GLU cc_start: 0.8335 (mp0) cc_final: 0.8125 (mp0) REVERT: C 244 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.8152 (tpt) REVERT: C 270 MET cc_start: 0.8675 (ptp) cc_final: 0.8418 (ptt) REVERT: B 44 LYS cc_start: 0.8936 (mmtp) cc_final: 0.8559 (tptt) REVERT: B 409 ARG cc_start: 0.7556 (ttp-110) cc_final: 0.7048 (ttp-110) REVERT: B 420 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8464 (mm) REVERT: E 62 LYS cc_start: 0.8539 (mptt) cc_final: 0.8124 (mptt) REVERT: E 197 LYS cc_start: 0.8740 (ptpp) cc_final: 0.8130 (mtpt) REVERT: E 211 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.7265 (mp10) REVERT: E 222 MET cc_start: 0.8411 (mmm) cc_final: 0.7948 (tpt) REVERT: E 251 TYR cc_start: 0.8110 (m-80) cc_final: 0.7894 (m-80) REVERT: E 262 ARG cc_start: 0.8572 (mpt-90) cc_final: 0.8362 (mmt90) REVERT: E 473 TYR cc_start: 0.7893 (m-80) cc_final: 0.7259 (m-10) outliers start: 44 outliers final: 18 residues processed: 326 average time/residue: 0.6870 time to fit residues: 242.1072 Evaluate side-chains 309 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 287 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 243 GLN Chi-restraints excluded: chain C residue 244 MET Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain E residue 136 CYS Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 211 GLN Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 303 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 42 optimal weight: 7.9990 chunk 128 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 153 optimal weight: 0.9980 chunk 64 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 160 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN D 334 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.114543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.093647 restraints weight = 20727.649| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.78 r_work: 0.2981 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14172 Z= 0.141 Angle : 0.561 10.040 19292 Z= 0.283 Chirality : 0.043 0.187 2188 Planarity : 0.004 0.055 2381 Dihedral : 4.494 45.244 2248 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 3.18 % Allowed : 17.64 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.21), residues: 1657 helix: 1.67 (0.23), residues: 528 sheet: 1.06 (0.27), residues: 431 loop : -0.16 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 83 TYR 0.017 0.001 TYR B 325 PHE 0.019 0.001 PHE C 428 TRP 0.008 0.001 TRP D 92 HIS 0.001 0.000 HIS D 133 Details of bonding type rmsd covalent geometry : bond 0.00338 (14166) covalent geometry : angle 0.55909 (19275) SS BOND : bond 0.00283 ( 1) SS BOND : angle 0.48263 ( 2) hydrogen bonds : bond 0.03988 ( 611) hydrogen bonds : angle 4.01539 ( 2151) link_NAG-ASN : bond 0.00348 ( 5) link_NAG-ASN : angle 1.77503 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 299 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.8562 (mp0) cc_final: 0.8012 (mp0) REVERT: A 171 MET cc_start: 0.8642 (mtm) cc_final: 0.8265 (mpp) REVERT: D 51 ARG cc_start: 0.8893 (mtm-85) cc_final: 0.8053 (mtp85) REVERT: D 121 ASP cc_start: 0.8958 (p0) cc_final: 0.8624 (p0) REVERT: D 244 MET cc_start: 0.7845 (mmm) cc_final: 0.7612 (mmm) REVERT: D 250 GLN cc_start: 0.7911 (tp40) cc_final: 0.7204 (tm-30) REVERT: D 406 ARG cc_start: 0.7534 (ttt180) cc_final: 0.7007 (mtp180) REVERT: C 40 LYS cc_start: 0.8808 (ptpp) cc_final: 0.8361 (ptpt) REVERT: C 270 MET cc_start: 0.8682 (ptp) cc_final: 0.8454 (ptt) REVERT: B 44 LYS cc_start: 0.8920 (mmtp) cc_final: 0.8593 (tptt) REVERT: B 409 ARG cc_start: 0.7581 (ttp-110) cc_final: 0.7092 (ttp-110) REVERT: B 420 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8497 (mm) REVERT: E 197 LYS cc_start: 0.8682 (ptpp) cc_final: 0.8094 (mtpt) REVERT: E 211 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.7332 (mp10) REVERT: E 231 ASP cc_start: 0.8604 (t0) cc_final: 0.8044 (t0) REVERT: E 232 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8402 (tp) REVERT: E 262 ARG cc_start: 0.8565 (mpt-90) cc_final: 0.8206 (mmt90) REVERT: E 469 ARG cc_start: 0.7109 (ptp90) cc_final: 0.6552 (pmt170) REVERT: E 473 TYR cc_start: 0.7911 (m-80) cc_final: 0.7272 (m-10) outliers start: 48 outliers final: 23 residues processed: 323 average time/residue: 0.6887 time to fit residues: 240.1967 Evaluate side-chains 297 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 271 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 243 GLN Chi-restraints excluded: chain D residue 414 SER Chi-restraints excluded: chain C residue 168 ASN Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain E residue 136 CYS Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 211 GLN Chi-restraints excluded: chain E residue 213 MET Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 303 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 143 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 125 optimal weight: 0.3980 chunk 72 optimal weight: 0.0370 chunk 127 optimal weight: 2.9990 chunk 151 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 overall best weight: 1.2662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 334 GLN C 133 HIS E 221 GLN E 354 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.114683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.093683 restraints weight = 20482.730| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.79 r_work: 0.2979 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14172 Z= 0.136 Angle : 0.570 11.997 19292 Z= 0.287 Chirality : 0.043 0.192 2188 Planarity : 0.004 0.063 2381 Dihedral : 4.455 44.593 2248 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.52 % Allowed : 18.70 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.21), residues: 1657 helix: 1.79 (0.23), residues: 527 sheet: 1.12 (0.28), residues: 429 loop : -0.14 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 83 TYR 0.016 0.001 TYR B 325 PHE 0.014 0.001 PHE E 340 TRP 0.008 0.001 TRP D 92 HIS 0.002 0.000 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00327 (14166) covalent geometry : angle 0.56796 (19275) SS BOND : bond 0.00273 ( 1) SS BOND : angle 0.46659 ( 2) hydrogen bonds : bond 0.03857 ( 611) hydrogen bonds : angle 3.95473 ( 2151) link_NAG-ASN : bond 0.00352 ( 5) link_NAG-ASN : angle 1.71137 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 292 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.8566 (mp0) cc_final: 0.8046 (mp0) REVERT: A 164 MET cc_start: 0.9260 (mtt) cc_final: 0.9018 (mtt) REVERT: A 171 MET cc_start: 0.8674 (mtm) cc_final: 0.8348 (mpp) REVERT: D 51 ARG cc_start: 0.8907 (mtm-85) cc_final: 0.8056 (mtp85) REVERT: D 121 ASP cc_start: 0.8956 (p0) cc_final: 0.8712 (p0) REVERT: D 244 MET cc_start: 0.7810 (mmm) cc_final: 0.7592 (mmm) REVERT: D 250 GLN cc_start: 0.7857 (tp40) cc_final: 0.7154 (tm-30) REVERT: D 406 ARG cc_start: 0.7447 (ttt180) cc_final: 0.6898 (mtp180) REVERT: C 36 GLU cc_start: 0.7611 (pm20) cc_final: 0.7160 (pm20) REVERT: C 40 LYS cc_start: 0.8803 (ptpp) cc_final: 0.8454 (ptpt) REVERT: C 83 ARG cc_start: 0.8751 (mtp-110) cc_final: 0.8303 (ttm110) REVERT: C 270 MET cc_start: 0.8710 (ptp) cc_final: 0.8441 (ptt) REVERT: B 44 LYS cc_start: 0.8915 (mmtp) cc_final: 0.8595 (tptt) REVERT: B 409 ARG cc_start: 0.7546 (ttp-110) cc_final: 0.7093 (ttp-110) REVERT: B 420 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8504 (mm) REVERT: E 197 LYS cc_start: 0.8652 (ptpp) cc_final: 0.8134 (mtpt) REVERT: E 211 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.7360 (mp10) REVERT: E 221 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.8287 (mp10) REVERT: E 231 ASP cc_start: 0.8597 (t0) cc_final: 0.8084 (t70) REVERT: E 232 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8432 (tp) REVERT: E 262 ARG cc_start: 0.8600 (mpt-90) cc_final: 0.8255 (mmt90) REVERT: E 469 ARG cc_start: 0.7093 (ptp90) cc_final: 0.6526 (pmt170) REVERT: E 473 TYR cc_start: 0.7913 (m-80) cc_final: 0.7256 (m-10) outliers start: 38 outliers final: 23 residues processed: 315 average time/residue: 0.6932 time to fit residues: 235.6466 Evaluate side-chains 313 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 286 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 243 GLN Chi-restraints excluded: chain D residue 414 SER Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 168 ASN Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain E residue 136 CYS Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 211 GLN Chi-restraints excluded: chain E residue 213 MET Chi-restraints excluded: chain E residue 221 GLN Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 303 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 95 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 119 optimal weight: 8.9990 chunk 59 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 68 optimal weight: 0.5980 chunk 69 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 chunk 30 optimal weight: 9.9990 chunk 120 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 334 GLN E 221 GLN E 354 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.114890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.094015 restraints weight = 20517.236| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.78 r_work: 0.2983 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14172 Z= 0.126 Angle : 0.571 13.724 19292 Z= 0.287 Chirality : 0.043 0.194 2188 Planarity : 0.004 0.071 2381 Dihedral : 4.403 44.831 2248 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 3.32 % Allowed : 18.50 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.21), residues: 1657 helix: 1.84 (0.23), residues: 527 sheet: 1.08 (0.28), residues: 435 loop : -0.11 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 83 TYR 0.015 0.001 TYR B 325 PHE 0.022 0.001 PHE C 428 TRP 0.008 0.001 TRP D 92 HIS 0.002 0.000 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00301 (14166) covalent geometry : angle 0.56978 (19275) SS BOND : bond 0.00249 ( 1) SS BOND : angle 0.40613 ( 2) hydrogen bonds : bond 0.03730 ( 611) hydrogen bonds : angle 3.90306 ( 2151) link_NAG-ASN : bond 0.00354 ( 5) link_NAG-ASN : angle 1.65250 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 300 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.8565 (mp0) cc_final: 0.8133 (mp0) REVERT: A 80 MET cc_start: 0.8799 (mmm) cc_final: 0.8155 (mtm) REVERT: A 164 MET cc_start: 0.9229 (mtt) cc_final: 0.8880 (mtt) REVERT: A 171 MET cc_start: 0.8664 (mtm) cc_final: 0.8356 (mpp) REVERT: D 51 ARG cc_start: 0.8903 (mtm-85) cc_final: 0.8044 (mtp85) REVERT: D 121 ASP cc_start: 0.8944 (p0) cc_final: 0.8697 (p0) REVERT: D 244 MET cc_start: 0.7818 (mmm) cc_final: 0.7417 (mmm) REVERT: D 250 GLN cc_start: 0.7841 (tp40) cc_final: 0.7126 (tm-30) REVERT: D 406 ARG cc_start: 0.7458 (ttt180) cc_final: 0.6914 (mtm180) REVERT: C 40 LYS cc_start: 0.8799 (ptpp) cc_final: 0.8381 (ptpt) REVERT: C 131 ASN cc_start: 0.8354 (m-40) cc_final: 0.7845 (p0) REVERT: C 241 GLU cc_start: 0.8544 (pt0) cc_final: 0.8186 (pt0) REVERT: C 270 MET cc_start: 0.8682 (ptp) cc_final: 0.8411 (ptt) REVERT: B 44 LYS cc_start: 0.8911 (mmtp) cc_final: 0.8606 (tptt) REVERT: B 409 ARG cc_start: 0.7518 (ttp-110) cc_final: 0.7066 (ttp-110) REVERT: B 420 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8495 (mm) REVERT: E 197 LYS cc_start: 0.8650 (ptpp) cc_final: 0.8127 (mtpt) REVERT: E 211 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.7332 (mp10) REVERT: E 231 ASP cc_start: 0.8572 (t0) cc_final: 0.8062 (t70) REVERT: E 232 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8439 (tp) REVERT: E 262 ARG cc_start: 0.8637 (mpt-90) cc_final: 0.8332 (mmt90) REVERT: E 469 ARG cc_start: 0.7074 (ptp90) cc_final: 0.6486 (pmm150) REVERT: E 473 TYR cc_start: 0.7896 (m-80) cc_final: 0.7231 (m-10) outliers start: 50 outliers final: 32 residues processed: 328 average time/residue: 0.7087 time to fit residues: 250.7331 Evaluate side-chains 317 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 282 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 243 GLN Chi-restraints excluded: chain D residue 251 MET Chi-restraints excluded: chain D residue 414 SER Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 168 ASN Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 136 CYS Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 211 GLN Chi-restraints excluded: chain E residue 213 MET Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 303 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 102 optimal weight: 5.9990 chunk 4 optimal weight: 0.0020 chunk 115 optimal weight: 0.9980 chunk 48 optimal weight: 0.0370 chunk 55 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 100 optimal weight: 8.9990 chunk 111 optimal weight: 4.9990 chunk 106 optimal weight: 0.0050 chunk 40 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 overall best weight: 0.4082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 334 GLN E 221 GLN E 354 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.117064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.096151 restraints weight = 20303.457| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.78 r_work: 0.3016 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 14172 Z= 0.107 Angle : 0.577 15.629 19292 Z= 0.289 Chirality : 0.042 0.195 2188 Planarity : 0.004 0.077 2381 Dihedral : 4.217 47.425 2248 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.52 % Allowed : 19.96 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.21), residues: 1657 helix: 1.92 (0.23), residues: 527 sheet: 1.10 (0.27), residues: 434 loop : -0.11 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 83 TYR 0.014 0.001 TYR B 325 PHE 0.013 0.001 PHE E 340 TRP 0.008 0.001 TRP D 92 HIS 0.001 0.000 HIS C 133 Details of bonding type rmsd covalent geometry : bond 0.00248 (14166) covalent geometry : angle 0.57572 (19275) SS BOND : bond 0.00183 ( 1) SS BOND : angle 0.30196 ( 2) hydrogen bonds : bond 0.03376 ( 611) hydrogen bonds : angle 3.78989 ( 2151) link_NAG-ASN : bond 0.00366 ( 5) link_NAG-ASN : angle 1.52813 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 307 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.8535 (mp0) cc_final: 0.8108 (mp0) REVERT: A 80 MET cc_start: 0.8772 (mmm) cc_final: 0.8122 (mtm) REVERT: A 164 MET cc_start: 0.9176 (mtt) cc_final: 0.8815 (mtt) REVERT: A 171 MET cc_start: 0.8701 (mtm) cc_final: 0.8360 (mpp) REVERT: D 51 ARG cc_start: 0.8914 (mtm-85) cc_final: 0.8069 (mtp85) REVERT: D 121 ASP cc_start: 0.8916 (p0) cc_final: 0.8661 (p0) REVERT: D 244 MET cc_start: 0.7904 (mmm) cc_final: 0.7610 (mmm) REVERT: D 250 GLN cc_start: 0.7784 (tp40) cc_final: 0.7059 (tm-30) REVERT: D 406 ARG cc_start: 0.7393 (ttt180) cc_final: 0.6887 (mtm180) REVERT: C 36 GLU cc_start: 0.7637 (pm20) cc_final: 0.7423 (pm20) REVERT: C 40 LYS cc_start: 0.8785 (ptpp) cc_final: 0.8414 (ptpt) REVERT: C 83 ARG cc_start: 0.8641 (mtp-110) cc_final: 0.8314 (ttm110) REVERT: C 102 TYR cc_start: 0.7565 (OUTLIER) cc_final: 0.7078 (m-80) REVERT: C 131 ASN cc_start: 0.8175 (m-40) cc_final: 0.7751 (p0) REVERT: C 168 ASN cc_start: 0.7634 (OUTLIER) cc_final: 0.6978 (m-40) REVERT: C 214 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8371 (mptt) REVERT: C 270 MET cc_start: 0.8630 (ptp) cc_final: 0.8355 (ptt) REVERT: B 44 LYS cc_start: 0.8907 (mmtp) cc_final: 0.8589 (tptm) REVERT: B 316 LEU cc_start: 0.8889 (mm) cc_final: 0.8646 (mm) REVERT: B 409 ARG cc_start: 0.7510 (ttp-110) cc_final: 0.7059 (ttp-110) REVERT: E 197 LYS cc_start: 0.8605 (ptpp) cc_final: 0.8169 (mtpt) REVERT: E 211 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.7268 (mp10) REVERT: E 231 ASP cc_start: 0.8507 (t0) cc_final: 0.8043 (t70) REVERT: E 232 ILE cc_start: 0.8724 (OUTLIER) cc_final: 0.8425 (tp) REVERT: E 262 ARG cc_start: 0.8620 (mpt-90) cc_final: 0.8344 (mmt90) REVERT: E 469 ARG cc_start: 0.7024 (ptp90) cc_final: 0.6438 (pmm150) REVERT: E 473 TYR cc_start: 0.7887 (m-80) cc_final: 0.7240 (m-10) outliers start: 38 outliers final: 20 residues processed: 323 average time/residue: 0.7169 time to fit residues: 249.7124 Evaluate side-chains 314 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 289 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain D residue 251 MET Chi-restraints excluded: chain C residue 102 TYR Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 168 ASN Chi-restraints excluded: chain C residue 214 LYS Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 136 CYS Chi-restraints excluded: chain E residue 211 GLN Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 285 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 37 optimal weight: 0.0370 chunk 142 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 147 optimal weight: 0.2980 chunk 137 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 144 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 overall best weight: 0.8462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 334 GLN E 221 GLN E 354 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.117930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.096347 restraints weight = 20687.163| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.73 r_work: 0.3049 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14172 Z= 0.119 Angle : 0.584 15.203 19292 Z= 0.292 Chirality : 0.042 0.194 2188 Planarity : 0.004 0.076 2381 Dihedral : 4.253 46.876 2248 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 2.06 % Allowed : 21.15 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.21), residues: 1657 helix: 1.98 (0.23), residues: 527 sheet: 1.30 (0.28), residues: 419 loop : -0.14 (0.23), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 83 TYR 0.016 0.001 TYR B 325 PHE 0.025 0.001 PHE C 428 TRP 0.008 0.001 TRP D 92 HIS 0.001 0.000 HIS C 133 Details of bonding type rmsd covalent geometry : bond 0.00288 (14166) covalent geometry : angle 0.58226 (19275) SS BOND : bond 0.00277 ( 1) SS BOND : angle 0.47372 ( 2) hydrogen bonds : bond 0.03438 ( 611) hydrogen bonds : angle 3.78148 ( 2151) link_NAG-ASN : bond 0.00341 ( 5) link_NAG-ASN : angle 1.55528 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 296 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.8566 (mp0) cc_final: 0.8144 (mp0) REVERT: A 80 MET cc_start: 0.8822 (mmm) cc_final: 0.8129 (mtm) REVERT: A 164 MET cc_start: 0.9168 (mtt) cc_final: 0.8792 (mtt) REVERT: A 171 MET cc_start: 0.8748 (mtm) cc_final: 0.8547 (mpp) REVERT: A 333 ARG cc_start: 0.7497 (ptp-110) cc_final: 0.7213 (ptp90) REVERT: D 51 ARG cc_start: 0.8946 (mtm-85) cc_final: 0.8133 (mtp85) REVERT: D 121 ASP cc_start: 0.8892 (p0) cc_final: 0.8602 (p0) REVERT: D 244 MET cc_start: 0.7795 (mmm) cc_final: 0.7510 (mmm) REVERT: D 250 GLN cc_start: 0.7864 (tp40) cc_final: 0.7164 (tm-30) REVERT: D 406 ARG cc_start: 0.7454 (ttt180) cc_final: 0.6966 (mtm180) REVERT: D 409 ARG cc_start: 0.8046 (tpt170) cc_final: 0.7777 (tpp-160) REVERT: C 40 LYS cc_start: 0.8783 (ptpp) cc_final: 0.8317 (ptpt) REVERT: C 83 ARG cc_start: 0.8594 (mtp-110) cc_final: 0.8313 (ttm110) REVERT: C 102 TYR cc_start: 0.7619 (OUTLIER) cc_final: 0.7144 (m-80) REVERT: C 131 ASN cc_start: 0.8172 (m-40) cc_final: 0.7825 (p0) REVERT: C 241 GLU cc_start: 0.8571 (pt0) cc_final: 0.8202 (pt0) REVERT: C 270 MET cc_start: 0.8610 (ptp) cc_final: 0.8340 (ptt) REVERT: B 44 LYS cc_start: 0.8860 (mmtp) cc_final: 0.8622 (tptt) REVERT: B 409 ARG cc_start: 0.7577 (ttp-110) cc_final: 0.7166 (ttp-110) REVERT: E 211 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.7433 (mp10) REVERT: E 221 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.6995 (mp-120) REVERT: E 231 ASP cc_start: 0.8521 (t0) cc_final: 0.8134 (t70) REVERT: E 232 ILE cc_start: 0.8751 (OUTLIER) cc_final: 0.8476 (tp) REVERT: E 262 ARG cc_start: 0.8656 (mpt-90) cc_final: 0.8430 (mtt-85) REVERT: E 469 ARG cc_start: 0.7099 (ptp90) cc_final: 0.6513 (pmm150) REVERT: E 473 TYR cc_start: 0.7868 (m-80) cc_final: 0.7287 (m-10) outliers start: 31 outliers final: 23 residues processed: 310 average time/residue: 0.6180 time to fit residues: 206.7009 Evaluate side-chains 312 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 285 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 251 MET Chi-restraints excluded: chain C residue 102 TYR Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 168 ASN Chi-restraints excluded: chain C residue 214 LYS Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 127 GLU Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 136 CYS Chi-restraints excluded: chain E residue 211 GLN Chi-restraints excluded: chain E residue 221 GLN Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 285 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 14 optimal weight: 6.9990 chunk 13 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 127 optimal weight: 0.8980 chunk 1 optimal weight: 10.0000 chunk 56 optimal weight: 0.8980 chunk 33 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 134 optimal weight: 0.0770 chunk 113 optimal weight: 8.9990 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 334 GLN E 221 GLN E 354 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.117876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.096374 restraints weight = 20554.892| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.71 r_work: 0.3049 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.157 14172 Z= 0.152 Angle : 0.837 59.196 19292 Z= 0.460 Chirality : 0.043 0.194 2188 Planarity : 0.005 0.113 2381 Dihedral : 4.248 46.874 2248 Min Nonbonded Distance : 1.662 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.99 % Allowed : 21.75 % Favored : 76.26 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.21), residues: 1657 helix: 1.99 (0.23), residues: 527 sheet: 1.30 (0.28), residues: 419 loop : -0.14 (0.23), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 83 TYR 0.018 0.001 TYR B 325 PHE 0.013 0.001 PHE E 340 TRP 0.007 0.001 TRP D 92 HIS 0.001 0.000 HIS C 133 Details of bonding type rmsd covalent geometry : bond 0.00358 (14166) covalent geometry : angle 0.83665 (19275) SS BOND : bond 0.00283 ( 1) SS BOND : angle 0.46241 ( 2) hydrogen bonds : bond 0.03441 ( 611) hydrogen bonds : angle 3.78225 ( 2151) link_NAG-ASN : bond 0.00341 ( 5) link_NAG-ASN : angle 1.55212 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 286 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.8570 (mp0) cc_final: 0.8148 (mp0) REVERT: A 80 MET cc_start: 0.8818 (mmm) cc_final: 0.8126 (mtm) REVERT: A 164 MET cc_start: 0.9172 (mtt) cc_final: 0.8798 (mtt) REVERT: A 333 ARG cc_start: 0.7499 (ptp-110) cc_final: 0.7202 (ptp90) REVERT: D 51 ARG cc_start: 0.8946 (mtm-85) cc_final: 0.8134 (mtp85) REVERT: D 121 ASP cc_start: 0.8891 (p0) cc_final: 0.8601 (p0) REVERT: D 244 MET cc_start: 0.7811 (mmm) cc_final: 0.7503 (mmm) REVERT: D 250 GLN cc_start: 0.7861 (tp40) cc_final: 0.7155 (tm-30) REVERT: D 406 ARG cc_start: 0.7456 (ttt180) cc_final: 0.6966 (mtm180) REVERT: D 409 ARG cc_start: 0.8040 (tpt170) cc_final: 0.7770 (tpp-160) REVERT: C 36 GLU cc_start: 0.7668 (pm20) cc_final: 0.7437 (pm20) REVERT: C 40 LYS cc_start: 0.8784 (ptpp) cc_final: 0.8423 (ptpt) REVERT: C 83 ARG cc_start: 0.8586 (mtp-110) cc_final: 0.8300 (ttm110) REVERT: C 102 TYR cc_start: 0.7624 (OUTLIER) cc_final: 0.7146 (m-80) REVERT: C 131 ASN cc_start: 0.8169 (m-40) cc_final: 0.7823 (p0) REVERT: C 214 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8474 (mptt) REVERT: C 270 MET cc_start: 0.8608 (ptp) cc_final: 0.8338 (ptt) REVERT: B 44 LYS cc_start: 0.8849 (mmtp) cc_final: 0.8621 (tptt) REVERT: B 409 ARG cc_start: 0.7583 (ttp-110) cc_final: 0.7171 (ttp-110) REVERT: E 211 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.7419 (mp10) REVERT: E 231 ASP cc_start: 0.8522 (t0) cc_final: 0.8118 (t70) REVERT: E 232 ILE cc_start: 0.8750 (OUTLIER) cc_final: 0.8469 (tp) REVERT: E 262 ARG cc_start: 0.8645 (mpt-90) cc_final: 0.8411 (mtp85) REVERT: E 469 ARG cc_start: 0.7100 (ptp90) cc_final: 0.6509 (pmm150) REVERT: E 473 TYR cc_start: 0.7862 (m-80) cc_final: 0.7280 (m-10) outliers start: 30 outliers final: 23 residues processed: 302 average time/residue: 0.6884 time to fit residues: 224.2300 Evaluate side-chains 315 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 288 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain C residue 102 TYR Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 168 ASN Chi-restraints excluded: chain C residue 214 LYS Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 127 GLU Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 136 CYS Chi-restraints excluded: chain E residue 211 GLN Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 343 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 0 optimal weight: 8.9990 chunk 158 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 97 optimal weight: 0.4980 chunk 135 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 138 optimal weight: 0.0050 chunk 141 optimal weight: 3.9990 chunk 127 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 334 GLN ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 354 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.117834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.096233 restraints weight = 20769.801| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.72 r_work: 0.3045 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.157 14172 Z= 0.152 Angle : 0.837 59.196 19292 Z= 0.460 Chirality : 0.043 0.194 2188 Planarity : 0.005 0.113 2381 Dihedral : 4.248 46.874 2248 Min Nonbonded Distance : 1.370 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.79 % Allowed : 22.08 % Favored : 76.13 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.21), residues: 1657 helix: 1.99 (0.23), residues: 527 sheet: 1.30 (0.28), residues: 419 loop : -0.14 (0.23), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 83 TYR 0.018 0.001 TYR B 325 PHE 0.013 0.001 PHE E 340 TRP 0.007 0.001 TRP D 92 HIS 0.001 0.000 HIS C 133 Details of bonding type rmsd covalent geometry : bond 0.00358 (14166) covalent geometry : angle 0.83665 (19275) SS BOND : bond 0.00283 ( 1) SS BOND : angle 0.46241 ( 2) hydrogen bonds : bond 0.03441 ( 611) hydrogen bonds : angle 3.78225 ( 2151) link_NAG-ASN : bond 0.00341 ( 5) link_NAG-ASN : angle 1.55212 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4876.96 seconds wall clock time: 83 minutes 55.41 seconds (5035.41 seconds total)