Starting phenix.real_space_refine on Wed Sep 17 17:07:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6mp6_9187/09_2025/6mp6_9187_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6mp6_9187/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/6mp6_9187/09_2025/6mp6_9187_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6mp6_9187/09_2025/6mp6_9187_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6mp6_9187/09_2025/6mp6_9187.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6mp6_9187/09_2025/6mp6_9187.map" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.026 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.41, per 1000 atoms: 0.24 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: 0.87 Conformation dependent library (CDL) restraints added in 471.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.34 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: 1.42 Time building geometry restraints manager: 1.16 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 0.700 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.200 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.580 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG C 465 TYR 0.017 0.002 TYR B 485 PHE 0.016 0.002 PHE C 201 TRP 0.010 0.001 TRP A 272 HIS 0.002 0.001 HIS B 452 Details of bonding type rmsd covalent geometry : bond 0.00609 (10116) covalent geometry : angle 1.09901 (13788) hydrogen bonds : bond 0.31034 ( 549) hydrogen bonds : angle 9.49545 ( 1629) link_NAG-ASN : bond 0.01083 ( 3) link_NAG-ASN : angle 5.73223 ( 9) *********************** 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 : 0.403 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: 0.0943 time to fit residues: 57.1352 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 : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 ASN ** 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 212 ASN C 224 GLN ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 483 GLN 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 = 0.101857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.079497 restraints weight = 24191.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.082058 restraints weight = 11988.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.083753 restraints weight = 7730.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.084871 restraints weight = 5866.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.085504 restraints weight = 4943.119| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10119 Z= 0.179 Angle : 0.785 9.591 13797 Z= 0.386 Chirality : 0.045 0.327 1728 Planarity : 0.005 0.038 1719 Dihedral : 5.582 55.834 1476 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 4.71 % Allowed : 19.69 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.20 (0.19), residues: 1332 helix: -1.48 (0.15), residues: 918 sheet: None (None), residues: 0 loop : -3.37 (0.25), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 98 TYR 0.025 0.002 TYR A 485 PHE 0.031 0.002 PHE C 192 TRP 0.023 0.002 TRP C 461 HIS 0.009 0.002 HIS B 316 Details of bonding type rmsd covalent geometry : bond 0.00393 (10116) covalent geometry : angle 0.78008 (13788) hydrogen bonds : bond 0.05750 ( 549) hydrogen bonds : angle 5.14302 ( 1629) link_NAG-ASN : bond 0.00607 ( 3) link_NAG-ASN : angle 3.64673 ( 9) *********************** 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 343 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 294 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: A 120 ASP cc_start: 0.9124 (t0) cc_final: 0.8864 (t0) REVERT: A 130 TRP cc_start: 0.7936 (m100) cc_final: 0.7564 (m100) REVERT: A 132 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8723 (tm) REVERT: A 217 ARG cc_start: 0.5783 (ttt90) cc_final: 0.4171 (ptt90) REVERT: A 256 ILE cc_start: 0.9350 (OUTLIER) cc_final: 0.9069 (pt) REVERT: A 291 GLU cc_start: 0.8390 (mm-30) cc_final: 0.7987 (mm-30) REVERT: A 311 LEU cc_start: 0.9397 (tp) cc_final: 0.9159 (tt) REVERT: A 343 PRO cc_start: 0.9352 (Cg_exo) cc_final: 0.9128 (Cg_endo) REVERT: A 413 LYS cc_start: 0.9251 (mttt) cc_final: 0.8819 (mmmt) REVERT: A 464 ASP cc_start: 0.8881 (t70) cc_final: 0.8597 (t70) REVERT: B 154 GLN cc_start: 0.9200 (mm-40) cc_final: 0.8907 (mm110) REVERT: B 282 MET cc_start: 0.8941 (ttt) cc_final: 0.8668 (ttm) REVERT: B 338 TRP cc_start: 0.8706 (t60) cc_final: 0.8201 (t60) REVERT: B 352 SER cc_start: 0.9312 (t) cc_final: 0.8886 (p) REVERT: B 363 CYS cc_start: 0.9053 (m) cc_final: 0.8509 (m) REVERT: B 365 GLU cc_start: 0.8682 (tt0) cc_final: 0.8472 (tp30) REVERT: B 366 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7610 (tm-30) REVERT: B 387 MET cc_start: 0.7919 (mmm) cc_final: 0.7603 (mmm) REVERT: B 473 GLU cc_start: 0.8815 (tm-30) cc_final: 0.8586 (tm-30) REVERT: C 50 ARG cc_start: 0.8884 (mmm160) cc_final: 0.8589 (mtm-85) REVERT: C 264 GLU cc_start: 0.8776 (tp30) cc_final: 0.8517 (tp30) REVERT: C 275 TRP cc_start: 0.8843 (m100) cc_final: 0.7967 (m-10) REVERT: C 282 MET cc_start: 0.9034 (tpt) cc_final: 0.8747 (tpt) REVERT: C 363 CYS cc_start: 0.8807 (m) cc_final: 0.8362 (m) REVERT: C 451 ASP cc_start: 0.5848 (t0) cc_final: 0.5574 (t0) REVERT: C 473 GLU cc_start: 0.8739 (tm-30) cc_final: 0.8445 (tm-30) outliers start: 49 outliers final: 23 residues processed: 324 average time/residue: 0.0846 time to fit residues: 39.6795 Evaluate side-chains 257 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 232 time to evaluate : 0.264 ------------------------------------------------------------------------------- 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 140 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 256 ILE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 308 CYS 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 132 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 268 VAL 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 268 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 46 optimal weight: 0.5980 chunk 11 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 224 GLN ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.102623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.081064 restraints weight = 24148.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.083612 restraints weight = 12010.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.085315 restraints weight = 7696.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.086359 restraints weight = 5798.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.087110 restraints weight = 4887.067| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.4286 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= 0.145 Angle : 0.728 10.863 13797 Z= 0.345 Chirality : 0.043 0.300 1728 Planarity : 0.004 0.031 1719 Dihedral : 4.964 50.273 1476 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 7.11 % Allowed : 19.69 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.70 (0.22), residues: 1332 helix: -0.19 (0.16), residues: 918 sheet: None (None), residues: 0 loop : -3.26 (0.25), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 301 TYR 0.025 0.002 TYR A 485 PHE 0.037 0.001 PHE C 192 TRP 0.011 0.001 TRP A 272 HIS 0.005 0.001 HIS B 316 Details of bonding type rmsd covalent geometry : bond 0.00325 (10116) covalent geometry : angle 0.72342 (13788) hydrogen bonds : bond 0.04789 ( 549) hydrogen bonds : angle 4.71600 ( 1629) link_NAG-ASN : bond 0.00539 ( 3) link_NAG-ASN : angle 3.17068 ( 9) *********************** 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 350 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 276 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: A 84 GLU cc_start: 0.7663 (tt0) cc_final: 0.7440 (tt0) REVERT: A 120 ASP cc_start: 0.9113 (t0) cc_final: 0.8835 (t0) REVERT: A 130 TRP cc_start: 0.7970 (m100) cc_final: 0.7259 (m100) REVERT: A 179 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7789 (mp0) REVERT: A 217 ARG cc_start: 0.5842 (ttt90) cc_final: 0.4152 (ptt90) REVERT: A 274 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8556 (mtt) REVERT: A 282 MET cc_start: 0.8354 (ttm) cc_final: 0.7701 (tmm) REVERT: A 413 LYS cc_start: 0.9233 (mttt) cc_final: 0.8848 (mmmt) REVERT: A 464 ASP cc_start: 0.8929 (t70) cc_final: 0.8468 (t70) REVERT: B 130 TRP cc_start: 0.7950 (m100) cc_final: 0.7064 (m100) REVERT: B 154 GLN cc_start: 0.9255 (mm-40) cc_final: 0.9013 (mm110) REVERT: B 182 ASP cc_start: 0.8889 (t0) cc_final: 0.8433 (t0) REVERT: B 282 MET cc_start: 0.8923 (ttt) cc_final: 0.8672 (ttm) REVERT: B 338 TRP cc_start: 0.8497 (t60) cc_final: 0.8138 (t60) REVERT: B 352 SER cc_start: 0.9298 (t) cc_final: 0.8857 (p) REVERT: B 363 CYS cc_start: 0.8960 (m) cc_final: 0.8459 (m) REVERT: B 366 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7544 (tm-30) REVERT: B 387 MET cc_start: 0.7744 (mmm) cc_final: 0.7413 (mmm) REVERT: B 473 GLU cc_start: 0.8873 (tm-30) cc_final: 0.8457 (tm-30) REVERT: C 50 ARG cc_start: 0.8808 (mmm160) cc_final: 0.8582 (mmm-85) REVERT: C 149 LEU cc_start: 0.9242 (tp) cc_final: 0.8967 (tt) REVERT: C 154 GLN cc_start: 0.8981 (mp10) cc_final: 0.8776 (mp10) REVERT: C 182 ASP cc_start: 0.8647 (t0) cc_final: 0.8339 (t0) REVERT: C 275 TRP cc_start: 0.8707 (m100) cc_final: 0.8475 (m-10) REVERT: C 282 MET cc_start: 0.9197 (tpt) cc_final: 0.8737 (tpt) REVERT: C 360 MET cc_start: 0.9414 (mmm) cc_final: 0.9139 (tpp) REVERT: C 363 CYS cc_start: 0.8901 (m) cc_final: 0.8588 (m) REVERT: C 403 GLN cc_start: 0.8577 (tp40) cc_final: 0.8174 (mt0) outliers start: 74 outliers final: 33 residues processed: 322 average time/residue: 0.0860 time to fit residues: 40.3462 Evaluate side-chains 275 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 241 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 CYS 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 192 PHE Chi-restraints excluded: chain A residue 236 VAL 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 395 CYS 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 268 VAL Chi-restraints excluded: chain C residue 79 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 268 VAL Chi-restraints excluded: chain C residue 323 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 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 100 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 chunk 129 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 122 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 17 optimal weight: 0.3980 chunk 60 optimal weight: 0.9980 chunk 91 optimal weight: 9.9990 chunk 71 optimal weight: 7.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.099669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.077046 restraints weight = 24348.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.079560 restraints weight = 12614.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.081233 restraints weight = 8329.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.082269 restraints weight = 6412.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.082770 restraints weight = 5488.598| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.4698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10119 Z= 0.155 Angle : 0.751 10.833 13797 Z= 0.350 Chirality : 0.043 0.319 1728 Planarity : 0.004 0.029 1719 Dihedral : 4.661 50.475 1476 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 7.20 % Allowed : 21.52 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.23), residues: 1332 helix: 0.51 (0.17), residues: 918 sheet: None (None), residues: 0 loop : -3.02 (0.26), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 301 TYR 0.024 0.002 TYR C 485 PHE 0.033 0.001 PHE C 192 TRP 0.018 0.001 TRP B 461 HIS 0.004 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00355 (10116) covalent geometry : angle 0.74699 (13788) hydrogen bonds : bond 0.04426 ( 549) hydrogen bonds : angle 4.65150 ( 1629) link_NAG-ASN : bond 0.00541 ( 3) link_NAG-ASN : angle 3.16830 ( 9) *********************** 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 334 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 259 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 GLU cc_start: 0.7596 (tt0) cc_final: 0.7388 (tt0) REVERT: A 120 ASP cc_start: 0.9164 (t70) cc_final: 0.8869 (t0) REVERT: A 179 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7648 (mp0) REVERT: A 217 ARG cc_start: 0.5715 (ttt90) cc_final: 0.4090 (ptt90) REVERT: A 282 MET cc_start: 0.8459 (ttm) cc_final: 0.7752 (tmm) REVERT: A 292 MET cc_start: 0.8544 (ptp) cc_final: 0.8123 (ptp) REVERT: A 302 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8980 (pp) REVERT: A 413 LYS cc_start: 0.9230 (mttt) cc_final: 0.8826 (mmmt) REVERT: A 464 ASP cc_start: 0.9022 (t70) cc_final: 0.8556 (t70) REVERT: B 130 TRP cc_start: 0.7878 (m100) cc_final: 0.6967 (m100) REVERT: B 143 SER cc_start: 0.9284 (t) cc_final: 0.9080 (p) REVERT: B 154 GLN cc_start: 0.9313 (mm-40) cc_final: 0.9071 (mm110) REVERT: B 282 MET cc_start: 0.8912 (ttt) cc_final: 0.8638 (ttm) REVERT: B 338 TRP cc_start: 0.8412 (t60) cc_final: 0.8143 (t60) REVERT: B 352 SER cc_start: 0.9178 (t) cc_final: 0.8698 (p) REVERT: B 362 LYS cc_start: 0.9145 (OUTLIER) cc_final: 0.8927 (tppt) REVERT: B 363 CYS cc_start: 0.9063 (m) cc_final: 0.8645 (m) REVERT: B 366 GLU cc_start: 0.7936 (tm-30) cc_final: 0.7644 (tm-30) REVERT: B 387 MET cc_start: 0.7814 (mmm) cc_final: 0.7411 (mmm) REVERT: B 473 GLU cc_start: 0.8862 (tm-30) cc_final: 0.8501 (tm-30) REVERT: C 50 ARG cc_start: 0.8914 (mmm160) cc_final: 0.8563 (mmm-85) REVERT: C 149 LEU cc_start: 0.9196 (tp) cc_final: 0.8919 (tt) REVERT: C 154 GLN cc_start: 0.9067 (mp10) cc_final: 0.8778 (mp10) REVERT: C 275 TRP cc_start: 0.8734 (m100) cc_final: 0.8446 (m-10) REVERT: C 311 LEU cc_start: 0.9497 (tt) cc_final: 0.9288 (tt) REVERT: C 360 MET cc_start: 0.9425 (mmm) cc_final: 0.9182 (tpp) REVERT: C 363 CYS cc_start: 0.8970 (m) cc_final: 0.8613 (m) REVERT: C 403 GLN cc_start: 0.8512 (tp40) cc_final: 0.8073 (mt0) outliers start: 75 outliers final: 45 residues processed: 307 average time/residue: 0.0849 time to fit residues: 38.2097 Evaluate side-chains 286 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 239 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 141 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 301 ARG Chi-restraints excluded: chain A residue 302 LEU 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 467 CYS 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 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 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 79 LEU 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 236 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 323 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 395 CYS Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 404 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 28 optimal weight: 0.0470 chunk 19 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 89 optimal weight: 0.3980 chunk 45 optimal weight: 0.7980 chunk 108 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 88 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- 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 195 ASN ** 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 = 0.3409 r_free = 0.3409 target = 0.101606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.079157 restraints weight = 24007.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.081757 restraints weight = 12350.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.083467 restraints weight = 8113.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.084564 restraints weight = 6207.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.084987 restraints weight = 5257.248| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.5023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10119 Z= 0.126 Angle : 0.733 10.397 13797 Z= 0.332 Chirality : 0.041 0.269 1728 Planarity : 0.003 0.028 1719 Dihedral : 4.467 50.829 1476 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 6.44 % Allowed : 24.78 % Favored : 68.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.23), residues: 1332 helix: 1.08 (0.18), residues: 882 sheet: None (None), residues: 0 loop : -2.94 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 376 TYR 0.023 0.002 TYR C 485 PHE 0.023 0.001 PHE C 192 TRP 0.020 0.001 TRP B 461 HIS 0.003 0.001 HIS B 316 Details of bonding type rmsd covalent geometry : bond 0.00279 (10116) covalent geometry : angle 0.73042 (13788) hydrogen bonds : bond 0.03935 ( 549) hydrogen bonds : angle 4.45406 ( 1629) link_NAG-ASN : bond 0.00514 ( 3) link_NAG-ASN : angle 2.73006 ( 9) *********************** 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 337 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 270 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ASN cc_start: 0.8452 (m-40) cc_final: 0.8130 (m-40) REVERT: A 120 ASP cc_start: 0.9061 (t70) cc_final: 0.8727 (t0) REVERT: A 179 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7595 (mp0) REVERT: A 217 ARG cc_start: 0.5691 (ttt90) cc_final: 0.3993 (ptt90) REVERT: A 247 LYS cc_start: 0.9067 (tppt) cc_final: 0.8440 (tmtt) REVERT: A 282 MET cc_start: 0.8414 (ttm) cc_final: 0.7739 (tmm) REVERT: A 387 MET cc_start: 0.8439 (mmp) cc_final: 0.8172 (mmp) REVERT: A 413 LYS cc_start: 0.9195 (mttt) cc_final: 0.8811 (mmmt) REVERT: A 464 ASP cc_start: 0.8983 (t70) cc_final: 0.8433 (t70) REVERT: B 130 TRP cc_start: 0.7859 (m100) cc_final: 0.6958 (m100) REVERT: B 141 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8549 (tt) REVERT: B 154 GLN cc_start: 0.9208 (mm-40) cc_final: 0.8895 (mm-40) REVERT: B 182 ASP cc_start: 0.8818 (t0) cc_final: 0.8352 (t0) REVERT: B 282 MET cc_start: 0.8883 (ttt) cc_final: 0.8598 (ttm) REVERT: B 338 TRP cc_start: 0.8364 (t60) cc_final: 0.8023 (t60) REVERT: B 352 SER cc_start: 0.9162 (t) cc_final: 0.8906 (t) REVERT: B 366 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7523 (tm-30) REVERT: B 387 MET cc_start: 0.7429 (OUTLIER) cc_final: 0.7103 (mmm) REVERT: B 473 GLU cc_start: 0.8809 (tm-30) cc_final: 0.8480 (tm-30) REVERT: C 50 ARG cc_start: 0.8941 (mmm160) cc_final: 0.8594 (mmm-85) REVERT: C 149 LEU cc_start: 0.9160 (tp) cc_final: 0.8912 (tt) REVERT: C 154 GLN cc_start: 0.9079 (mp10) cc_final: 0.8789 (mp10) REVERT: C 182 ASP cc_start: 0.8517 (t0) cc_final: 0.8272 (t0) REVERT: C 267 MET cc_start: 0.8677 (mmm) cc_final: 0.7945 (mmm) REVERT: C 270 VAL cc_start: 0.9429 (OUTLIER) cc_final: 0.9226 (p) REVERT: C 275 TRP cc_start: 0.8685 (m100) cc_final: 0.8401 (m-10) REVERT: C 284 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9127 (mm) REVERT: C 362 LYS cc_start: 0.9112 (tppp) cc_final: 0.8611 (tppp) REVERT: C 363 CYS cc_start: 0.8936 (m) cc_final: 0.8624 (m) REVERT: C 403 GLN cc_start: 0.8390 (tp40) cc_final: 0.8005 (mt0) outliers start: 67 outliers final: 40 residues processed: 310 average time/residue: 0.0875 time to fit residues: 39.5421 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 : 0.373 ------------------------------------------------------------------------------- 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 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 451 ASP 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 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 311 LEU Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 485 TYR Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 323 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 436 VAL Chi-restraints excluded: chain C residue 437 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 25 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 chunk 127 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 chunk 35 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 128 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 40 optimal weight: 0.2980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3401 r_free = 0.3401 target = 0.101149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.078504 restraints weight = 24056.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.081079 restraints weight = 12463.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.082784 restraints weight = 8223.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.083880 restraints weight = 6319.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.084575 restraints weight = 5368.259| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.5210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10119 Z= 0.131 Angle : 0.737 10.054 13797 Z= 0.336 Chirality : 0.042 0.276 1728 Planarity : 0.003 0.027 1719 Dihedral : 4.415 51.091 1476 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 6.44 % Allowed : 26.22 % Favored : 67.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.23), residues: 1332 helix: 1.32 (0.18), residues: 882 sheet: None (None), residues: 0 loop : -2.87 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 376 TYR 0.023 0.001 TYR C 485 PHE 0.036 0.001 PHE A 134 TRP 0.020 0.001 TRP B 461 HIS 0.002 0.001 HIS A 316 Details of bonding type rmsd covalent geometry : bond 0.00301 (10116) covalent geometry : angle 0.73410 (13788) hydrogen bonds : bond 0.03879 ( 549) hydrogen bonds : angle 4.47323 ( 1629) link_NAG-ASN : bond 0.00530 ( 3) link_NAG-ASN : angle 2.70721 ( 9) *********************** 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 326 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 259 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ASN cc_start: 0.8576 (m-40) cc_final: 0.8140 (m-40) REVERT: A 120 ASP cc_start: 0.9063 (t70) cc_final: 0.8712 (t0) REVERT: A 179 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7588 (mp0) REVERT: A 217 ARG cc_start: 0.5699 (ttt90) cc_final: 0.4007 (ptt90) REVERT: A 247 LYS cc_start: 0.9050 (tppt) cc_final: 0.8420 (tmtt) REVERT: A 282 MET cc_start: 0.8460 (ttm) cc_final: 0.7841 (tmm) REVERT: A 387 MET cc_start: 0.8425 (mmp) cc_final: 0.8171 (mmp) REVERT: A 413 LYS cc_start: 0.9202 (mttt) cc_final: 0.8809 (mmmt) REVERT: A 464 ASP cc_start: 0.9005 (t70) cc_final: 0.8494 (t70) REVERT: B 130 TRP cc_start: 0.7861 (m100) cc_final: 0.6862 (m100) REVERT: B 141 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8566 (tt) REVERT: B 154 GLN cc_start: 0.9226 (mm-40) cc_final: 0.8913 (mm-40) REVERT: B 182 ASP cc_start: 0.8749 (t0) cc_final: 0.8156 (t0) REVERT: B 275 TRP cc_start: 0.8784 (m100) cc_final: 0.8141 (m-10) REVERT: B 282 MET cc_start: 0.8923 (ttt) cc_final: 0.8617 (ttm) REVERT: B 331 LYS cc_start: 0.9312 (tptp) cc_final: 0.8986 (tptp) REVERT: B 352 SER cc_start: 0.9113 (t) cc_final: 0.8846 (t) REVERT: B 366 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7605 (tm-30) REVERT: B 387 MET cc_start: 0.7351 (OUTLIER) cc_final: 0.7118 (mmm) REVERT: B 403 GLN cc_start: 0.8728 (mm-40) cc_final: 0.8415 (mm-40) REVERT: B 473 GLU cc_start: 0.8834 (tm-30) cc_final: 0.8496 (tm-30) REVERT: C 50 ARG cc_start: 0.8940 (mmm160) cc_final: 0.8581 (mmm-85) REVERT: C 81 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8713 (tp) REVERT: C 149 LEU cc_start: 0.9158 (tp) cc_final: 0.8919 (tt) REVERT: C 154 GLN cc_start: 0.9094 (mp10) cc_final: 0.8784 (mp10) REVERT: C 275 TRP cc_start: 0.8672 (m100) cc_final: 0.8361 (m-10) REVERT: C 282 MET cc_start: 0.9229 (tpt) cc_final: 0.8790 (tpt) REVERT: C 284 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9103 (mm) REVERT: C 363 CYS cc_start: 0.8811 (m) cc_final: 0.8554 (m) REVERT: C 403 GLN cc_start: 0.8451 (tp40) cc_final: 0.8019 (mt0) outliers start: 67 outliers final: 41 residues processed: 300 average time/residue: 0.0844 time to fit residues: 36.9713 Evaluate side-chains 284 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 239 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 311 LEU 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 387 MET Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 482 LEU 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 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 323 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 436 VAL Chi-restraints excluded: chain C residue 437 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 95 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 105 optimal weight: 20.0000 chunk 89 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 121 optimal weight: 0.4980 chunk 28 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 GLN ** B 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.101417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.079131 restraints weight = 23977.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.081699 restraints weight = 12375.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.083399 restraints weight = 8117.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.084503 restraints weight = 6208.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.085084 restraints weight = 5260.029| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.5391 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= 0.129 Angle : 0.766 13.640 13797 Z= 0.343 Chirality : 0.042 0.268 1728 Planarity : 0.003 0.026 1719 Dihedral : 4.389 51.310 1476 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 5.76 % Allowed : 28.15 % Favored : 66.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.24), residues: 1332 helix: 1.42 (0.18), residues: 888 sheet: None (None), residues: 0 loop : -2.72 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 47 TYR 0.022 0.002 TYR C 485 PHE 0.022 0.001 PHE A 134 TRP 0.021 0.001 TRP B 461 HIS 0.002 0.001 HIS A 316 Details of bonding type rmsd covalent geometry : bond 0.00294 (10116) covalent geometry : angle 0.76312 (13788) hydrogen bonds : bond 0.03795 ( 549) hydrogen bonds : angle 4.47840 ( 1629) link_NAG-ASN : bond 0.00510 ( 3) link_NAG-ASN : angle 2.58856 ( 9) *********************** 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 311 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 251 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ASN cc_start: 0.8651 (m-40) cc_final: 0.8232 (m-40) REVERT: A 120 ASP cc_start: 0.9058 (t70) cc_final: 0.8711 (t0) REVERT: A 179 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7620 (mp0) REVERT: A 217 ARG cc_start: 0.5636 (ttt90) cc_final: 0.4031 (ptt90) REVERT: A 247 LYS cc_start: 0.9066 (tppt) cc_final: 0.8423 (tmtt) REVERT: A 282 MET cc_start: 0.8484 (ttm) cc_final: 0.7886 (tmm) REVERT: A 288 LYS cc_start: 0.8829 (tppt) cc_final: 0.8601 (tppt) REVERT: A 387 MET cc_start: 0.8380 (mmp) cc_final: 0.8134 (mmp) REVERT: A 413 LYS cc_start: 0.9206 (mttt) cc_final: 0.8816 (mmmt) REVERT: A 464 ASP cc_start: 0.8999 (t70) cc_final: 0.8483 (t70) REVERT: B 130 TRP cc_start: 0.7831 (m100) cc_final: 0.6880 (m100) REVERT: B 141 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8597 (tt) REVERT: B 154 GLN cc_start: 0.9230 (mm-40) cc_final: 0.8944 (mm-40) REVERT: B 182 ASP cc_start: 0.8652 (t0) cc_final: 0.8209 (t0) REVERT: B 227 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7666 (tt0) REVERT: B 275 TRP cc_start: 0.8748 (m100) cc_final: 0.8088 (m-10) REVERT: B 282 MET cc_start: 0.8938 (ttt) cc_final: 0.8605 (ttm) REVERT: B 352 SER cc_start: 0.9103 (t) cc_final: 0.8829 (t) REVERT: B 366 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7527 (tm-30) REVERT: B 387 MET cc_start: 0.7340 (OUTLIER) cc_final: 0.7101 (mmm) REVERT: B 403 GLN cc_start: 0.8767 (mm-40) cc_final: 0.8507 (mm-40) REVERT: B 473 GLU cc_start: 0.8854 (tm-30) cc_final: 0.8540 (tm-30) REVERT: C 81 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8773 (tp) REVERT: C 130 TRP cc_start: 0.8326 (m100) cc_final: 0.7919 (m-10) REVERT: C 149 LEU cc_start: 0.9211 (tp) cc_final: 0.8739 (tt) REVERT: C 153 LEU cc_start: 0.8731 (tt) cc_final: 0.8500 (mm) REVERT: C 154 GLN cc_start: 0.9020 (mp10) cc_final: 0.8659 (mp10) REVERT: C 179 GLU cc_start: 0.7822 (mp0) cc_final: 0.7045 (mp0) REVERT: C 275 TRP cc_start: 0.8707 (m100) cc_final: 0.8387 (m-10) REVERT: C 284 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.9149 (mm) REVERT: C 363 CYS cc_start: 0.8759 (m) cc_final: 0.8518 (m) REVERT: C 403 GLN cc_start: 0.8435 (tp40) cc_final: 0.8021 (mt0) outliers start: 60 outliers final: 47 residues processed: 290 average time/residue: 0.0855 time to fit residues: 36.5629 Evaluate side-chains 287 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 235 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 141 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 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 48 CYS Chi-restraints excluded: chain B residue 57 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 132 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 227 GLU 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 379 LEU Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 482 LEU 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 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 323 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 436 VAL Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 482 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 85 optimal weight: 4.9990 chunk 11 optimal weight: 0.5980 chunk 27 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 chunk 125 optimal weight: 0.3980 chunk 56 optimal weight: 0.8980 chunk 123 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 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 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 GLN A 483 GLN ** B 316 HIS ** 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 = 0.3433 r_free = 0.3433 target = 0.103375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.081879 restraints weight = 23434.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.084474 restraints weight = 12195.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.086232 restraints weight = 7992.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.087371 restraints weight = 6084.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.088103 restraints weight = 5122.026| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.5529 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= 0.131 Angle : 0.779 11.809 13797 Z= 0.348 Chirality : 0.043 0.265 1728 Planarity : 0.003 0.026 1719 Dihedral : 4.394 51.487 1476 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 5.86 % Allowed : 28.43 % Favored : 65.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.24), residues: 1332 helix: 1.50 (0.18), residues: 888 sheet: -0.08 (1.00), residues: 30 loop : -2.73 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 376 TYR 0.025 0.001 TYR C 485 PHE 0.049 0.001 PHE C 192 TRP 0.022 0.001 TRP B 461 HIS 0.003 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00302 (10116) covalent geometry : angle 0.77613 (13788) hydrogen bonds : bond 0.03775 ( 549) hydrogen bonds : angle 4.46940 ( 1629) link_NAG-ASN : bond 0.00509 ( 3) link_NAG-ASN : angle 2.52852 ( 9) *********************** 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 310 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 249 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ASP cc_start: 0.9004 (t70) cc_final: 0.8695 (t0) REVERT: A 184 PHE cc_start: 0.8165 (OUTLIER) cc_final: 0.7587 (t80) REVERT: A 217 ARG cc_start: 0.5818 (ttt90) cc_final: 0.4139 (ptt90) REVERT: A 247 LYS cc_start: 0.9150 (tppt) cc_final: 0.8544 (tmtt) REVERT: A 282 MET cc_start: 0.8410 (ttm) cc_final: 0.7929 (tmm) REVERT: A 288 LYS cc_start: 0.9012 (tppt) cc_final: 0.8801 (tppt) REVERT: A 387 MET cc_start: 0.8201 (mmp) cc_final: 0.7873 (mmp) REVERT: A 413 LYS cc_start: 0.9190 (mttt) cc_final: 0.8829 (mmmt) REVERT: A 464 ASP cc_start: 0.8751 (t70) cc_final: 0.8261 (t70) REVERT: B 130 TRP cc_start: 0.7926 (m100) cc_final: 0.7123 (m100) REVERT: B 141 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8745 (tt) REVERT: B 182 ASP cc_start: 0.8647 (t0) cc_final: 0.8206 (t0) REVERT: B 227 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7602 (tp30) REVERT: B 275 TRP cc_start: 0.8707 (m100) cc_final: 0.8154 (m-10) REVERT: B 282 MET cc_start: 0.8856 (ttt) cc_final: 0.8590 (ttm) REVERT: B 352 SER cc_start: 0.9246 (t) cc_final: 0.9009 (t) REVERT: B 366 GLU cc_start: 0.7735 (tm-30) cc_final: 0.7441 (tm-30) REVERT: B 403 GLN cc_start: 0.8789 (mm-40) cc_final: 0.8571 (mm-40) REVERT: B 473 GLU cc_start: 0.8791 (tm-30) cc_final: 0.8552 (tm-30) REVERT: C 81 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8741 (tp) REVERT: C 145 LEU cc_start: 0.9127 (tt) cc_final: 0.8820 (tp) REVERT: C 154 GLN cc_start: 0.9044 (mp10) cc_final: 0.8774 (mp10) REVERT: C 179 GLU cc_start: 0.7837 (mp0) cc_final: 0.7116 (mp0) REVERT: C 284 LEU cc_start: 0.9572 (OUTLIER) cc_final: 0.9257 (mm) REVERT: C 363 CYS cc_start: 0.8503 (m) cc_final: 0.8300 (m) REVERT: C 403 GLN cc_start: 0.8415 (tp40) cc_final: 0.8118 (mt0) outliers start: 61 outliers final: 46 residues processed: 284 average time/residue: 0.0787 time to fit residues: 32.9787 Evaluate side-chains 294 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 243 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU 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 B residue 48 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 103 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 136 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 227 GLU 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 379 LEU Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 482 LEU 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 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 319 LEU Chi-restraints excluded: chain C residue 323 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 436 VAL Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 482 LEU 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 115 optimal weight: 0.5980 chunk 118 optimal weight: 0.8980 chunk 130 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 110 optimal weight: 0.6980 chunk 4 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 33 optimal weight: 0.0570 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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 403 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.101942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.080223 restraints weight = 23903.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.082783 restraints weight = 12220.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.084490 restraints weight = 7950.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.085622 restraints weight = 6028.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.086155 restraints weight = 5054.242| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.5743 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= 0.128 Angle : 0.788 12.752 13797 Z= 0.351 Chirality : 0.043 0.254 1728 Planarity : 0.003 0.027 1719 Dihedral : 4.381 51.525 1476 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 5.67 % Allowed : 28.63 % Favored : 65.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.24), residues: 1332 helix: 1.58 (0.18), residues: 885 sheet: None (None), residues: 0 loop : -2.67 (0.26), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 376 TYR 0.024 0.001 TYR C 485 PHE 0.049 0.001 PHE C 192 TRP 0.031 0.002 TRP C 461 HIS 0.002 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00289 (10116) covalent geometry : angle 0.78567 (13788) hydrogen bonds : bond 0.03670 ( 549) hydrogen bonds : angle 4.42715 ( 1629) link_NAG-ASN : bond 0.00495 ( 3) link_NAG-ASN : angle 2.39552 ( 9) *********************** 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 319 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 260 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ASP cc_start: 0.9099 (t70) cc_final: 0.8781 (t0) REVERT: A 184 PHE cc_start: 0.8079 (OUTLIER) cc_final: 0.7591 (t80) REVERT: A 217 ARG cc_start: 0.5624 (ttt90) cc_final: 0.4036 (ptt90) REVERT: A 247 LYS cc_start: 0.9059 (tppt) cc_final: 0.8407 (tmtt) REVERT: A 282 MET cc_start: 0.8529 (ttm) cc_final: 0.7935 (tmm) REVERT: A 387 MET cc_start: 0.8295 (mmp) cc_final: 0.8023 (mmp) REVERT: A 413 LYS cc_start: 0.9173 (mttt) cc_final: 0.8789 (mmmt) REVERT: A 464 ASP cc_start: 0.8980 (t70) cc_final: 0.8501 (t70) REVERT: B 130 TRP cc_start: 0.7817 (m100) cc_final: 0.6945 (m100) REVERT: B 141 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8521 (tt) REVERT: B 182 ASP cc_start: 0.8701 (t0) cc_final: 0.8295 (t0) REVERT: B 227 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7628 (tt0) REVERT: B 275 TRP cc_start: 0.8664 (m100) cc_final: 0.8010 (m-10) REVERT: B 282 MET cc_start: 0.8977 (ttt) cc_final: 0.8707 (ttm) REVERT: B 352 SER cc_start: 0.9044 (t) cc_final: 0.8780 (t) REVERT: B 366 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7534 (tm-30) REVERT: B 473 GLU cc_start: 0.8857 (tm-30) cc_final: 0.8501 (tm-30) REVERT: C 81 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8727 (tp) REVERT: C 145 LEU cc_start: 0.9025 (tt) cc_final: 0.8803 (tp) REVERT: C 154 GLN cc_start: 0.8945 (mp10) cc_final: 0.8644 (mp10) REVERT: C 179 GLU cc_start: 0.7849 (mp0) cc_final: 0.7035 (mp0) REVERT: C 224 GLN cc_start: 0.8907 (pt0) cc_final: 0.8478 (pm20) REVERT: C 284 LEU cc_start: 0.9420 (OUTLIER) cc_final: 0.9110 (mm) REVERT: C 361 MET cc_start: 0.9076 (tpp) cc_final: 0.8687 (mmm) REVERT: C 403 GLN cc_start: 0.8411 (tp40) cc_final: 0.8011 (mt0) outliers start: 59 outliers final: 44 residues processed: 290 average time/residue: 0.0808 time to fit residues: 34.7727 Evaluate side-chains 295 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 246 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU 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 328 PHE Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 136 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 227 GLU 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 379 LEU Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 464 ASP Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 482 LEU 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 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 319 LEU Chi-restraints excluded: chain C residue 323 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 436 VAL Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 482 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 86 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 67 optimal weight: 0.3980 chunk 55 optimal weight: 0.0870 chunk 119 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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 483 GLN ** C 313 HIS ** 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 = 0.3421 r_free = 0.3421 target = 0.102541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.079994 restraints weight = 23727.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.082550 restraints weight = 12385.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.084283 restraints weight = 8169.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.085406 restraints weight = 6258.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.085935 restraints weight = 5297.418| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.5844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10119 Z= 0.136 Angle : 0.814 12.766 13797 Z= 0.363 Chirality : 0.043 0.256 1728 Planarity : 0.004 0.055 1719 Dihedral : 4.351 51.659 1476 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 5.00 % Allowed : 29.39 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.24), residues: 1332 helix: 1.58 (0.18), residues: 885 sheet: None (None), residues: 0 loop : -2.66 (0.26), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 376 TYR 0.025 0.001 TYR C 485 PHE 0.048 0.001 PHE C 192 TRP 0.026 0.001 TRP C 461 HIS 0.003 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00316 (10116) covalent geometry : angle 0.81187 (13788) hydrogen bonds : bond 0.03733 ( 549) hydrogen bonds : angle 4.48590 ( 1629) link_NAG-ASN : bond 0.00499 ( 3) link_NAG-ASN : angle 2.37084 ( 9) ********************** 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 306 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 254 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ASP cc_start: 0.9094 (t70) cc_final: 0.8769 (t0) REVERT: A 184 PHE cc_start: 0.8161 (OUTLIER) cc_final: 0.7697 (t80) REVERT: A 217 ARG cc_start: 0.5623 (ttt90) cc_final: 0.4043 (ptt90) REVERT: A 247 LYS cc_start: 0.9068 (tppt) cc_final: 0.8426 (tmtt) REVERT: A 274 MET cc_start: 0.8625 (ttm) cc_final: 0.8123 (ttp) REVERT: A 282 MET cc_start: 0.8525 (ttm) cc_final: 0.7932 (tmm) REVERT: A 387 MET cc_start: 0.8335 (mmp) cc_final: 0.8036 (mmp) REVERT: A 413 LYS cc_start: 0.9154 (mttt) cc_final: 0.8772 (mmmt) REVERT: A 464 ASP cc_start: 0.8947 (t70) cc_final: 0.8444 (t70) REVERT: B 130 TRP cc_start: 0.7795 (m100) cc_final: 0.6941 (m100) REVERT: B 141 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8536 (tt) REVERT: B 182 ASP cc_start: 0.8697 (t0) cc_final: 0.8291 (t0) REVERT: B 227 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7646 (tt0) REVERT: B 275 TRP cc_start: 0.8661 (m100) cc_final: 0.8025 (m-10) REVERT: B 282 MET cc_start: 0.8971 (ttt) cc_final: 0.8711 (ttm) REVERT: B 352 SER cc_start: 0.9060 (t) cc_final: 0.8787 (t) REVERT: B 361 MET cc_start: 0.9116 (tpp) cc_final: 0.8821 (mmm) REVERT: B 366 GLU cc_start: 0.7744 (tm-30) cc_final: 0.7461 (tm-30) REVERT: B 473 GLU cc_start: 0.8850 (tm-30) cc_final: 0.8510 (tm-30) REVERT: C 145 LEU cc_start: 0.8931 (tt) cc_final: 0.8640 (tp) REVERT: C 154 GLN cc_start: 0.9080 (mp10) cc_final: 0.8633 (mp10) REVERT: C 179 GLU cc_start: 0.7830 (mp0) cc_final: 0.7003 (mp0) REVERT: C 224 GLN cc_start: 0.8904 (pt0) cc_final: 0.8491 (pm20) REVERT: C 284 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.9117 (mm) REVERT: C 403 GLN cc_start: 0.8383 (tp40) cc_final: 0.8082 (mt0) outliers start: 52 outliers final: 45 residues processed: 280 average time/residue: 0.0854 time to fit residues: 35.2829 Evaluate side-chains 293 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 244 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU 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 328 PHE Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 463 VAL 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 119 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 227 GLU 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 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 462 LEU Chi-restraints excluded: chain B residue 464 ASP Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 485 TYR Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 110 CYS 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 319 LEU Chi-restraints excluded: chain C residue 323 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 436 VAL Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 482 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 79 optimal weight: 0.8980 chunk 118 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 59 optimal weight: 0.2980 chunk 103 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 3 optimal weight: 8.9990 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 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 GLN ** B 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.102542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.080105 restraints weight = 23975.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.082729 restraints weight = 12412.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.084489 restraints weight = 8104.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.085621 restraints weight = 6165.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.086223 restraints weight = 5189.006| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.5934 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= 0.136 Angle : 0.825 12.856 13797 Z= 0.367 Chirality : 0.043 0.256 1728 Planarity : 0.003 0.046 1719 Dihedral : 4.396 51.756 1476 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 5.09 % Allowed : 30.45 % Favored : 64.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.24), residues: 1332 helix: 1.55 (0.18), residues: 885 sheet: None (None), residues: 0 loop : -2.67 (0.26), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 376 TYR 0.025 0.001 TYR C 485 PHE 0.048 0.001 PHE C 192 TRP 0.026 0.001 TRP C 461 HIS 0.003 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00314 (10116) covalent geometry : angle 0.82269 (13788) hydrogen bonds : bond 0.03776 ( 549) hydrogen bonds : angle 4.41743 ( 1629) link_NAG-ASN : bond 0.00488 ( 3) link_NAG-ASN : angle 2.35561 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1867.12 seconds wall clock time: 32 minutes 50.48 seconds (1970.48 seconds total)