Starting phenix.real_space_refine on Fri Feb 14 07:49:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6mp6_9187/02_2025/6mp6_9187_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6mp6_9187/02_2025/6mp6_9187.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6mp6_9187/02_2025/6mp6_9187.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6mp6_9187/02_2025/6mp6_9187.map" model { file = "/net/cci-nas-00/data/ceres_data/6mp6_9187/02_2025/6mp6_9187_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6mp6_9187/02_2025/6mp6_9187_neut.cif" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.026 sd= 0.373 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 6483 2.51 5 N 1650 2.21 5 O 1758 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9939 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3299 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 17, 'TRANS': 428} Chain: "B" Number of atoms: 3299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3299 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 17, 'TRANS': 428} Chain: "C" Number of atoms: 3299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3299 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 17, 'TRANS': 428} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.90, per 1000 atoms: 0.59 Number of scatterers: 9939 At special positions: 0 Unit cell: (118.374, 119.46, 116.202, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 1758 8.00 N 1650 7.00 C 6483 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 601 " - " ASN A 163 " " NAG B 601 " - " ASN B 163 " " NAG C 601 " - " ASN C 163 " Time building additional restraints: 2.32 Conformation dependent library (CDL) restraints added in 1.2 seconds 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2418 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 3 sheets defined 75.6% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 44 through 52 Processing helix chain 'A' and resid 52 through 75 removed outlier: 3.613A pdb=" N VAL A 59 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 63 " --> pdb=" O VAL A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 102 Proline residue: A 83 - end of helix removed outlier: 4.183A pdb=" N SER A 87 " --> pdb=" O PRO A 83 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ALA A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE A 89 " --> pdb=" O ARG A 85 " (cutoff:3.500A) Proline residue: A 92 - end of helix removed outlier: 4.090A pdb=" N LEU A 96 " --> pdb=" O PRO A 92 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N MET A 102 " --> pdb=" O ARG A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 116 removed outlier: 3.820A pdb=" N VAL A 109 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N CYS A 110 " --> pdb=" O PRO A 106 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 112 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ILE A 113 " --> pdb=" O VAL A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 152 removed outlier: 3.625A pdb=" N TRP A 130 " --> pdb=" O ARG A 126 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY A 148 " --> pdb=" O ALA A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 169 removed outlier: 3.516A pdb=" N ALA A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ALA A 169 " --> pdb=" O SER A 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 164 through 169' Processing helix chain 'A' and resid 179 through 191 removed outlier: 3.768A pdb=" N PHE A 184 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA A 188 " --> pdb=" O PHE A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 201 removed outlier: 3.746A pdb=" N PHE A 201 " --> pdb=" O SER A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 248 removed outlier: 3.586A pdb=" N PHE A 237 " --> pdb=" O GLY A 233 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A 240 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A 245 " --> pdb=" O PHE A 241 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG A 246 " --> pdb=" O GLY A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 251 No H-bonds generated for 'chain 'A' and resid 249 through 251' Processing helix chain 'A' and resid 252 through 292 removed outlier: 3.596A pdb=" N ARG A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N THR A 266 " --> pdb=" O PHE A 262 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TRP A 272 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N TRP A 275 " --> pdb=" O SER A 271 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYR A 276 " --> pdb=" O TRP A 272 " (cutoff:3.500A) Proline residue: A 278 - end of helix removed outlier: 3.795A pdb=" N MET A 282 " --> pdb=" O PRO A 278 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE A 283 " --> pdb=" O VAL A 279 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA A 286 " --> pdb=" O MET A 282 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 316 removed outlier: 3.597A pdb=" N ILE A 306 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 311 " --> pdb=" O LEU A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 330 Processing helix chain 'A' and resid 332 through 339 removed outlier: 3.718A pdb=" N PHE A 336 " --> pdb=" O ASN A 332 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY A 339 " --> pdb=" O ARG A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 351 removed outlier: 3.610A pdb=" N LEU A 344 " --> pdb=" O ILE A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 355 No H-bonds generated for 'chain 'A' and resid 353 through 355' Processing helix chain 'A' and resid 356 through 368 removed outlier: 3.678A pdb=" N GLU A 365 " --> pdb=" O MET A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 382 removed outlier: 3.660A pdb=" N PHE A 377 " --> pdb=" O HIS A 373 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE A 378 " --> pdb=" O ILE A 374 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU A 379 " --> pdb=" O SER A 375 " (cutoff:3.500A) Proline residue: A 380 - end of helix Processing helix chain 'A' and resid 387 through 404 removed outlier: 3.532A pdb=" N VAL A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA A 398 " --> pdb=" O GLN A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 425 removed outlier: 3.703A pdb=" N ILE A 415 " --> pdb=" O PHE A 411 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR A 416 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA A 421 " --> pdb=" O ILE A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 438 Processing helix chain 'A' and resid 439 through 445 removed outlier: 3.609A pdb=" N ALA A 445 " --> pdb=" O ILE A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 483 removed outlier: 3.506A pdb=" N VAL A 463 " --> pdb=" O VAL A 459 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG A 465 " --> pdb=" O TRP A 461 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL A 469 " --> pdb=" O ARG A 465 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ASP A 475 " --> pdb=" O ASN A 471 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ALA A 476 " --> pdb=" O VAL A 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 52 Processing helix chain 'B' and resid 52 through 75 removed outlier: 3.612A pdb=" N VAL B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL B 63 " --> pdb=" O VAL B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 102 Proline residue: B 83 - end of helix removed outlier: 4.183A pdb=" N SER B 87 " --> pdb=" O PRO B 83 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ALA B 88 " --> pdb=" O GLU B 84 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE B 89 " --> pdb=" O ARG B 85 " (cutoff:3.500A) Proline residue: B 92 - end of helix removed outlier: 4.090A pdb=" N LEU B 96 " --> pdb=" O PRO B 92 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG B 101 " --> pdb=" O LEU B 97 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N MET B 102 " --> pdb=" O ARG B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 116 removed outlier: 3.821A pdb=" N VAL B 109 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N CYS B 110 " --> pdb=" O PRO B 106 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU B 112 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ILE B 113 " --> pdb=" O VAL B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 152 removed outlier: 3.626A pdb=" N TRP B 130 " --> pdb=" O ARG B 126 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU B 136 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 169 removed outlier: 3.516A pdb=" N ALA B 168 " --> pdb=" O ALA B 164 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ALA B 169 " --> pdb=" O SER B 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 164 through 169' Processing helix chain 'B' and resid 179 through 191 removed outlier: 3.767A pdb=" N PHE B 184 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA B 188 " --> pdb=" O PHE B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 201 removed outlier: 3.746A pdb=" N PHE B 201 " --> pdb=" O SER B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 248 removed outlier: 3.586A pdb=" N PHE B 237 " --> pdb=" O GLY B 233 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU B 245 " --> pdb=" O PHE B 241 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG B 246 " --> pdb=" O GLY B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 251 No H-bonds generated for 'chain 'B' and resid 249 through 251' Processing helix chain 'B' and resid 252 through 292 removed outlier: 3.596A pdb=" N ARG B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N THR B 266 " --> pdb=" O PHE B 262 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TRP B 272 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE B 273 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N TRP B 275 " --> pdb=" O SER B 271 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYR B 276 " --> pdb=" O TRP B 272 " (cutoff:3.500A) Proline residue: B 278 - end of helix removed outlier: 3.795A pdb=" N MET B 282 " --> pdb=" O PRO B 278 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE B 283 " --> pdb=" O VAL B 279 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA B 286 " --> pdb=" O MET B 282 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL B 290 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 316 removed outlier: 3.598A pdb=" N ILE B 306 " --> pdb=" O LEU B 302 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU B 311 " --> pdb=" O LEU B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 330 Processing helix chain 'B' and resid 332 through 339 removed outlier: 3.718A pdb=" N PHE B 336 " --> pdb=" O ASN B 332 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY B 339 " --> pdb=" O ARG B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 351 removed outlier: 3.610A pdb=" N LEU B 344 " --> pdb=" O ILE B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 355 No H-bonds generated for 'chain 'B' and resid 353 through 355' Processing helix chain 'B' and resid 356 through 368 removed outlier: 3.679A pdb=" N GLU B 365 " --> pdb=" O MET B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 382 removed outlier: 3.659A pdb=" N PHE B 377 " --> pdb=" O HIS B 373 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU B 379 " --> pdb=" O SER B 375 " (cutoff:3.500A) Proline residue: B 380 - end of helix Processing helix chain 'B' and resid 387 through 404 removed outlier: 3.532A pdb=" N VAL B 396 " --> pdb=" O LEU B 392 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA B 398 " --> pdb=" O GLN B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 425 removed outlier: 3.703A pdb=" N ILE B 415 " --> pdb=" O PHE B 411 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR B 416 " --> pdb=" O VAL B 412 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA B 421 " --> pdb=" O ILE B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 438 Processing helix chain 'B' and resid 439 through 445 removed outlier: 3.609A pdb=" N ALA B 445 " --> pdb=" O ILE B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 483 removed outlier: 3.507A pdb=" N VAL B 463 " --> pdb=" O VAL B 459 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ARG B 465 " --> pdb=" O TRP B 461 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL B 469 " --> pdb=" O ARG B 465 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY B 474 " --> pdb=" O LEU B 470 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ASP B 475 " --> pdb=" O ASN B 471 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ALA B 476 " --> pdb=" O VAL B 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 52 Processing helix chain 'C' and resid 52 through 75 removed outlier: 3.613A pdb=" N VAL C 59 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL C 63 " --> pdb=" O VAL C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 102 Proline residue: C 83 - end of helix removed outlier: 4.183A pdb=" N SER C 87 " --> pdb=" O PRO C 83 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ALA C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE C 89 " --> pdb=" O ARG C 85 " (cutoff:3.500A) Proline residue: C 92 - end of helix removed outlier: 4.090A pdb=" N LEU C 96 " --> pdb=" O PRO C 92 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG C 101 " --> pdb=" O LEU C 97 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N MET C 102 " --> pdb=" O ARG C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 116 removed outlier: 3.820A pdb=" N VAL C 109 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N CYS C 110 " --> pdb=" O PRO C 106 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU C 112 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ILE C 113 " --> pdb=" O VAL C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 152 removed outlier: 3.625A pdb=" N TRP C 130 " --> pdb=" O ARG C 126 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU C 136 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY C 148 " --> pdb=" O ALA C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 169 removed outlier: 3.516A pdb=" N ALA C 168 " --> pdb=" O ALA C 164 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ALA C 169 " --> pdb=" O SER C 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 164 through 169' Processing helix chain 'C' and resid 179 through 191 removed outlier: 3.769A pdb=" N PHE C 184 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA C 188 " --> pdb=" O PHE C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 201 removed outlier: 3.746A pdb=" N PHE C 201 " --> pdb=" O SER C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 248 removed outlier: 3.585A pdb=" N PHE C 237 " --> pdb=" O GLY C 233 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL C 240 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU C 245 " --> pdb=" O PHE C 241 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG C 246 " --> pdb=" O GLY C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 252 through 292 removed outlier: 3.596A pdb=" N ARG C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N THR C 266 " --> pdb=" O PHE C 262 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TRP C 272 " --> pdb=" O VAL C 268 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE C 273 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N TRP C 275 " --> pdb=" O SER C 271 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYR C 276 " --> pdb=" O TRP C 272 " (cutoff:3.500A) Proline residue: C 278 - end of helix removed outlier: 3.794A pdb=" N MET C 282 " --> pdb=" O PRO C 278 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE C 283 " --> pdb=" O VAL C 279 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA C 286 " --> pdb=" O MET C 282 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL C 290 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET C 292 " --> pdb=" O LYS C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 316 removed outlier: 3.597A pdb=" N ILE C 306 " --> pdb=" O LEU C 302 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU C 311 " --> pdb=" O LEU C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 330 Processing helix chain 'C' and resid 332 through 339 removed outlier: 3.717A pdb=" N PHE C 336 " --> pdb=" O ASN C 332 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY C 339 " --> pdb=" O ARG C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 351 removed outlier: 3.611A pdb=" N LEU C 344 " --> pdb=" O ILE C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 355 No H-bonds generated for 'chain 'C' and resid 353 through 355' Processing helix chain 'C' and resid 356 through 368 removed outlier: 3.679A pdb=" N GLU C 365 " --> pdb=" O MET C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 382 removed outlier: 3.659A pdb=" N PHE C 377 " --> pdb=" O HIS C 373 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE C 378 " --> pdb=" O ILE C 374 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU C 379 " --> pdb=" O SER C 375 " (cutoff:3.500A) Proline residue: C 380 - end of helix Processing helix chain 'C' and resid 387 through 404 removed outlier: 3.532A pdb=" N VAL C 396 " --> pdb=" O LEU C 392 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA C 398 " --> pdb=" O GLN C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 425 removed outlier: 3.703A pdb=" N ILE C 415 " --> pdb=" O PHE C 411 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR C 416 " --> pdb=" O VAL C 412 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA C 421 " --> pdb=" O ILE C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 438 Processing helix chain 'C' and resid 439 through 445 removed outlier: 3.609A pdb=" N ALA C 445 " --> pdb=" O ILE C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 483 removed outlier: 3.507A pdb=" N VAL C 463 " --> pdb=" O VAL C 459 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG C 465 " --> pdb=" O TRP C 461 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL C 469 " --> pdb=" O ARG C 465 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY C 474 " --> pdb=" O LEU C 470 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ASP C 475 " --> pdb=" O ASN C 471 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA C 476 " --> pdb=" O VAL C 472 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 212 removed outlier: 4.634A pdb=" N ARG A 211 " --> pdb=" O VAL A 218 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N VAL A 218 " --> pdb=" O ARG A 211 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 207 through 212 removed outlier: 4.634A pdb=" N ARG B 211 " --> pdb=" O VAL B 218 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N VAL B 218 " --> pdb=" O ARG B 211 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 207 through 212 removed outlier: 4.635A pdb=" N ARG C 211 " --> pdb=" O VAL C 218 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N VAL C 218 " --> pdb=" O ARG C 211 " (cutoff:3.500A) 549 hydrogen bonds defined for protein. 1629 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.70 Time building geometry restraints manager: 2.68 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 23.780 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.550 ------------------------------------------------------------------------------- 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 10116 Z= 0.399 Angle : 1.099 11.238 13788 Z= 0.536 Chirality : 0.061 0.457 1728 Planarity : 0.007 0.049 1719 Dihedral : 10.388 69.243 3576 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 0.00 % Allowed : 9.51 % Favored : 90.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.02 (0.14), residues: 1332 helix: -3.96 (0.08), residues: 867 sheet: None (None), residues: 0 loop : -3.67 (0.22), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 272 HIS 0.002 0.001 HIS B 452 PHE 0.016 0.002 PHE C 201 TYR 0.017 0.002 TYR B 485 ARG 0.002 0.000 ARG C 465 *********************** 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 : 1.074 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: 0.2199 time to fit residues: 130.6422 Evaluate side-chains 270 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 0.8980 chunk 100 optimal weight: 0.2980 chunk 55 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 103 optimal weight: 0.2980 chunk 40 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 119 optimal weight: 0.0970 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 ASN ** B 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 483 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.105604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.083517 restraints weight = 23735.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.086139 restraints weight = 11830.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.087873 restraints weight = 7631.444| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10116 Z= 0.197 Angle : 0.760 9.704 13788 Z= 0.367 Chirality : 0.044 0.280 1728 Planarity : 0.005 0.037 1719 Dihedral : 5.490 58.350 1476 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 4.51 % Allowed : 19.60 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.24 (0.19), residues: 1332 helix: -1.48 (0.14), residues: 900 sheet: None (None), residues: 0 loop : -3.44 (0.24), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 461 HIS 0.009 0.001 HIS B 316 PHE 0.028 0.001 PHE C 192 TYR 0.024 0.002 TYR A 485 ARG 0.006 0.000 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 301 time to evaluate : 1.102 Fit side-chains revert: symmetry clash REVERT: A 85 ARG cc_start: 0.7658 (mtm180) cc_final: 0.6781 (mmt180) REVERT: A 120 ASP cc_start: 0.9036 (t0) cc_final: 0.8803 (t0) REVERT: A 130 TRP cc_start: 0.7749 (m100) cc_final: 0.7382 (m100) REVERT: A 132 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8620 (tm) REVERT: A 217 ARG cc_start: 0.5754 (ttt90) cc_final: 0.4187 (ptt90) REVERT: A 256 ILE cc_start: 0.9315 (OUTLIER) cc_final: 0.9072 (pt) REVERT: A 284 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8708 (mt) REVERT: A 304 LYS cc_start: 0.9295 (tppp) cc_final: 0.9070 (tttm) REVERT: A 310 LEU cc_start: 0.8969 (mt) cc_final: 0.8572 (mt) REVERT: A 311 LEU cc_start: 0.9381 (tp) cc_final: 0.9175 (tt) REVERT: A 413 LYS cc_start: 0.9231 (mttt) cc_final: 0.8836 (mmmt) REVERT: A 464 ASP cc_start: 0.8936 (t70) cc_final: 0.8654 (t70) REVERT: B 154 GLN cc_start: 0.9195 (mm-40) cc_final: 0.8890 (mm110) REVERT: B 179 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8271 (mp0) REVERT: B 182 ASP cc_start: 0.8751 (t0) cc_final: 0.8318 (t0) REVERT: B 282 MET cc_start: 0.8900 (ttt) cc_final: 0.8647 (ttm) REVERT: B 338 TRP cc_start: 0.8649 (t60) cc_final: 0.8159 (t60) REVERT: B 352 SER cc_start: 0.9316 (t) cc_final: 0.8921 (p) REVERT: B 363 CYS cc_start: 0.9090 (m) cc_final: 0.8538 (m) REVERT: B 387 MET cc_start: 0.7669 (mmm) cc_final: 0.7435 (mmm) REVERT: B 473 GLU cc_start: 0.8724 (tm-30) cc_final: 0.8427 (tm-30) REVERT: B 477 LEU cc_start: 0.9606 (mt) cc_final: 0.9312 (mp) REVERT: C 50 ARG cc_start: 0.8843 (mmm160) cc_final: 0.8520 (mtm-85) REVERT: C 182 ASP cc_start: 0.8716 (t0) cc_final: 0.8059 (t0) REVERT: C 264 GLU cc_start: 0.8783 (tp30) cc_final: 0.8462 (tp30) REVERT: C 275 TRP cc_start: 0.8775 (m100) cc_final: 0.7837 (m-10) REVERT: C 282 MET cc_start: 0.9040 (tpt) cc_final: 0.8764 (tpt) REVERT: C 338 TRP cc_start: 0.8871 (t60) cc_final: 0.8635 (t-100) REVERT: C 363 CYS cc_start: 0.8887 (m) cc_final: 0.8413 (m) REVERT: C 451 ASP cc_start: 0.5680 (t0) cc_final: 0.5376 (t0) REVERT: C 473 GLU cc_start: 0.8746 (tm-30) cc_final: 0.8478 (tm-30) outliers start: 47 outliers final: 22 residues processed: 331 average time/residue: 0.2084 time to fit residues: 97.2965 Evaluate side-chains 274 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 249 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 342 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 61 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 54 optimal weight: 0.8980 chunk 56 optimal weight: 0.0020 chunk 12 optimal weight: 0.0770 chunk 69 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 overall best weight: 0.9548 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN A 212 ASN ** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 GLN ** B 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.102975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.081461 restraints weight = 24122.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.084036 restraints weight = 11999.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.085741 restraints weight = 7709.561| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.4308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10116 Z= 0.210 Angle : 0.728 11.001 13788 Z= 0.345 Chirality : 0.043 0.296 1728 Planarity : 0.004 0.029 1719 Dihedral : 4.924 50.857 1476 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 6.63 % Allowed : 20.37 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.22), residues: 1332 helix: -0.21 (0.16), residues: 915 sheet: None (None), residues: 0 loop : -3.10 (0.26), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 461 HIS 0.005 0.001 HIS B 316 PHE 0.031 0.001 PHE C 192 TYR 0.027 0.002 TYR A 485 ARG 0.003 0.000 ARG A 98 *********************** 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 346 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 277 time to evaluate : 1.169 Fit side-chains revert: symmetry clash REVERT: A 120 ASP cc_start: 0.9101 (t0) cc_final: 0.8817 (t0) REVERT: A 130 TRP cc_start: 0.7951 (m100) cc_final: 0.7435 (m100) REVERT: A 179 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7693 (mp0) REVERT: A 217 ARG cc_start: 0.5779 (ttt90) cc_final: 0.4121 (ptt90) REVERT: A 274 MET cc_start: 0.8843 (OUTLIER) cc_final: 0.8537 (mtt) REVERT: A 302 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8890 (pp) REVERT: A 413 LYS cc_start: 0.9236 (mttt) cc_final: 0.8853 (mmmt) REVERT: A 464 ASP cc_start: 0.8963 (t70) cc_final: 0.8504 (t70) REVERT: B 130 TRP cc_start: 0.7983 (m100) cc_final: 0.7039 (m100) REVERT: B 154 GLN cc_start: 0.9277 (mm-40) cc_final: 0.9047 (mm110) REVERT: B 179 GLU cc_start: 0.8421 (mm-30) cc_final: 0.7960 (mp0) REVERT: B 208 TYR cc_start: 0.7123 (m-80) cc_final: 0.6604 (m-80) REVERT: B 282 MET cc_start: 0.8932 (ttt) cc_final: 0.8706 (ttm) REVERT: B 338 TRP cc_start: 0.8600 (t60) cc_final: 0.8166 (t60) REVERT: B 352 SER cc_start: 0.9312 (t) cc_final: 0.9086 (t) REVERT: B 363 CYS cc_start: 0.9003 (m) cc_final: 0.8540 (m) REVERT: B 387 MET cc_start: 0.7806 (mmm) cc_final: 0.7493 (mmm) REVERT: B 473 GLU cc_start: 0.8804 (tm-30) cc_final: 0.8455 (tm-30) REVERT: C 50 ARG cc_start: 0.8786 (mmm160) cc_final: 0.8560 (mmm-85) REVERT: C 149 LEU cc_start: 0.9215 (tp) cc_final: 0.8916 (tt) REVERT: C 275 TRP cc_start: 0.8688 (m100) cc_final: 0.8444 (m-10) REVERT: C 282 MET cc_start: 0.9214 (tpt) cc_final: 0.8785 (tpp) REVERT: C 360 MET cc_start: 0.9415 (mmm) cc_final: 0.9042 (tpp) REVERT: C 363 CYS cc_start: 0.8947 (m) cc_final: 0.8599 (m) REVERT: C 403 GLN cc_start: 0.8490 (tp40) cc_final: 0.8162 (mt0) outliers start: 69 outliers final: 28 residues processed: 321 average time/residue: 0.1968 time to fit residues: 90.7433 Evaluate side-chains 272 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 242 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 467 CYS Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 362 LYS Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 351 SER Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 437 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 62 optimal weight: 0.3980 chunk 21 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 121 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 5 optimal weight: 0.4980 chunk 11 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3416 r_free = 0.3416 target = 0.102098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.079585 restraints weight = 23819.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.082162 restraints weight = 12407.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.083882 restraints weight = 8164.456| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.4746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10116 Z= 0.187 Angle : 0.744 11.241 13788 Z= 0.338 Chirality : 0.042 0.284 1728 Planarity : 0.003 0.028 1719 Dihedral : 4.560 50.867 1476 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 6.05 % Allowed : 23.92 % Favored : 70.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.23), residues: 1332 helix: 0.64 (0.18), residues: 885 sheet: None (None), residues: 0 loop : -3.07 (0.25), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 461 HIS 0.003 0.001 HIS A 313 PHE 0.033 0.001 PHE C 192 TYR 0.026 0.002 TYR A 485 ARG 0.004 0.000 ARG A 376 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 283 time to evaluate : 1.159 Fit side-chains revert: symmetry clash REVERT: A 52 ASN cc_start: 0.8296 (m-40) cc_final: 0.8021 (m-40) REVERT: A 120 ASP cc_start: 0.9127 (t0) cc_final: 0.8812 (t0) REVERT: A 130 TRP cc_start: 0.8026 (m100) cc_final: 0.7522 (m-10) REVERT: A 179 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7665 (mp0) REVERT: A 217 ARG cc_start: 0.5618 (ttt90) cc_final: 0.4024 (ptt90) REVERT: A 247 LYS cc_start: 0.9038 (tppt) cc_final: 0.8501 (tmtt) REVERT: A 282 MET cc_start: 0.8404 (ttm) cc_final: 0.7669 (tmm) REVERT: A 292 MET cc_start: 0.8404 (ptp) cc_final: 0.8080 (ptp) REVERT: A 302 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8945 (pp) REVERT: A 413 LYS cc_start: 0.9202 (mttt) cc_final: 0.8816 (mmmt) REVERT: A 464 ASP cc_start: 0.9096 (t70) cc_final: 0.8581 (t70) REVERT: B 130 TRP cc_start: 0.7886 (m100) cc_final: 0.6956 (m100) REVERT: B 154 GLN cc_start: 0.9277 (mm-40) cc_final: 0.8937 (mm-40) REVERT: B 179 GLU cc_start: 0.8331 (mm-30) cc_final: 0.7881 (mp0) REVERT: B 208 TYR cc_start: 0.6922 (m-80) cc_final: 0.6353 (m-80) REVERT: B 282 MET cc_start: 0.8956 (ttt) cc_final: 0.8740 (ttm) REVERT: B 338 TRP cc_start: 0.8402 (t60) cc_final: 0.8087 (t60) REVERT: B 352 SER cc_start: 0.9213 (t) cc_final: 0.8980 (t) REVERT: B 363 CYS cc_start: 0.9061 (m) cc_final: 0.8665 (m) REVERT: B 473 GLU cc_start: 0.8834 (tm-30) cc_final: 0.8478 (tm-30) REVERT: C 50 ARG cc_start: 0.8880 (mmm160) cc_final: 0.8536 (mmm-85) REVERT: C 149 LEU cc_start: 0.9123 (tp) cc_final: 0.8868 (tt) REVERT: C 182 ASP cc_start: 0.8599 (t0) cc_final: 0.8364 (t0) REVERT: C 275 TRP cc_start: 0.8647 (m100) cc_final: 0.8350 (m-10) REVERT: C 282 MET cc_start: 0.9228 (tpt) cc_final: 0.8772 (tpp) REVERT: C 284 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.9070 (mm) REVERT: C 360 MET cc_start: 0.9418 (mmm) cc_final: 0.9125 (tpp) REVERT: C 363 CYS cc_start: 0.8896 (m) cc_final: 0.8561 (m) REVERT: C 403 GLN cc_start: 0.8443 (tp40) cc_final: 0.8015 (mt0) outliers start: 63 outliers final: 41 residues processed: 323 average time/residue: 0.1908 time to fit residues: 88.6997 Evaluate side-chains 296 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 253 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 467 CYS Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain B residue 362 LYS Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 328 PHE Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 351 SER Chi-restraints excluded: chain C residue 401 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 44 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 120 optimal weight: 0.1980 chunk 34 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 85 optimal weight: 0.7980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 GLN C 386 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.102419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.079882 restraints weight = 23692.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.082454 restraints weight = 12392.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.084194 restraints weight = 8184.514| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.5018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10116 Z= 0.188 Angle : 0.734 10.537 13788 Z= 0.336 Chirality : 0.041 0.274 1728 Planarity : 0.003 0.027 1719 Dihedral : 4.432 51.309 1476 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 6.44 % Allowed : 24.88 % Favored : 68.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.23), residues: 1332 helix: 1.08 (0.18), residues: 879 sheet: None (None), residues: 0 loop : -2.93 (0.25), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 461 HIS 0.003 0.001 HIS A 313 PHE 0.031 0.001 PHE C 192 TYR 0.025 0.002 TYR C 485 ARG 0.002 0.000 ARG A 376 *********************** 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 330 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 263 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ASN cc_start: 0.8367 (m-40) cc_final: 0.8130 (m-40) REVERT: A 120 ASP cc_start: 0.9102 (t70) cc_final: 0.8783 (t0) REVERT: A 179 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7662 (mp0) REVERT: A 217 ARG cc_start: 0.5651 (ttt90) cc_final: 0.3967 (ptt90) REVERT: A 247 LYS cc_start: 0.9062 (tppt) cc_final: 0.8409 (tmtt) REVERT: A 282 MET cc_start: 0.8450 (ttm) cc_final: 0.7735 (tmm) REVERT: A 292 MET cc_start: 0.8499 (ptp) cc_final: 0.8193 (ptp) REVERT: A 387 MET cc_start: 0.8376 (mmp) cc_final: 0.8163 (mmp) REVERT: A 413 LYS cc_start: 0.9220 (mttt) cc_final: 0.8816 (mmmt) REVERT: A 464 ASP cc_start: 0.9017 (t70) cc_final: 0.8432 (t70) REVERT: B 94 GLU cc_start: 0.8713 (tt0) cc_final: 0.8458 (tt0) REVERT: B 130 TRP cc_start: 0.7815 (m100) cc_final: 0.6859 (m100) REVERT: B 141 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8686 (tt) REVERT: B 154 GLN cc_start: 0.9240 (mm-40) cc_final: 0.8938 (mm-40) REVERT: B 179 GLU cc_start: 0.8304 (mm-30) cc_final: 0.7869 (mp0) REVERT: B 182 ASP cc_start: 0.8854 (t0) cc_final: 0.8417 (t0) REVERT: B 208 TYR cc_start: 0.6955 (m-80) cc_final: 0.6416 (m-80) REVERT: B 282 MET cc_start: 0.8883 (ttt) cc_final: 0.8623 (ttm) REVERT: B 352 SER cc_start: 0.9184 (t) cc_final: 0.8933 (t) REVERT: B 363 CYS cc_start: 0.9035 (m) cc_final: 0.8637 (m) REVERT: B 366 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7576 (tm-30) REVERT: B 473 GLU cc_start: 0.8809 (tm-30) cc_final: 0.8461 (tm-30) REVERT: C 50 ARG cc_start: 0.8918 (mmm160) cc_final: 0.8565 (mmm-85) REVERT: C 149 LEU cc_start: 0.9150 (tp) cc_final: 0.8883 (tt) REVERT: C 209 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7923 (mt-10) REVERT: C 256 ILE cc_start: 0.9417 (tp) cc_final: 0.9195 (pt) REVERT: C 275 TRP cc_start: 0.8629 (m100) cc_final: 0.8349 (m-10) REVERT: C 284 LEU cc_start: 0.9430 (OUTLIER) cc_final: 0.9114 (mm) REVERT: C 360 MET cc_start: 0.9488 (mmm) cc_final: 0.9207 (tpp) REVERT: C 363 CYS cc_start: 0.8873 (m) cc_final: 0.8566 (m) REVERT: C 403 GLN cc_start: 0.8502 (tp40) cc_final: 0.8125 (mt0) outliers start: 67 outliers final: 43 residues processed: 302 average time/residue: 0.1920 time to fit residues: 83.7148 Evaluate side-chains 292 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 247 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 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 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 70 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 255 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 328 PHE Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 351 SER Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 467 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 100 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 46 optimal weight: 0.0980 chunk 11 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 34 optimal weight: 3.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- 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 = 0.3413 r_free = 0.3413 target = 0.101950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.079253 restraints weight = 24005.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.081833 restraints weight = 12548.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.083555 restraints weight = 8301.455| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.5189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10116 Z= 0.183 Angle : 0.726 10.458 13788 Z= 0.332 Chirality : 0.042 0.266 1728 Planarity : 0.003 0.027 1719 Dihedral : 4.363 51.380 1476 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 6.44 % Allowed : 25.74 % Favored : 67.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.23), residues: 1332 helix: 1.30 (0.18), residues: 879 sheet: None (None), residues: 0 loop : -2.67 (0.26), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 461 HIS 0.002 0.001 HIS A 313 PHE 0.031 0.001 PHE C 192 TYR 0.023 0.002 TYR C 485 ARG 0.002 0.000 ARG B 189 *********************** 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 343 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 276 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ASN cc_start: 0.8446 (m-40) cc_final: 0.8204 (m-40) REVERT: A 120 ASP cc_start: 0.9066 (t70) cc_final: 0.8715 (t0) REVERT: A 179 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7583 (mp0) REVERT: A 217 ARG cc_start: 0.5552 (ttt90) cc_final: 0.3903 (ptt90) REVERT: A 247 LYS cc_start: 0.9056 (tppt) cc_final: 0.8426 (tmtt) REVERT: A 282 MET cc_start: 0.8463 (ttm) cc_final: 0.8081 (ttp) REVERT: A 374 ILE cc_start: 0.9607 (tp) cc_final: 0.9369 (tp) REVERT: A 387 MET cc_start: 0.8407 (mmp) cc_final: 0.8181 (mmp) REVERT: A 413 LYS cc_start: 0.9205 (mttt) cc_final: 0.8786 (mmmt) REVERT: A 464 ASP cc_start: 0.8927 (t70) cc_final: 0.8343 (t70) REVERT: B 94 GLU cc_start: 0.8691 (tt0) cc_final: 0.8404 (tt0) REVERT: B 130 TRP cc_start: 0.7827 (m100) cc_final: 0.6996 (m100) REVERT: B 141 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8678 (tt) REVERT: B 154 GLN cc_start: 0.9243 (mm-40) cc_final: 0.8974 (mm-40) REVERT: B 179 GLU cc_start: 0.8271 (mm-30) cc_final: 0.7857 (mp0) REVERT: B 182 ASP cc_start: 0.8854 (t0) cc_final: 0.8416 (t0) REVERT: B 208 TYR cc_start: 0.6990 (m-80) cc_final: 0.6456 (m-80) REVERT: B 275 TRP cc_start: 0.8825 (m100) cc_final: 0.8172 (m-10) REVERT: B 282 MET cc_start: 0.8917 (ttt) cc_final: 0.8620 (ttm) REVERT: B 331 LYS cc_start: 0.8668 (tppt) cc_final: 0.8304 (ttpt) REVERT: B 352 SER cc_start: 0.9162 (t) cc_final: 0.8923 (t) REVERT: B 363 CYS cc_start: 0.8990 (m) cc_final: 0.8490 (m) REVERT: B 366 GLU cc_start: 0.7891 (tm-30) cc_final: 0.7456 (tm-30) REVERT: B 387 MET cc_start: 0.7465 (mmt) cc_final: 0.7067 (mmm) REVERT: B 473 GLU cc_start: 0.8821 (tm-30) cc_final: 0.8437 (tm-30) REVERT: C 50 ARG cc_start: 0.8928 (mmm160) cc_final: 0.8566 (mmm-85) REVERT: C 81 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8715 (tp) REVERT: C 149 LEU cc_start: 0.9159 (tp) cc_final: 0.8899 (tt) REVERT: C 179 GLU cc_start: 0.7888 (mp0) cc_final: 0.7085 (mp0) REVERT: C 209 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7954 (mt-10) REVERT: C 256 ILE cc_start: 0.9404 (tp) cc_final: 0.9194 (pt) REVERT: C 275 TRP cc_start: 0.8680 (m100) cc_final: 0.8354 (m-10) REVERT: C 284 LEU cc_start: 0.9455 (OUTLIER) cc_final: 0.9116 (mm) REVERT: C 360 MET cc_start: 0.9542 (mmm) cc_final: 0.9108 (tpp) REVERT: C 363 CYS cc_start: 0.8800 (m) cc_final: 0.8479 (m) REVERT: C 403 GLN cc_start: 0.8495 (tp40) cc_final: 0.8143 (mt0) REVERT: C 460 ASP cc_start: 0.9136 (p0) cc_final: 0.8526 (t0) outliers start: 67 outliers final: 46 residues processed: 313 average time/residue: 0.1944 time to fit residues: 88.2171 Evaluate side-chains 297 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 248 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 CYS Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 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 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 79 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 328 PHE Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 485 TYR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 328 PHE Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 467 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.9148 > 50: distance: 62 - 87: 22.130 distance: 70 - 95: 24.081 distance: 73 - 79: 20.890 distance: 79 - 80: 38.597 distance: 80 - 81: 22.078 distance: 80 - 83: 32.591 distance: 81 - 82: 17.302 distance: 81 - 87: 49.450 distance: 83 - 84: 12.366 distance: 83 - 85: 22.913 distance: 84 - 86: 13.395 distance: 87 - 88: 11.527 distance: 88 - 89: 34.594 distance: 88 - 91: 12.658 distance: 89 - 90: 42.333 distance: 89 - 95: 23.306 distance: 91 - 92: 40.584 distance: 92 - 93: 18.432 distance: 92 - 94: 10.196 distance: 95 - 96: 24.243 distance: 96 - 97: 27.840 distance: 96 - 99: 33.877 distance: 97 - 98: 6.792 distance: 97 - 104: 44.065 distance: 99 - 100: 24.237 distance: 100 - 101: 46.816 distance: 101 - 102: 10.361 distance: 104 - 105: 34.904 distance: 105 - 106: 36.287 distance: 105 - 108: 39.040 distance: 106 - 107: 30.722 distance: 106 - 109: 8.411 distance: 109 - 110: 19.095 distance: 110 - 111: 35.443 distance: 110 - 113: 30.472 distance: 111 - 112: 44.173 distance: 111 - 116: 27.219 distance: 113 - 114: 43.323 distance: 113 - 115: 39.897 distance: 116 - 117: 21.408 distance: 117 - 118: 13.774 distance: 117 - 120: 28.734 distance: 118 - 124: 56.890 distance: 120 - 121: 52.333 distance: 121 - 122: 6.597 distance: 121 - 123: 32.770 distance: 124 - 125: 27.946 distance: 125 - 126: 7.318 distance: 125 - 128: 33.194 distance: 126 - 127: 28.792 distance: 126 - 132: 48.924 distance: 128 - 129: 31.351 distance: 129 - 130: 6.833 distance: 129 - 131: 50.616 distance: 132 - 133: 10.703 distance: 132 - 138: 41.305 distance: 133 - 134: 5.775 distance: 133 - 136: 33.568 distance: 134 - 135: 59.386 distance: 134 - 139: 14.222 distance: 136 - 137: 40.611 distance: 137 - 138: 45.804 distance: 140 - 143: 8.895 distance: 141 - 146: 35.548 distance: 143 - 144: 31.242 distance: 143 - 145: 6.831 distance: 146 - 147: 24.671 distance: 147 - 148: 24.687 distance: 147 - 150: 29.078 distance: 148 - 149: 18.772 distance: 148 - 154: 23.887 distance: 150 - 151: 38.775 distance: 151 - 152: 55.396 distance: 151 - 153: 37.542