Starting phenix.real_space_refine on Wed Apr 30 22:22:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6mp6_9187/04_2025/6mp6_9187_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6mp6_9187/04_2025/6mp6_9187.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6mp6_9187/04_2025/6mp6_9187.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6mp6_9187/04_2025/6mp6_9187.map" model { file = "/net/cci-nas-00/data/ceres_data/6mp6_9187/04_2025/6mp6_9187_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6mp6_9187/04_2025/6mp6_9187_neut.cif" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.026 sd= 0.373 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 48 5.16 5 C 6483 2.51 5 N 1650 2.21 5 O 1758 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 9939 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3299 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 17, 'TRANS': 428} Chain: "B" Number of atoms: 3299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3299 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 17, 'TRANS': 428} Chain: "C" Number of atoms: 3299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3299 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 17, 'TRANS': 428} Chain: "A" 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: "B" 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: 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 Time building chain proxies: 5.78, per 1000 atoms: 0.58 Number of scatterers: 9939 At special positions: 0 Unit cell: (118.374, 119.46, 116.202, 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 48 16.00 O 1758 8.00 N 1650 7.00 C 6483 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 601 " - " ASN A 163 " " NAG B 601 " - " ASN B 163 " " NAG C 601 " - " ASN C 163 " Time building additional restraints: 2.34 Conformation dependent library (CDL) restraints added in 1.1 seconds 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2418 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 3 sheets defined 75.6% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 44 through 52 Processing helix chain 'A' and resid 52 through 75 removed outlier: 3.613A pdb=" N VAL A 59 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 63 " --> pdb=" O VAL A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 102 Proline residue: A 83 - end of helix removed outlier: 4.183A pdb=" N SER A 87 " --> pdb=" O PRO A 83 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ALA A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE A 89 " --> pdb=" O ARG A 85 " (cutoff:3.500A) Proline residue: A 92 - end of helix removed outlier: 4.090A pdb=" N LEU A 96 " --> pdb=" O PRO A 92 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N MET A 102 " --> pdb=" O ARG A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 116 removed outlier: 3.820A pdb=" N VAL A 109 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N CYS A 110 " --> pdb=" O PRO A 106 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 112 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ILE A 113 " --> pdb=" O VAL A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 152 removed outlier: 3.625A pdb=" N TRP A 130 " --> pdb=" O ARG A 126 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY A 148 " --> pdb=" O ALA A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 169 removed outlier: 3.516A pdb=" N ALA A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ALA A 169 " --> pdb=" O SER A 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 164 through 169' Processing helix chain 'A' and resid 179 through 191 removed outlier: 3.768A pdb=" N PHE A 184 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA A 188 " --> pdb=" O PHE A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 201 removed outlier: 3.746A pdb=" N PHE A 201 " --> pdb=" O SER A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 248 removed outlier: 3.586A pdb=" N PHE A 237 " --> pdb=" O GLY A 233 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A 240 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A 245 " --> pdb=" O PHE A 241 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG A 246 " --> pdb=" O GLY A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 251 No H-bonds generated for 'chain 'A' and resid 249 through 251' Processing helix chain 'A' and resid 252 through 292 removed outlier: 3.596A pdb=" N ARG A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N THR A 266 " --> pdb=" O PHE A 262 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TRP A 272 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N TRP A 275 " --> pdb=" O SER A 271 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYR A 276 " --> pdb=" O TRP A 272 " (cutoff:3.500A) Proline residue: A 278 - end of helix removed outlier: 3.795A pdb=" N MET A 282 " --> pdb=" O PRO A 278 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE A 283 " --> pdb=" O VAL A 279 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA A 286 " --> pdb=" O MET A 282 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 316 removed outlier: 3.597A pdb=" N ILE A 306 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 311 " --> pdb=" O LEU A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 330 Processing helix chain 'A' and resid 332 through 339 removed outlier: 3.718A pdb=" N PHE A 336 " --> pdb=" O ASN A 332 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY A 339 " --> pdb=" O ARG A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 351 removed outlier: 3.610A pdb=" N LEU A 344 " --> pdb=" O ILE A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 355 No H-bonds generated for 'chain 'A' and resid 353 through 355' Processing helix chain 'A' and resid 356 through 368 removed outlier: 3.678A pdb=" N GLU A 365 " --> pdb=" O MET A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 382 removed outlier: 3.660A pdb=" N PHE A 377 " --> pdb=" O HIS A 373 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE A 378 " --> pdb=" O ILE A 374 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU A 379 " --> pdb=" O SER A 375 " (cutoff:3.500A) Proline residue: A 380 - end of helix Processing helix chain 'A' and resid 387 through 404 removed outlier: 3.532A pdb=" N VAL A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA A 398 " --> pdb=" O GLN A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 425 removed outlier: 3.703A pdb=" N ILE A 415 " --> pdb=" O PHE A 411 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR A 416 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA A 421 " --> pdb=" O ILE A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 438 Processing helix chain 'A' and resid 439 through 445 removed outlier: 3.609A pdb=" N ALA A 445 " --> pdb=" O ILE A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 483 removed outlier: 3.506A pdb=" N VAL A 463 " --> pdb=" O VAL A 459 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG A 465 " --> pdb=" O TRP A 461 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL A 469 " --> pdb=" O ARG A 465 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ASP A 475 " --> pdb=" O ASN A 471 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ALA A 476 " --> pdb=" O VAL A 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 52 Processing helix chain 'B' and resid 52 through 75 removed outlier: 3.612A pdb=" N VAL B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL B 63 " --> pdb=" O VAL B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 102 Proline residue: B 83 - end of helix removed outlier: 4.183A pdb=" N SER B 87 " --> pdb=" O PRO B 83 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ALA B 88 " --> pdb=" O GLU B 84 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE B 89 " --> pdb=" O ARG B 85 " (cutoff:3.500A) Proline residue: B 92 - end of helix removed outlier: 4.090A pdb=" N LEU B 96 " --> pdb=" O PRO B 92 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG B 101 " --> pdb=" O LEU B 97 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N MET B 102 " --> pdb=" O ARG B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 116 removed outlier: 3.821A pdb=" N VAL B 109 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N CYS B 110 " --> pdb=" O PRO B 106 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU B 112 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ILE B 113 " --> pdb=" O VAL B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 152 removed outlier: 3.626A pdb=" N TRP B 130 " --> pdb=" O ARG B 126 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU B 136 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 169 removed outlier: 3.516A pdb=" N ALA B 168 " --> pdb=" O ALA B 164 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ALA B 169 " --> pdb=" O SER B 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 164 through 169' Processing helix chain 'B' and resid 179 through 191 removed outlier: 3.767A pdb=" N PHE B 184 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA B 188 " --> pdb=" O PHE B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 201 removed outlier: 3.746A pdb=" N PHE B 201 " --> pdb=" O SER B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 248 removed outlier: 3.586A pdb=" N PHE B 237 " --> pdb=" O GLY B 233 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU B 245 " --> pdb=" O PHE B 241 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG B 246 " --> pdb=" O GLY B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 251 No H-bonds generated for 'chain 'B' and resid 249 through 251' Processing helix chain 'B' and resid 252 through 292 removed outlier: 3.596A pdb=" N ARG B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N THR B 266 " --> pdb=" O PHE B 262 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TRP B 272 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE B 273 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N TRP B 275 " --> pdb=" O SER B 271 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYR B 276 " --> pdb=" O TRP B 272 " (cutoff:3.500A) Proline residue: B 278 - end of helix removed outlier: 3.795A pdb=" N MET B 282 " --> pdb=" O PRO B 278 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE B 283 " --> pdb=" O VAL B 279 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA B 286 " --> pdb=" O MET B 282 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL B 290 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 316 removed outlier: 3.598A pdb=" N ILE B 306 " --> pdb=" O LEU B 302 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU B 311 " --> pdb=" O LEU B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 330 Processing helix chain 'B' and resid 332 through 339 removed outlier: 3.718A pdb=" N PHE B 336 " --> pdb=" O ASN B 332 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY B 339 " --> pdb=" O ARG B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 351 removed outlier: 3.610A pdb=" N LEU B 344 " --> pdb=" O ILE B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 355 No H-bonds generated for 'chain 'B' and resid 353 through 355' Processing helix chain 'B' and resid 356 through 368 removed outlier: 3.679A pdb=" N GLU B 365 " --> pdb=" O MET B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 382 removed outlier: 3.659A pdb=" N PHE B 377 " --> pdb=" O HIS B 373 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU B 379 " --> pdb=" O SER B 375 " (cutoff:3.500A) Proline residue: B 380 - end of helix Processing helix chain 'B' and resid 387 through 404 removed outlier: 3.532A pdb=" N VAL B 396 " --> pdb=" O LEU B 392 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA B 398 " --> pdb=" O GLN B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 425 removed outlier: 3.703A pdb=" N ILE B 415 " --> pdb=" O PHE B 411 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR B 416 " --> pdb=" O VAL B 412 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA B 421 " --> pdb=" O ILE B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 438 Processing helix chain 'B' and resid 439 through 445 removed outlier: 3.609A pdb=" N ALA B 445 " --> pdb=" O ILE B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 483 removed outlier: 3.507A pdb=" N VAL B 463 " --> pdb=" O VAL B 459 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ARG B 465 " --> pdb=" O TRP B 461 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL B 469 " --> pdb=" O ARG B 465 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY B 474 " --> pdb=" O LEU B 470 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ASP B 475 " --> pdb=" O ASN B 471 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ALA B 476 " --> pdb=" O VAL B 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 52 Processing helix chain 'C' and resid 52 through 75 removed outlier: 3.613A pdb=" N VAL C 59 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL C 63 " --> pdb=" O VAL C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 102 Proline residue: C 83 - end of helix removed outlier: 4.183A pdb=" N SER C 87 " --> pdb=" O PRO C 83 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ALA C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE C 89 " --> pdb=" O ARG C 85 " (cutoff:3.500A) Proline residue: C 92 - end of helix removed outlier: 4.090A pdb=" N LEU C 96 " --> pdb=" O PRO C 92 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG C 101 " --> pdb=" O LEU C 97 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N MET C 102 " --> pdb=" O ARG C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 116 removed outlier: 3.820A pdb=" N VAL C 109 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N CYS C 110 " --> pdb=" O PRO C 106 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU C 112 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ILE C 113 " --> pdb=" O VAL C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 152 removed outlier: 3.625A pdb=" N TRP C 130 " --> pdb=" O ARG C 126 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU C 136 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY C 148 " --> pdb=" O ALA C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 169 removed outlier: 3.516A pdb=" N ALA C 168 " --> pdb=" O ALA C 164 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ALA C 169 " --> pdb=" O SER C 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 164 through 169' Processing helix chain 'C' and resid 179 through 191 removed outlier: 3.769A pdb=" N PHE C 184 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA C 188 " --> pdb=" O PHE C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 201 removed outlier: 3.746A pdb=" N PHE C 201 " --> pdb=" O SER C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 248 removed outlier: 3.585A pdb=" N PHE C 237 " --> pdb=" O GLY C 233 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL C 240 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU C 245 " --> pdb=" O PHE C 241 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG C 246 " --> pdb=" O GLY C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 252 through 292 removed outlier: 3.596A pdb=" N ARG C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N THR C 266 " --> pdb=" O PHE C 262 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TRP C 272 " --> pdb=" O VAL C 268 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE C 273 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N TRP C 275 " --> pdb=" O SER C 271 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYR C 276 " --> pdb=" O TRP C 272 " (cutoff:3.500A) Proline residue: C 278 - end of helix removed outlier: 3.794A pdb=" N MET C 282 " --> pdb=" O PRO C 278 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE C 283 " --> pdb=" O VAL C 279 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA C 286 " --> pdb=" O MET C 282 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL C 290 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET C 292 " --> pdb=" O LYS C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 316 removed outlier: 3.597A pdb=" N ILE C 306 " --> pdb=" O LEU C 302 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU C 311 " --> pdb=" O LEU C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 330 Processing helix chain 'C' and resid 332 through 339 removed outlier: 3.717A pdb=" N PHE C 336 " --> pdb=" O ASN C 332 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY C 339 " --> pdb=" O ARG C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 351 removed outlier: 3.611A pdb=" N LEU C 344 " --> pdb=" O ILE C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 355 No H-bonds generated for 'chain 'C' and resid 353 through 355' Processing helix chain 'C' and resid 356 through 368 removed outlier: 3.679A pdb=" N GLU C 365 " --> pdb=" O MET C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 382 removed outlier: 3.659A pdb=" N PHE C 377 " --> pdb=" O HIS C 373 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE C 378 " --> pdb=" O ILE C 374 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU C 379 " --> pdb=" O SER C 375 " (cutoff:3.500A) Proline residue: C 380 - end of helix Processing helix chain 'C' and resid 387 through 404 removed outlier: 3.532A pdb=" N VAL C 396 " --> pdb=" O LEU C 392 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA C 398 " --> pdb=" O GLN C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 425 removed outlier: 3.703A pdb=" N ILE C 415 " --> pdb=" O PHE C 411 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR C 416 " --> pdb=" O VAL C 412 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA C 421 " --> pdb=" O ILE C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 438 Processing helix chain 'C' and resid 439 through 445 removed outlier: 3.609A pdb=" N ALA C 445 " --> pdb=" O ILE C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 483 removed outlier: 3.507A pdb=" N VAL C 463 " --> pdb=" O VAL C 459 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG C 465 " --> pdb=" O TRP C 461 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL C 469 " --> pdb=" O ARG C 465 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY C 474 " --> pdb=" O LEU C 470 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ASP C 475 " --> pdb=" O ASN C 471 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA C 476 " --> pdb=" O VAL C 472 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 212 removed outlier: 4.634A pdb=" N ARG A 211 " --> pdb=" O VAL A 218 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N VAL A 218 " --> pdb=" O ARG A 211 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 207 through 212 removed outlier: 4.634A pdb=" N ARG B 211 " --> pdb=" O VAL B 218 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N VAL B 218 " --> pdb=" O ARG B 211 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 207 through 212 removed outlier: 4.635A pdb=" N ARG C 211 " --> pdb=" O VAL C 218 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N VAL C 218 " --> pdb=" O ARG C 211 " (cutoff:3.500A) 549 hydrogen bonds defined for protein. 1629 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: 2.52 Time building geometry restraints manager: 2.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3105 1.34 - 1.45: 1342 1.45 - 1.57: 5594 1.57 - 1.69: 0 1.69 - 1.80: 75 Bond restraints: 10116 Sorted by residual: bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.29e+00 bond pdb=" C1 NAG B 601 " pdb=" O5 NAG B 601 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.05e+00 bond pdb=" C1 NAG C 601 " pdb=" O5 NAG C 601 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.87e+00 bond pdb=" N ASN B 447 " pdb=" CA ASN B 447 " ideal model delta sigma weight residual 1.457 1.479 -0.021 1.29e-02 6.01e+03 2.72e+00 bond pdb=" N ASN C 447 " pdb=" CA ASN C 447 " ideal model delta sigma weight residual 1.457 1.478 -0.021 1.29e-02 6.01e+03 2.61e+00 ... (remaining 10111 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 13153 2.25 - 4.50: 483 4.50 - 6.74: 79 6.74 - 8.99: 67 8.99 - 11.24: 6 Bond angle restraints: 13788 Sorted by residual: angle pdb=" N VAL A 459 " pdb=" CA VAL A 459 " pdb=" C VAL A 459 " ideal model delta sigma weight residual 113.20 106.15 7.05 9.60e-01 1.09e+00 5.39e+01 angle pdb=" N VAL C 459 " pdb=" CA VAL C 459 " pdb=" C VAL C 459 " ideal model delta sigma weight residual 113.20 106.17 7.03 9.60e-01 1.09e+00 5.36e+01 angle pdb=" N VAL B 459 " pdb=" CA VAL B 459 " pdb=" C VAL B 459 " ideal model delta sigma weight residual 113.20 106.18 7.02 9.60e-01 1.09e+00 5.34e+01 angle pdb=" C VAL C 446 " pdb=" N ASN C 447 " pdb=" CA ASN C 447 " ideal model delta sigma weight residual 121.54 129.83 -8.29 1.91e+00 2.74e-01 1.88e+01 angle pdb=" C VAL A 446 " pdb=" N ASN A 447 " pdb=" CA ASN A 447 " ideal model delta sigma weight residual 121.54 129.83 -8.29 1.91e+00 2.74e-01 1.88e+01 ... (remaining 13783 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.85: 5561 13.85 - 27.70: 316 27.70 - 41.55: 107 41.55 - 55.39: 2 55.39 - 69.24: 8 Dihedral angle restraints: 5994 sinusoidal: 2220 harmonic: 3774 Sorted by residual: dihedral pdb=" CA SER B 405 " pdb=" C SER B 405 " pdb=" N GLN B 406 " pdb=" CA GLN B 406 " ideal model delta harmonic sigma weight residual 180.00 158.28 21.72 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA SER A 405 " pdb=" C SER A 405 " pdb=" N GLN A 406 " pdb=" CA GLN A 406 " ideal model delta harmonic sigma weight residual 180.00 158.36 21.64 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA SER C 405 " pdb=" C SER C 405 " pdb=" N GLN C 406 " pdb=" CA GLN C 406 " ideal model delta harmonic sigma weight residual 180.00 158.36 21.64 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 5991 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 1550 0.091 - 0.183: 157 0.183 - 0.274: 15 0.274 - 0.366: 5 0.366 - 0.457: 1 Chirality restraints: 1728 Sorted by residual: chirality pdb=" C1 NAG A 601 " pdb=" ND2 ASN A 163 " pdb=" C2 NAG A 601 " pdb=" O5 NAG A 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.23e+00 chirality pdb=" C1 NAG C 601 " pdb=" ND2 ASN C 163 " pdb=" C2 NAG C 601 " pdb=" O5 NAG C 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" C1 NAG B 601 " pdb=" ND2 ASN B 163 " pdb=" C2 NAG B 601 " pdb=" O5 NAG B 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.15e+00 ... (remaining 1725 not shown) Planarity restraints: 1722 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 379 " 0.033 5.00e-02 4.00e+02 4.85e-02 3.77e+00 pdb=" N PRO B 380 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 380 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 380 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 379 " -0.033 5.00e-02 4.00e+02 4.85e-02 3.76e+00 pdb=" N PRO A 380 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 380 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 380 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 379 " 0.033 5.00e-02 4.00e+02 4.85e-02 3.76e+00 pdb=" N PRO C 380 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO C 380 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 380 " 0.028 5.00e-02 4.00e+02 ... (remaining 1719 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.93: 3940 2.93 - 3.42: 10539 3.42 - 3.92: 15276 3.92 - 4.41: 17280 4.41 - 4.90: 27912 Nonbonded interactions: 74947 Sorted by model distance: nonbonded pdb=" O TYR A 325 " pdb=" OG1 THR A 329 " model vdw 2.439 3.040 nonbonded pdb=" O TYR C 325 " pdb=" OG1 THR C 329 " model vdw 2.440 3.040 nonbonded pdb=" O TYR B 325 " pdb=" OG1 THR B 329 " model vdw 2.440 3.040 nonbonded pdb=" O PHE A 328 " pdb=" ND2 ASN A 484 " model vdw 2.500 3.120 nonbonded pdb=" O PHE B 328 " pdb=" ND2 ASN B 484 " model vdw 2.500 3.120 ... (remaining 74942 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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 group one per residue 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: 0.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 23.740 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 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 : 0.006 0.062 10119 Z= 0.265 Angle : 1.108 11.238 13797 Z= 0.538 Chirality : 0.061 0.457 1728 Planarity : 0.007 0.049 1719 Dihedral : 10.388 69.243 3576 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 0.00 % Allowed : 9.51 % Favored : 90.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.02 (0.14), residues: 1332 helix: -3.96 (0.08), residues: 867 sheet: None (None), residues: 0 loop : -3.67 (0.22), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 272 HIS 0.002 0.001 HIS B 452 PHE 0.016 0.002 PHE C 201 TYR 0.017 0.002 TYR B 485 ARG 0.002 0.000 ARG C 465 Details of bonding type rmsd link_NAG-ASN : bond 0.01083 ( 3) link_NAG-ASN : angle 5.73223 ( 9) hydrogen bonds : bond 0.31034 ( 549) hydrogen bonds : angle 9.49545 ( 1629) covalent geometry : bond 0.00609 (10116) covalent geometry : angle 1.09901 (13788) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 431 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 ARG cc_start: 0.7365 (mtm180) cc_final: 0.6902 (mmt180) REVERT: A 130 TRP cc_start: 0.7582 (m100) cc_final: 0.7230 (m100) REVERT: A 217 ARG cc_start: 0.6274 (ttt90) cc_final: 0.4543 (ptt90) REVERT: A 275 TRP cc_start: 0.8768 (m100) cc_final: 0.8444 (m-10) REVERT: A 282 MET cc_start: 0.8268 (ttt) cc_final: 0.8037 (ttm) REVERT: A 288 LYS cc_start: 0.8900 (tppt) cc_final: 0.8365 (tppp) REVERT: A 297 LEU cc_start: 0.8405 (tt) cc_final: 0.7209 (pp) REVERT: A 392 LEU cc_start: 0.9293 (tm) cc_final: 0.8944 (tp) REVERT: A 413 LYS cc_start: 0.9095 (mttt) cc_final: 0.8868 (mmmt) REVERT: B 130 TRP cc_start: 0.8149 (m100) cc_final: 0.7412 (m100) REVERT: B 145 LEU cc_start: 0.9377 (tp) cc_final: 0.9159 (tt) REVERT: B 182 ASP cc_start: 0.8576 (t0) cc_final: 0.8074 (t0) REVERT: B 282 MET cc_start: 0.8766 (ttt) cc_final: 0.8549 (ttm) REVERT: B 305 TYR cc_start: 0.8753 (t80) cc_final: 0.8546 (t80) REVERT: B 338 TRP cc_start: 0.8479 (t60) cc_final: 0.8055 (t60) REVERT: B 352 SER cc_start: 0.9287 (t) cc_final: 0.9037 (p) REVERT: B 363 CYS cc_start: 0.9028 (m) cc_final: 0.8658 (m) REVERT: B 365 GLU cc_start: 0.8614 (tt0) cc_final: 0.8330 (tp30) REVERT: B 388 ASP cc_start: 0.9182 (p0) cc_final: 0.8930 (p0) REVERT: B 464 ASP cc_start: 0.9257 (t70) cc_final: 0.9056 (t70) REVERT: B 473 GLU cc_start: 0.8921 (tm-30) cc_final: 0.8568 (tm-30) REVERT: C 50 ARG cc_start: 0.8416 (mmm160) cc_final: 0.8210 (tpt170) REVERT: C 263 ASN cc_start: 0.9201 (t0) cc_final: 0.9000 (t0) REVERT: C 264 GLU cc_start: 0.8802 (tp30) cc_final: 0.8599 (tp30) REVERT: C 275 TRP cc_start: 0.8661 (m100) cc_final: 0.7889 (m-10) REVERT: C 363 CYS cc_start: 0.8939 (m) cc_final: 0.8675 (m) REVERT: C 451 ASP cc_start: 0.5694 (t0) cc_final: 0.5303 (t0) REVERT: C 473 GLU cc_start: 0.8534 (tm-30) cc_final: 0.8258 (tm-30) outliers start: 0 outliers final: 0 residues processed: 431 average time/residue: 0.2208 time to fit residues: 132.6945 Evaluate side-chains 270 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 0.8980 chunk 100 optimal weight: 0.2980 chunk 55 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 103 optimal weight: 0.2980 chunk 40 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 119 optimal weight: 0.0970 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 ASN ** B 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 483 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.105620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.083337 restraints weight = 23733.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.085985 restraints weight = 11748.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.087740 restraints weight = 7546.872| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10119 Z= 0.146 Angle : 0.764 9.704 13797 Z= 0.368 Chirality : 0.044 0.280 1728 Planarity : 0.005 0.037 1719 Dihedral : 5.490 58.350 1476 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 4.51 % Allowed : 19.60 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.24 (0.19), residues: 1332 helix: -1.48 (0.14), residues: 900 sheet: None (None), residues: 0 loop : -3.44 (0.24), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 461 HIS 0.009 0.001 HIS B 316 PHE 0.028 0.001 PHE C 192 TYR 0.024 0.002 TYR A 485 ARG 0.006 0.000 ARG A 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00663 ( 3) link_NAG-ASN : angle 3.34949 ( 9) hydrogen bonds : bond 0.05427 ( 549) hydrogen bonds : angle 5.08427 ( 1629) covalent geometry : bond 0.00307 (10116) covalent geometry : angle 0.75961 (13788) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 301 time to evaluate : 1.174 Fit side-chains revert: symmetry clash REVERT: A 85 ARG cc_start: 0.7659 (mtm180) cc_final: 0.6783 (mmt180) REVERT: A 120 ASP cc_start: 0.9035 (t0) cc_final: 0.8802 (t0) REVERT: A 130 TRP cc_start: 0.7747 (m100) cc_final: 0.7382 (m100) REVERT: A 132 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8621 (tm) REVERT: A 217 ARG cc_start: 0.5756 (ttt90) cc_final: 0.4187 (ptt90) REVERT: A 256 ILE cc_start: 0.9316 (OUTLIER) cc_final: 0.9074 (pt) REVERT: A 284 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8708 (mt) REVERT: A 304 LYS cc_start: 0.9296 (tppp) cc_final: 0.9071 (tttm) REVERT: A 310 LEU cc_start: 0.8969 (mt) cc_final: 0.8571 (mt) REVERT: A 311 LEU cc_start: 0.9381 (tp) cc_final: 0.9176 (tt) REVERT: A 413 LYS cc_start: 0.9230 (mttt) cc_final: 0.8837 (mmmt) REVERT: A 464 ASP cc_start: 0.8936 (t70) cc_final: 0.8655 (t70) REVERT: B 154 GLN cc_start: 0.9194 (mm-40) cc_final: 0.8889 (mm110) REVERT: B 179 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8272 (mp0) REVERT: B 182 ASP cc_start: 0.8755 (t0) cc_final: 0.8321 (t0) REVERT: B 282 MET cc_start: 0.8899 (ttt) cc_final: 0.8645 (ttm) REVERT: B 338 TRP cc_start: 0.8647 (t60) cc_final: 0.8158 (t60) REVERT: B 352 SER cc_start: 0.9316 (t) cc_final: 0.8921 (p) REVERT: B 363 CYS cc_start: 0.9088 (m) cc_final: 0.8538 (m) REVERT: B 387 MET cc_start: 0.7667 (mmm) cc_final: 0.7433 (mmm) REVERT: B 473 GLU cc_start: 0.8724 (tm-30) cc_final: 0.8426 (tm-30) REVERT: B 477 LEU cc_start: 0.9607 (mt) cc_final: 0.9313 (mp) REVERT: C 50 ARG cc_start: 0.8845 (mmm160) cc_final: 0.8520 (mtm-85) REVERT: C 182 ASP cc_start: 0.8718 (t0) cc_final: 0.8059 (t0) REVERT: C 264 GLU cc_start: 0.8777 (tp30) cc_final: 0.8457 (tp30) REVERT: C 275 TRP cc_start: 0.8776 (m100) cc_final: 0.7836 (m-10) REVERT: C 282 MET cc_start: 0.9044 (tpt) cc_final: 0.8765 (tpt) REVERT: C 338 TRP cc_start: 0.8870 (t60) cc_final: 0.8635 (t-100) REVERT: C 363 CYS cc_start: 0.8884 (m) cc_final: 0.8413 (m) REVERT: C 451 ASP cc_start: 0.5679 (t0) cc_final: 0.5377 (t0) REVERT: C 473 GLU cc_start: 0.8745 (tm-30) cc_final: 0.8479 (tm-30) outliers start: 47 outliers final: 22 residues processed: 331 average time/residue: 0.2196 time to fit residues: 104.1116 Evaluate side-chains 274 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 249 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 342 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 61 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 54 optimal weight: 0.8980 chunk 56 optimal weight: 0.4980 chunk 12 optimal weight: 0.0770 chunk 69 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 overall best weight: 1.0540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN A 212 ASN ** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 GLN ** B 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 GLN C 212 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.102348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.080819 restraints weight = 24142.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.083377 restraints weight = 11985.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.085074 restraints weight = 7725.812| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.4302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10119 Z= 0.152 Angle : 0.735 10.995 13797 Z= 0.348 Chirality : 0.043 0.302 1728 Planarity : 0.004 0.029 1719 Dihedral : 4.929 50.837 1476 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 6.63 % Allowed : 20.37 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.21), residues: 1332 helix: -0.23 (0.16), residues: 918 sheet: None (None), residues: 0 loop : -3.12 (0.26), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 461 HIS 0.006 0.001 HIS B 316 PHE 0.032 0.001 PHE C 192 TYR 0.027 0.002 TYR A 485 ARG 0.004 0.000 ARG B 189 Details of bonding type rmsd link_NAG-ASN : bond 0.00540 ( 3) link_NAG-ASN : angle 3.09820 ( 9) hydrogen bonds : bond 0.04821 ( 549) hydrogen bonds : angle 4.68982 ( 1629) covalent geometry : bond 0.00346 (10116) covalent geometry : angle 0.73117 (13788) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 273 time to evaluate : 1.062 Fit side-chains revert: symmetry clash REVERT: A 120 ASP cc_start: 0.9107 (t0) cc_final: 0.8813 (t0) REVERT: A 130 TRP cc_start: 0.7968 (m100) cc_final: 0.7448 (m100) REVERT: A 179 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7699 (mp0) REVERT: A 217 ARG cc_start: 0.5787 (ttt90) cc_final: 0.4126 (ptt90) REVERT: A 274 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.8541 (mtt) REVERT: A 302 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8957 (pp) REVERT: A 413 LYS cc_start: 0.9242 (mttt) cc_final: 0.8857 (mmmt) REVERT: A 464 ASP cc_start: 0.8940 (t70) cc_final: 0.8486 (t70) REVERT: B 130 TRP cc_start: 0.7980 (m100) cc_final: 0.7041 (m100) REVERT: B 154 GLN cc_start: 0.9277 (mm-40) cc_final: 0.9046 (mm110) REVERT: B 179 GLU cc_start: 0.8425 (mm-30) cc_final: 0.7962 (mp0) REVERT: B 208 TYR cc_start: 0.7140 (m-80) cc_final: 0.6614 (m-80) REVERT: B 282 MET cc_start: 0.8948 (ttt) cc_final: 0.8718 (ttm) REVERT: B 338 TRP cc_start: 0.8604 (t60) cc_final: 0.8171 (t60) REVERT: B 352 SER cc_start: 0.9310 (t) cc_final: 0.9082 (t) REVERT: B 363 CYS cc_start: 0.9006 (m) cc_final: 0.8545 (m) REVERT: B 387 MET cc_start: 0.7836 (mmm) cc_final: 0.7513 (mmm) REVERT: B 473 GLU cc_start: 0.8841 (tm-30) cc_final: 0.8500 (tm-30) REVERT: C 50 ARG cc_start: 0.8789 (mmm160) cc_final: 0.8562 (mmm-85) REVERT: C 149 LEU cc_start: 0.9200 (tp) cc_final: 0.8902 (tt) REVERT: C 275 TRP cc_start: 0.8700 (m100) cc_final: 0.8448 (m-10) REVERT: C 282 MET cc_start: 0.9209 (tpt) cc_final: 0.8781 (tpp) REVERT: C 360 MET cc_start: 0.9441 (mmm) cc_final: 0.9039 (tpp) REVERT: C 363 CYS cc_start: 0.8949 (m) cc_final: 0.8599 (m) REVERT: C 403 GLN cc_start: 0.8507 (tp40) cc_final: 0.8177 (mt0) REVERT: C 451 ASP cc_start: 0.5836 (t0) cc_final: 0.5572 (t0) outliers start: 69 outliers final: 29 residues processed: 319 average time/residue: 0.1883 time to fit residues: 86.2542 Evaluate side-chains 270 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 239 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 467 CYS Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 362 LYS Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 351 SER Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 437 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 62 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 121 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 117 optimal weight: 0.9990 chunk 5 optimal weight: 0.0980 chunk 11 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 GLN ** B 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 GLN ** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.101986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.079449 restraints weight = 23802.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.082013 restraints weight = 12329.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.083727 restraints weight = 8137.055| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.4776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10119 Z= 0.129 Angle : 0.750 11.262 13797 Z= 0.341 Chirality : 0.042 0.285 1728 Planarity : 0.004 0.029 1719 Dihedral : 4.561 50.863 1476 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 6.24 % Allowed : 22.67 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.23), residues: 1332 helix: 0.66 (0.18), residues: 885 sheet: None (None), residues: 0 loop : -3.06 (0.25), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 461 HIS 0.003 0.001 HIS B 316 PHE 0.033 0.001 PHE C 192 TYR 0.026 0.002 TYR A 485 ARG 0.003 0.000 ARG A 376 Details of bonding type rmsd link_NAG-ASN : bond 0.00521 ( 3) link_NAG-ASN : angle 2.77014 ( 9) hydrogen bonds : bond 0.04109 ( 549) hydrogen bonds : angle 4.51821 ( 1629) covalent geometry : bond 0.00286 (10116) covalent geometry : angle 0.74728 (13788) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 281 time to evaluate : 1.028 Fit side-chains revert: symmetry clash REVERT: A 52 ASN cc_start: 0.8311 (m-40) cc_final: 0.8034 (m-40) REVERT: A 120 ASP cc_start: 0.9130 (t0) cc_final: 0.8819 (t0) REVERT: A 130 TRP cc_start: 0.8040 (m100) cc_final: 0.7527 (m-10) REVERT: A 179 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7734 (mp0) REVERT: A 217 ARG cc_start: 0.5617 (ttt90) cc_final: 0.4025 (ptt90) REVERT: A 282 MET cc_start: 0.8406 (ttm) cc_final: 0.7671 (tmm) REVERT: A 302 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8995 (pp) REVERT: A 413 LYS cc_start: 0.9204 (mttt) cc_final: 0.8817 (mmmt) REVERT: A 464 ASP cc_start: 0.9039 (t70) cc_final: 0.8525 (t70) REVERT: B 130 TRP cc_start: 0.7888 (m100) cc_final: 0.6945 (m100) REVERT: B 154 GLN cc_start: 0.9275 (mm-40) cc_final: 0.8943 (mm-40) REVERT: B 179 GLU cc_start: 0.8334 (mm-30) cc_final: 0.7883 (mp0) REVERT: B 208 TYR cc_start: 0.6951 (m-80) cc_final: 0.6375 (m-80) REVERT: B 282 MET cc_start: 0.8956 (ttt) cc_final: 0.8664 (ttm) REVERT: B 338 TRP cc_start: 0.8411 (t60) cc_final: 0.8085 (t60) REVERT: B 352 SER cc_start: 0.9204 (t) cc_final: 0.8967 (t) REVERT: B 363 CYS cc_start: 0.9080 (m) cc_final: 0.8675 (m) REVERT: B 473 GLU cc_start: 0.8830 (tm-30) cc_final: 0.8452 (tm-30) REVERT: C 50 ARG cc_start: 0.8886 (mmm160) cc_final: 0.8535 (mmm-85) REVERT: C 149 LEU cc_start: 0.9144 (tp) cc_final: 0.8876 (tt) REVERT: C 182 ASP cc_start: 0.8609 (t0) cc_final: 0.8369 (t0) REVERT: C 275 TRP cc_start: 0.8651 (m100) cc_final: 0.8359 (m-10) REVERT: C 282 MET cc_start: 0.9234 (tpt) cc_final: 0.8779 (tpp) REVERT: C 284 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9079 (mm) REVERT: C 311 LEU cc_start: 0.9501 (tt) cc_final: 0.9291 (tt) REVERT: C 360 MET cc_start: 0.9411 (mmm) cc_final: 0.9093 (tpp) REVERT: C 363 CYS cc_start: 0.8923 (m) cc_final: 0.8583 (m) REVERT: C 372 LYS cc_start: 0.8928 (mtmm) cc_final: 0.8665 (mtmm) REVERT: C 403 GLN cc_start: 0.8450 (tp40) cc_final: 0.8028 (mt0) outliers start: 65 outliers final: 40 residues processed: 319 average time/residue: 0.1807 time to fit residues: 83.5601 Evaluate side-chains 294 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 252 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 467 CYS Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain B residue 362 LYS Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 328 PHE Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 351 SER Chi-restraints excluded: chain C residue 401 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 44 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 103 optimal weight: 0.6980 chunk 120 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 85 optimal weight: 0.0070 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.102416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.080112 restraints weight = 23802.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.082691 restraints weight = 12386.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.084400 restraints weight = 8166.559| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.5031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10119 Z= 0.128 Angle : 0.732 11.056 13797 Z= 0.334 Chirality : 0.041 0.273 1728 Planarity : 0.003 0.027 1719 Dihedral : 4.421 51.271 1476 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 6.44 % Allowed : 24.50 % Favored : 69.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.23), residues: 1332 helix: 1.06 (0.18), residues: 879 sheet: None (None), residues: 0 loop : -2.93 (0.25), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 461 HIS 0.002 0.001 HIS B 316 PHE 0.031 0.001 PHE C 192 TYR 0.024 0.002 TYR C 485 ARG 0.003 0.000 ARG A 376 Details of bonding type rmsd link_NAG-ASN : bond 0.00525 ( 3) link_NAG-ASN : angle 2.64348 ( 9) hydrogen bonds : bond 0.03896 ( 549) hydrogen bonds : angle 4.41129 ( 1629) covalent geometry : bond 0.00290 (10116) covalent geometry : angle 0.72910 (13788) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 265 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ASN cc_start: 0.8362 (m-40) cc_final: 0.8110 (m-40) REVERT: A 120 ASP cc_start: 0.9103 (t70) cc_final: 0.8785 (t0) REVERT: A 179 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7669 (mp0) REVERT: A 217 ARG cc_start: 0.5675 (ttt90) cc_final: 0.3978 (ptt90) REVERT: A 247 LYS cc_start: 0.9064 (tppt) cc_final: 0.8394 (tmtt) REVERT: A 282 MET cc_start: 0.8453 (ttm) cc_final: 0.7736 (tmm) REVERT: A 413 LYS cc_start: 0.9220 (mttt) cc_final: 0.8815 (mmmt) REVERT: A 464 ASP cc_start: 0.8977 (t70) cc_final: 0.8442 (t70) REVERT: B 130 TRP cc_start: 0.7853 (m100) cc_final: 0.6892 (m100) REVERT: B 141 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8679 (tt) REVERT: B 154 GLN cc_start: 0.9245 (mm-40) cc_final: 0.8944 (mm-40) REVERT: B 179 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7840 (mp0) REVERT: B 182 ASP cc_start: 0.8858 (t0) cc_final: 0.8420 (t0) REVERT: B 208 TYR cc_start: 0.6965 (m-80) cc_final: 0.6422 (m-80) REVERT: B 352 SER cc_start: 0.9190 (t) cc_final: 0.8941 (t) REVERT: B 363 CYS cc_start: 0.9030 (m) cc_final: 0.8542 (m) REVERT: B 366 GLU cc_start: 0.8011 (tm-30) cc_final: 0.7529 (tm-30) REVERT: B 473 GLU cc_start: 0.8812 (tm-30) cc_final: 0.8479 (tm-30) REVERT: C 50 ARG cc_start: 0.8914 (mmm160) cc_final: 0.8567 (mmm-85) REVERT: C 149 LEU cc_start: 0.9142 (tp) cc_final: 0.8890 (tt) REVERT: C 209 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7914 (mt-10) REVERT: C 256 ILE cc_start: 0.9415 (tp) cc_final: 0.9194 (pt) REVERT: C 275 TRP cc_start: 0.8629 (m100) cc_final: 0.8356 (m-10) REVERT: C 284 LEU cc_start: 0.9432 (OUTLIER) cc_final: 0.9121 (mm) REVERT: C 360 MET cc_start: 0.9503 (mmm) cc_final: 0.9114 (tpp) REVERT: C 363 CYS cc_start: 0.8858 (m) cc_final: 0.8533 (m) REVERT: C 403 GLN cc_start: 0.8503 (tp40) cc_final: 0.8120 (mt0) REVERT: C 460 ASP cc_start: 0.9141 (p0) cc_final: 0.8521 (t0) outliers start: 67 outliers final: 44 residues processed: 303 average time/residue: 0.1919 time to fit residues: 84.0400 Evaluate side-chains 294 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 248 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 467 CYS Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain B residue 362 LYS Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 485 TYR Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 328 PHE Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 351 SER Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 467 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 100 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 11 optimal weight: 0.0670 chunk 59 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 68 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 34 optimal weight: 3.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 GLN ** B 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.104051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.082246 restraints weight = 24045.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.084806 restraints weight = 12023.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.086543 restraints weight = 7768.010| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.5250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10119 Z= 0.128 Angle : 0.736 10.487 13797 Z= 0.335 Chirality : 0.042 0.266 1728 Planarity : 0.003 0.027 1719 Dihedral : 4.355 51.383 1476 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 6.44 % Allowed : 26.03 % Favored : 67.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.23), residues: 1332 helix: 1.33 (0.18), residues: 879 sheet: None (None), residues: 0 loop : -2.66 (0.26), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 461 HIS 0.002 0.001 HIS B 316 PHE 0.031 0.001 PHE C 192 TYR 0.024 0.002 TYR C 485 ARG 0.002 0.000 ARG A 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00514 ( 3) link_NAG-ASN : angle 2.53400 ( 9) hydrogen bonds : bond 0.03788 ( 549) hydrogen bonds : angle 4.35676 ( 1629) covalent geometry : bond 0.00293 (10116) covalent geometry : angle 0.73385 (13788) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 271 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ASN cc_start: 0.8430 (m-40) cc_final: 0.8193 (m-40) REVERT: A 120 ASP cc_start: 0.9055 (t70) cc_final: 0.8708 (t0) REVERT: A 217 ARG cc_start: 0.5745 (ttt90) cc_final: 0.4018 (ptt90) REVERT: A 247 LYS cc_start: 0.9081 (tppt) cc_final: 0.8455 (tmtt) REVERT: A 282 MET cc_start: 0.8454 (ttm) cc_final: 0.8090 (ttp) REVERT: A 292 MET cc_start: 0.8325 (ptp) cc_final: 0.8052 (ptp) REVERT: A 413 LYS cc_start: 0.9245 (mttt) cc_final: 0.8821 (mmmt) REVERT: A 464 ASP cc_start: 0.8944 (t70) cc_final: 0.8420 (t70) REVERT: B 130 TRP cc_start: 0.7872 (m100) cc_final: 0.7049 (m100) REVERT: B 141 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8745 (tt) REVERT: B 154 GLN cc_start: 0.9234 (mm-40) cc_final: 0.8985 (mm-40) REVERT: B 179 GLU cc_start: 0.8293 (mm-30) cc_final: 0.7905 (mp0) REVERT: B 182 ASP cc_start: 0.8862 (t0) cc_final: 0.8425 (t0) REVERT: B 208 TYR cc_start: 0.7188 (m-80) cc_final: 0.6669 (m-80) REVERT: B 275 TRP cc_start: 0.8827 (m100) cc_final: 0.8203 (m-10) REVERT: B 282 MET cc_start: 0.8664 (ttm) cc_final: 0.8438 (ttm) REVERT: B 331 LYS cc_start: 0.8749 (tppt) cc_final: 0.8397 (ttpt) REVERT: B 352 SER cc_start: 0.9210 (t) cc_final: 0.8979 (t) REVERT: B 363 CYS cc_start: 0.8941 (m) cc_final: 0.8491 (m) REVERT: B 366 GLU cc_start: 0.7903 (tm-30) cc_final: 0.7511 (tm-30) REVERT: B 387 MET cc_start: 0.7518 (mmt) cc_final: 0.7142 (mmm) REVERT: B 473 GLU cc_start: 0.8799 (tm-30) cc_final: 0.8474 (tm-30) REVERT: C 50 ARG cc_start: 0.8892 (mmm160) cc_final: 0.8581 (mmm-85) REVERT: C 81 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8715 (tp) REVERT: C 149 LEU cc_start: 0.9217 (tp) cc_final: 0.8987 (tt) REVERT: C 179 GLU cc_start: 0.7925 (mp0) cc_final: 0.7180 (mp0) REVERT: C 209 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7911 (mt-10) REVERT: C 256 ILE cc_start: 0.9425 (tp) cc_final: 0.9216 (pt) REVERT: C 275 TRP cc_start: 0.8681 (m100) cc_final: 0.8388 (m-10) REVERT: C 284 LEU cc_start: 0.9513 (OUTLIER) cc_final: 0.9156 (mm) REVERT: C 363 CYS cc_start: 0.8819 (m) cc_final: 0.8552 (m) REVERT: C 403 GLN cc_start: 0.8478 (tp40) cc_final: 0.8165 (mt0) REVERT: C 460 ASP cc_start: 0.9061 (p0) cc_final: 0.8609 (t0) outliers start: 67 outliers final: 44 residues processed: 307 average time/residue: 0.1891 time to fit residues: 83.6580 Evaluate side-chains 290 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 243 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 CYS Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 467 CYS Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 328 PHE Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 485 TYR Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 328 PHE Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 467 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 62 optimal weight: 1.9990 chunk 88 optimal weight: 10.0000 chunk 128 optimal weight: 0.9980 chunk 72 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 110 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 61 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.102419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.079919 restraints weight = 24172.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.082497 restraints weight = 12503.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.084212 restraints weight = 8229.772| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.5425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10119 Z= 0.130 Angle : 0.748 10.156 13797 Z= 0.340 Chirality : 0.042 0.264 1728 Planarity : 0.003 0.025 1719 Dihedral : 4.326 51.541 1476 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 5.76 % Allowed : 27.86 % Favored : 66.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.24), residues: 1332 helix: 1.48 (0.18), residues: 879 sheet: None (None), residues: 0 loop : -2.60 (0.26), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 461 HIS 0.002 0.001 HIS B 316 PHE 0.046 0.001 PHE C 192 TYR 0.025 0.002 TYR C 485 ARG 0.002 0.000 ARG C 47 Details of bonding type rmsd link_NAG-ASN : bond 0.00509 ( 3) link_NAG-ASN : angle 2.48977 ( 9) hydrogen bonds : bond 0.03801 ( 549) hydrogen bonds : angle 4.37280 ( 1629) covalent geometry : bond 0.00300 (10116) covalent geometry : angle 0.74599 (13788) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 263 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ASN cc_start: 0.8408 (m-40) cc_final: 0.8139 (m-40) REVERT: A 102 MET cc_start: 0.8954 (tmm) cc_final: 0.8676 (ttm) REVERT: A 120 ASP cc_start: 0.9102 (t70) cc_final: 0.8758 (t0) REVERT: A 179 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7625 (mp0) REVERT: A 217 ARG cc_start: 0.5646 (ttt90) cc_final: 0.3971 (ptt90) REVERT: A 247 LYS cc_start: 0.9060 (tppt) cc_final: 0.8429 (tmtt) REVERT: A 282 MET cc_start: 0.8492 (ttm) cc_final: 0.8113 (ttp) REVERT: A 413 LYS cc_start: 0.9211 (mttt) cc_final: 0.8778 (mmmt) REVERT: A 464 ASP cc_start: 0.9020 (t70) cc_final: 0.8487 (t70) REVERT: B 130 TRP cc_start: 0.7826 (m100) cc_final: 0.7543 (m100) REVERT: B 141 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8697 (tt) REVERT: B 154 GLN cc_start: 0.9243 (mm-40) cc_final: 0.8998 (mm-40) REVERT: B 179 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7923 (mp0) REVERT: B 182 ASP cc_start: 0.8811 (t0) cc_final: 0.8356 (t0) REVERT: B 275 TRP cc_start: 0.8805 (m100) cc_final: 0.8141 (m-10) REVERT: B 282 MET cc_start: 0.8677 (ttm) cc_final: 0.8405 (ttm) REVERT: B 352 SER cc_start: 0.9139 (t) cc_final: 0.8889 (t) REVERT: B 363 CYS cc_start: 0.8986 (m) cc_final: 0.8498 (m) REVERT: B 366 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7672 (tm-30) REVERT: B 403 GLN cc_start: 0.8808 (mm-40) cc_final: 0.8573 (mm-40) REVERT: B 473 GLU cc_start: 0.8884 (tm-30) cc_final: 0.8684 (tm-30) REVERT: C 81 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8756 (tp) REVERT: C 145 LEU cc_start: 0.9141 (tt) cc_final: 0.8903 (tp) REVERT: C 179 GLU cc_start: 0.7893 (mp0) cc_final: 0.7093 (mp0) REVERT: C 209 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7969 (mt-10) REVERT: C 256 ILE cc_start: 0.9390 (tp) cc_final: 0.9186 (pt) REVERT: C 275 TRP cc_start: 0.8700 (m100) cc_final: 0.8383 (m-10) REVERT: C 284 LEU cc_start: 0.9457 (OUTLIER) cc_final: 0.9098 (mm) REVERT: C 363 CYS cc_start: 0.8838 (m) cc_final: 0.8513 (m) REVERT: C 387 MET cc_start: 0.8106 (mmp) cc_final: 0.7837 (mmm) REVERT: C 403 GLN cc_start: 0.8499 (tp40) cc_final: 0.8135 (mt0) outliers start: 60 outliers final: 44 residues processed: 295 average time/residue: 0.1944 time to fit residues: 84.1047 Evaluate side-chains 291 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 244 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 CYS Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 467 CYS Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 328 PHE Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 464 ASP Chi-restraints excluded: chain B residue 485 TYR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 328 PHE Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 467 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 8 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 40 optimal weight: 0.0870 chunk 88 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 128 optimal weight: 4.9990 chunk 127 optimal weight: 6.9990 chunk 130 optimal weight: 0.6980 chunk 24 optimal weight: 6.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 ASN A 483 GLN ** B 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.101500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.079462 restraints weight = 24118.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.082031 restraints weight = 12412.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.083745 restraints weight = 8104.296| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.5569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10119 Z= 0.130 Angle : 0.769 10.145 13797 Z= 0.348 Chirality : 0.042 0.256 1728 Planarity : 0.003 0.026 1719 Dihedral : 4.306 51.656 1476 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 5.76 % Allowed : 28.43 % Favored : 65.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.24), residues: 1332 helix: 1.54 (0.18), residues: 879 sheet: None (None), residues: 0 loop : -2.54 (0.26), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 461 HIS 0.003 0.001 HIS A 313 PHE 0.041 0.001 PHE C 192 TYR 0.024 0.002 TYR C 485 ARG 0.002 0.000 ARG A 47 Details of bonding type rmsd link_NAG-ASN : bond 0.00502 ( 3) link_NAG-ASN : angle 2.39076 ( 9) hydrogen bonds : bond 0.03775 ( 549) hydrogen bonds : angle 4.34085 ( 1629) covalent geometry : bond 0.00297 (10116) covalent geometry : angle 0.76671 (13788) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 252 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ASN cc_start: 0.8423 (m-40) cc_final: 0.8196 (m-40) REVERT: A 102 MET cc_start: 0.8919 (tmm) cc_final: 0.8717 (ttm) REVERT: A 120 ASP cc_start: 0.9097 (t70) cc_final: 0.8762 (t0) REVERT: A 179 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7611 (mp0) REVERT: A 184 PHE cc_start: 0.8090 (OUTLIER) cc_final: 0.7587 (t80) REVERT: A 217 ARG cc_start: 0.5580 (ttt90) cc_final: 0.3994 (ptt90) REVERT: A 247 LYS cc_start: 0.9058 (tppt) cc_final: 0.8409 (tmtt) REVERT: A 282 MET cc_start: 0.8494 (ttm) cc_final: 0.8124 (ttp) REVERT: A 362 LYS cc_start: 0.8703 (ttmt) cc_final: 0.8352 (ttpp) REVERT: A 413 LYS cc_start: 0.9207 (mttt) cc_final: 0.8776 (mmmt) REVERT: A 464 ASP cc_start: 0.9027 (t70) cc_final: 0.8418 (t70) REVERT: B 130 TRP cc_start: 0.7820 (m100) cc_final: 0.6982 (m100) REVERT: B 141 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8674 (tt) REVERT: B 154 GLN cc_start: 0.9244 (mm-40) cc_final: 0.8975 (mm-40) REVERT: B 179 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7895 (mp0) REVERT: B 182 ASP cc_start: 0.8766 (t0) cc_final: 0.8303 (t0) REVERT: B 275 TRP cc_start: 0.8780 (m100) cc_final: 0.8135 (m-10) REVERT: B 282 MET cc_start: 0.8656 (ttm) cc_final: 0.8405 (ttm) REVERT: B 352 SER cc_start: 0.9133 (t) cc_final: 0.8878 (t) REVERT: B 363 CYS cc_start: 0.8959 (m) cc_final: 0.8490 (m) REVERT: B 366 GLU cc_start: 0.7950 (tm-30) cc_final: 0.7728 (tm-30) REVERT: B 403 GLN cc_start: 0.8796 (mm-40) cc_final: 0.8568 (mm-40) REVERT: C 81 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8692 (tp) REVERT: C 145 LEU cc_start: 0.9104 (tt) cc_final: 0.8848 (tp) REVERT: C 179 GLU cc_start: 0.7886 (mp0) cc_final: 0.7059 (mp0) REVERT: C 275 TRP cc_start: 0.8764 (m100) cc_final: 0.8388 (m-10) REVERT: C 284 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9113 (mm) REVERT: C 360 MET cc_start: 0.9606 (mmm) cc_final: 0.9228 (tpp) REVERT: C 363 CYS cc_start: 0.8942 (m) cc_final: 0.8597 (m) REVERT: C 387 MET cc_start: 0.8109 (mmp) cc_final: 0.7867 (mmm) REVERT: C 403 GLN cc_start: 0.8464 (tp40) cc_final: 0.8112 (mt0) outliers start: 60 outliers final: 41 residues processed: 287 average time/residue: 0.1967 time to fit residues: 81.7940 Evaluate side-chains 290 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 245 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 CYS Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 467 CYS Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 328 PHE Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 464 ASP Chi-restraints excluded: chain B residue 485 TYR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 328 PHE Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 467 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 0.0060 chunk 34 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 126 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 33 optimal weight: 0.0770 chunk 14 optimal weight: 0.3980 chunk 29 optimal weight: 0.9980 overall best weight: 0.4954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.102602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.080667 restraints weight = 23770.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.083254 restraints weight = 12250.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.084971 restraints weight = 8005.705| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.5716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10119 Z= 0.129 Angle : 0.782 12.708 13797 Z= 0.352 Chirality : 0.043 0.247 1728 Planarity : 0.003 0.026 1719 Dihedral : 4.267 51.725 1476 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 4.90 % Allowed : 29.49 % Favored : 65.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.24), residues: 1332 helix: 1.57 (0.18), residues: 882 sheet: None (None), residues: 0 loop : -2.59 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 461 HIS 0.003 0.001 HIS A 313 PHE 0.040 0.001 PHE C 192 TYR 0.024 0.001 TYR C 485 ARG 0.002 0.000 ARG B 189 Details of bonding type rmsd link_NAG-ASN : bond 0.00497 ( 3) link_NAG-ASN : angle 2.27932 ( 9) hydrogen bonds : bond 0.03692 ( 549) hydrogen bonds : angle 4.35761 ( 1629) covalent geometry : bond 0.00291 (10116) covalent geometry : angle 0.77971 (13788) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 248 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ASP cc_start: 0.9140 (t70) cc_final: 0.8822 (t0) REVERT: A 184 PHE cc_start: 0.8119 (OUTLIER) cc_final: 0.7673 (t80) REVERT: A 217 ARG cc_start: 0.5592 (ttt90) cc_final: 0.4001 (ptt90) REVERT: A 247 LYS cc_start: 0.9040 (tppt) cc_final: 0.8387 (tmtt) REVERT: A 282 MET cc_start: 0.8510 (ttm) cc_final: 0.8130 (ttp) REVERT: A 301 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.7373 (ttp-110) REVERT: A 413 LYS cc_start: 0.9177 (mttt) cc_final: 0.8751 (mmmt) REVERT: A 464 ASP cc_start: 0.8980 (t70) cc_final: 0.8467 (t70) REVERT: B 130 TRP cc_start: 0.7857 (m100) cc_final: 0.7593 (m100) REVERT: B 141 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8643 (tt) REVERT: B 154 GLN cc_start: 0.9244 (mm-40) cc_final: 0.8984 (mm-40) REVERT: B 179 GLU cc_start: 0.8268 (mm-30) cc_final: 0.8024 (mp0) REVERT: B 182 ASP cc_start: 0.8762 (t0) cc_final: 0.8351 (t0) REVERT: B 275 TRP cc_start: 0.8666 (m100) cc_final: 0.8008 (m-10) REVERT: B 352 SER cc_start: 0.9123 (t) cc_final: 0.8874 (t) REVERT: B 366 GLU cc_start: 0.7919 (tm-30) cc_final: 0.7708 (tm-30) REVERT: B 403 GLN cc_start: 0.8783 (mm-40) cc_final: 0.8567 (mm-40) REVERT: B 473 GLU cc_start: 0.8841 (tm-30) cc_final: 0.8511 (tm-30) REVERT: C 81 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8709 (tp) REVERT: C 179 GLU cc_start: 0.7893 (mp0) cc_final: 0.7106 (mp0) REVERT: C 267 MET cc_start: 0.9244 (tpp) cc_final: 0.9011 (mmm) REVERT: C 275 TRP cc_start: 0.8753 (m100) cc_final: 0.8364 (m-10) REVERT: C 284 LEU cc_start: 0.9467 (OUTLIER) cc_final: 0.9111 (mm) REVERT: C 360 MET cc_start: 0.9615 (mmm) cc_final: 0.9279 (tpp) REVERT: C 363 CYS cc_start: 0.8886 (m) cc_final: 0.8546 (m) REVERT: C 387 MET cc_start: 0.8043 (mmp) cc_final: 0.7807 (mmm) REVERT: C 403 GLN cc_start: 0.8457 (tp40) cc_final: 0.8092 (mt0) REVERT: C 461 TRP cc_start: 0.9067 (p-90) cc_final: 0.8843 (p-90) outliers start: 51 outliers final: 39 residues processed: 276 average time/residue: 0.2119 time to fit residues: 84.7318 Evaluate side-chains 287 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 243 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 301 ARG Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 467 CYS Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 328 PHE Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 464 ASP Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 485 TYR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 328 PHE Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 467 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 94 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 27 optimal weight: 0.0980 chunk 82 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 GLN ** B 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.100923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.079056 restraints weight = 23903.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.081590 restraints weight = 12328.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.083286 restraints weight = 8087.982| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.5728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10119 Z= 0.143 Angle : 0.802 12.865 13797 Z= 0.363 Chirality : 0.043 0.267 1728 Planarity : 0.003 0.025 1719 Dihedral : 4.309 51.781 1476 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 5.00 % Allowed : 29.11 % Favored : 65.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.24), residues: 1332 helix: 1.63 (0.18), residues: 882 sheet: -0.34 (0.92), residues: 30 loop : -2.63 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 461 HIS 0.003 0.001 HIS A 313 PHE 0.039 0.001 PHE C 192 TYR 0.024 0.002 TYR C 485 ARG 0.002 0.000 ARG B 189 Details of bonding type rmsd link_NAG-ASN : bond 0.00498 ( 3) link_NAG-ASN : angle 2.44389 ( 9) hydrogen bonds : bond 0.03843 ( 549) hydrogen bonds : angle 4.38411 ( 1629) covalent geometry : bond 0.00335 (10116) covalent geometry : angle 0.79984 (13788) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 245 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ASP cc_start: 0.9116 (t70) cc_final: 0.8789 (t0) REVERT: A 184 PHE cc_start: 0.8148 (OUTLIER) cc_final: 0.7686 (t80) REVERT: A 217 ARG cc_start: 0.5721 (ttt90) cc_final: 0.4056 (ptt90) REVERT: A 247 LYS cc_start: 0.9065 (tppt) cc_final: 0.8418 (tmtt) REVERT: A 282 MET cc_start: 0.8523 (ttm) cc_final: 0.8148 (ttp) REVERT: A 301 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.7367 (ttp-110) REVERT: A 362 LYS cc_start: 0.9134 (ptmt) cc_final: 0.8619 (tmmt) REVERT: A 366 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7713 (mt-10) REVERT: A 413 LYS cc_start: 0.9182 (mttt) cc_final: 0.8782 (mmmt) REVERT: A 464 ASP cc_start: 0.8977 (t70) cc_final: 0.8423 (t70) REVERT: B 130 TRP cc_start: 0.7865 (m100) cc_final: 0.7603 (m100) REVERT: B 141 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8624 (tt) REVERT: B 154 GLN cc_start: 0.9245 (mm-40) cc_final: 0.8981 (mm-40) REVERT: B 179 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7927 (mp0) REVERT: B 182 ASP cc_start: 0.8789 (t0) cc_final: 0.8329 (t0) REVERT: B 209 GLU cc_start: 0.8652 (tt0) cc_final: 0.8393 (tt0) REVERT: B 275 TRP cc_start: 0.8711 (m100) cc_final: 0.8016 (m-10) REVERT: B 352 SER cc_start: 0.9113 (t) cc_final: 0.8853 (t) REVERT: B 403 GLN cc_start: 0.8791 (mm-40) cc_final: 0.8583 (mm-40) REVERT: B 473 GLU cc_start: 0.8834 (tm-30) cc_final: 0.8512 (tm-30) REVERT: C 81 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8722 (tp) REVERT: C 145 LEU cc_start: 0.9058 (tt) cc_final: 0.8831 (tp) REVERT: C 179 GLU cc_start: 0.7848 (mp0) cc_final: 0.7075 (mp0) REVERT: C 267 MET cc_start: 0.9203 (tpp) cc_final: 0.9003 (mmm) REVERT: C 275 TRP cc_start: 0.8699 (m100) cc_final: 0.8255 (m-10) REVERT: C 284 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9132 (mm) REVERT: C 360 MET cc_start: 0.9624 (mmm) cc_final: 0.9352 (tpp) REVERT: C 362 LYS cc_start: 0.8975 (tppp) cc_final: 0.8576 (tptt) REVERT: C 363 CYS cc_start: 0.8955 (m) cc_final: 0.8607 (m) REVERT: C 403 GLN cc_start: 0.8440 (tp40) cc_final: 0.8118 (mt0) REVERT: C 461 TRP cc_start: 0.9096 (p-90) cc_final: 0.8854 (p-90) outliers start: 52 outliers final: 42 residues processed: 271 average time/residue: 0.1875 time to fit residues: 73.3951 Evaluate side-chains 287 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 240 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 301 ARG Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 467 CYS Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 328 PHE Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 464 ASP Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 485 TYR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 328 PHE Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 467 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 0.9990 chunk 47 optimal weight: 9.9990 chunk 19 optimal weight: 0.9990 chunk 131 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 124 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.101435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.079139 restraints weight = 23887.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.081704 restraints weight = 12460.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.083417 restraints weight = 8211.460| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.5841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10119 Z= 0.139 Angle : 0.808 13.056 13797 Z= 0.366 Chirality : 0.043 0.261 1728 Planarity : 0.003 0.025 1719 Dihedral : 4.293 51.700 1476 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 4.80 % Allowed : 30.45 % Favored : 64.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.24), residues: 1332 helix: 1.64 (0.18), residues: 882 sheet: None (None), residues: 0 loop : -2.57 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 461 HIS 0.003 0.001 HIS A 313 PHE 0.039 0.001 PHE C 192 TYR 0.024 0.002 TYR C 485 ARG 0.002 0.000 ARG A 47 Details of bonding type rmsd link_NAG-ASN : bond 0.00487 ( 3) link_NAG-ASN : angle 2.42208 ( 9) hydrogen bonds : bond 0.03758 ( 549) hydrogen bonds : angle 4.39473 ( 1629) covalent geometry : bond 0.00325 (10116) covalent geometry : angle 0.80552 (13788) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3743.63 seconds wall clock time: 66 minutes 11.93 seconds (3971.93 seconds total)