Starting phenix.real_space_refine on Thu Mar 14 22:17:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mp6_9187/03_2024/6mp6_9187_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mp6_9187/03_2024/6mp6_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mp6_9187/03_2024/6mp6_9187.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mp6_9187/03_2024/6mp6_9187.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mp6_9187/03_2024/6mp6_9187_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mp6_9187/03_2024/6mp6_9187_neut.pdb" } 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 Residue "A ARG 98": "NH1" <-> "NH2" Residue "A ARG 101": "NH1" <-> "NH2" Residue "A ARG 202": "NH1" <-> "NH2" Residue "A ARG 217": "NH1" <-> "NH2" Residue "A ARG 246": "NH1" <-> "NH2" Residue "A ARG 257": "NH1" <-> "NH2" Residue "A ARG 335": "NH1" <-> "NH2" Residue "A ARG 488": "NH1" <-> "NH2" Residue "B ARG 98": "NH1" <-> "NH2" Residue "B ARG 101": "NH1" <-> "NH2" Residue "B ARG 202": "NH1" <-> "NH2" Residue "B ARG 217": "NH1" <-> "NH2" Residue "B ARG 246": "NH1" <-> "NH2" Residue "B ARG 257": "NH1" <-> "NH2" Residue "B ARG 335": "NH1" <-> "NH2" Residue "B ARG 488": "NH1" <-> "NH2" Residue "C ARG 98": "NH1" <-> "NH2" Residue "C ARG 101": "NH1" <-> "NH2" Residue "C ARG 202": "NH1" <-> "NH2" Residue "C ARG 217": "NH1" <-> "NH2" Residue "C ARG 246": "NH1" <-> "NH2" Residue "C ARG 257": "NH1" <-> "NH2" Residue "C ARG 335": "NH1" <-> "NH2" Residue "C ARG 488": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 5.77, per 1000 atoms: 0.58 Number of scatterers: 9939 At special positions: 0 Unit cell: (118.374, 119.46, 116.202, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 1758 8.00 N 1650 7.00 C 6483 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 3.90 Conformation dependent library (CDL) restraints added in 1.9 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: 1.08 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: 2.76 Time building geometry restraints manager: 4.26 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: 98.90 - 105.92: 231 105.92 - 112.94: 5543 112.94 - 119.96: 3576 119.96 - 126.99: 4327 126.99 - 134.01: 111 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 2.440 nonbonded pdb=" O TYR C 325 " pdb=" OG1 THR C 329 " model vdw 2.440 2.440 nonbonded pdb=" O TYR B 325 " pdb=" OG1 THR B 329 " model vdw 2.440 2.440 nonbonded pdb=" O PHE A 328 " pdb=" ND2 ASN A 484 " model vdw 2.500 2.520 nonbonded pdb=" O PHE B 328 " pdb=" ND2 ASN B 484 " model vdw 2.500 2.520 ... (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 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: 0.470 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: 2.850 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 29.520 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.070 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.640 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 431 time to evaluate : 0.845 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: 0.2098 time to fit residues: 124.4561 Evaluate side-chains 270 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 1.057 ------------------------------------------------------------------------------- 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: 3.9990 chunk 100 optimal weight: 0.0970 chunk 55 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 67 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 103 optimal weight: 0.0370 chunk 40 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 chunk 119 optimal weight: 0.9990 overall best weight: 0.4456 ------------------------------------------------------------------------------- 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 224 GLN ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 483 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10116 Z= 0.190 Angle : 0.750 9.572 13788 Z= 0.362 Chirality : 0.043 0.279 1728 Planarity : 0.005 0.036 1719 Dihedral : 5.519 59.445 1476 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 4.71 % Allowed : 19.40 % 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: -3.19 (0.19), residues: 1332 helix: -1.44 (0.15), residues: 879 sheet: None (None), residues: 0 loop : -3.34 (0.24), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 461 HIS 0.009 0.001 HIS B 316 PHE 0.030 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 353 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 304 time to evaluate : 1.159 Fit side-chains REVERT: A 52 ASN cc_start: 0.8624 (m-40) cc_final: 0.8368 (m110) REVERT: A 85 ARG cc_start: 0.7307 (mtm180) cc_final: 0.6903 (mmt180) REVERT: A 130 TRP cc_start: 0.7665 (m100) cc_final: 0.7339 (m100) REVERT: A 132 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8705 (tm) REVERT: A 217 ARG cc_start: 0.6142 (ttt90) cc_final: 0.4474 (ptt90) REVERT: A 256 ILE cc_start: 0.9280 (tp) cc_final: 0.9041 (pt) REVERT: A 284 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8797 (mt) REVERT: A 304 LYS cc_start: 0.9337 (tppp) cc_final: 0.9116 (tttm) REVERT: A 311 LEU cc_start: 0.9400 (tp) cc_final: 0.9190 (tt) REVERT: A 343 PRO cc_start: 0.9229 (Cg_exo) cc_final: 0.8970 (Cg_endo) REVERT: A 413 LYS cc_start: 0.9052 (mttt) cc_final: 0.8777 (mmmt) REVERT: A 464 ASP cc_start: 0.8732 (t70) cc_final: 0.8506 (t70) REVERT: B 182 ASP cc_start: 0.8422 (t0) cc_final: 0.7990 (t0) REVERT: B 282 MET cc_start: 0.8739 (ttt) cc_final: 0.8507 (ttm) REVERT: B 338 TRP cc_start: 0.8561 (t60) cc_final: 0.8105 (t60) REVERT: B 352 SER cc_start: 0.9295 (t) cc_final: 0.8898 (p) REVERT: B 363 CYS cc_start: 0.9023 (m) cc_final: 0.8487 (m) REVERT: B 387 MET cc_start: 0.7917 (mmm) cc_final: 0.7557 (mmm) REVERT: B 473 GLU cc_start: 0.8656 (tm-30) cc_final: 0.8394 (tm-30) REVERT: B 477 LEU cc_start: 0.9622 (mt) cc_final: 0.9318 (mp) REVERT: C 182 ASP cc_start: 0.8530 (t0) cc_final: 0.7890 (t0) REVERT: C 264 GLU cc_start: 0.8642 (tp30) cc_final: 0.8346 (tp30) REVERT: C 275 TRP cc_start: 0.8619 (m100) cc_final: 0.7797 (m-10) REVERT: C 282 MET cc_start: 0.8860 (tpt) cc_final: 0.8641 (tpt) REVERT: C 338 TRP cc_start: 0.8835 (t60) cc_final: 0.8633 (t-100) REVERT: C 363 CYS cc_start: 0.8793 (m) cc_final: 0.8320 (m) REVERT: C 387 MET cc_start: 0.7448 (mmm) cc_final: 0.7127 (mmm) REVERT: C 451 ASP cc_start: 0.5596 (t0) cc_final: 0.5281 (t0) REVERT: C 473 GLU cc_start: 0.8687 (tm-30) cc_final: 0.8440 (tm-30) outliers start: 49 outliers final: 25 residues processed: 334 average time/residue: 0.2008 time to fit residues: 94.7342 Evaluate side-chains 273 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 246 time to evaluate : 1.126 ------------------------------------------------------------------------------- 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 268 VAL Chi-restraints excluded: chain A residue 284 LEU 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 475 ASP 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 B residue 384 THR Chi-restraints excluded: chain C residue 79 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 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 66 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 99 optimal weight: 7.9990 chunk 81 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 120 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 chunk 106 optimal weight: 0.1980 chunk 119 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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** A 483 GLN ** B 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 GLN C 212 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.4328 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= 0.191 Angle : 0.713 11.052 13788 Z= 0.334 Chirality : 0.042 0.286 1728 Planarity : 0.004 0.030 1719 Dihedral : 4.916 50.766 1476 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 6.72 % Allowed : 21.61 % Favored : 71.66 % 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: -1.53 (0.22), residues: 1332 helix: -0.05 (0.16), residues: 894 sheet: None (None), residues: 0 loop : -3.03 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 461 HIS 0.006 0.001 HIS B 316 PHE 0.031 0.001 PHE C 192 TYR 0.025 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 349 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 279 time to evaluate : 1.117 Fit side-chains revert: symmetry clash REVERT: A 52 ASN cc_start: 0.8366 (m-40) cc_final: 0.8162 (m-40) REVERT: A 130 TRP cc_start: 0.7872 (m100) cc_final: 0.7412 (m100) REVERT: A 217 ARG cc_start: 0.6138 (ttt90) cc_final: 0.4401 (ptt90) REVERT: A 304 LYS cc_start: 0.9313 (tppp) cc_final: 0.9109 (tttm) REVERT: A 413 LYS cc_start: 0.9089 (mttt) cc_final: 0.8854 (mmmt) REVERT: A 464 ASP cc_start: 0.8895 (t70) cc_final: 0.8462 (t70) REVERT: B 130 TRP cc_start: 0.7990 (m100) cc_final: 0.7077 (m100) REVERT: B 179 GLU cc_start: 0.8009 (mp0) cc_final: 0.7639 (mp0) REVERT: B 182 ASP cc_start: 0.8535 (t0) cc_final: 0.8080 (t0) REVERT: B 338 TRP cc_start: 0.8508 (t60) cc_final: 0.8110 (t60) REVERT: B 352 SER cc_start: 0.9274 (t) cc_final: 0.9035 (t) REVERT: B 362 LYS cc_start: 0.9180 (OUTLIER) cc_final: 0.8963 (tppt) REVERT: B 363 CYS cc_start: 0.8935 (m) cc_final: 0.8571 (m) REVERT: B 366 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7681 (tm-30) REVERT: B 387 MET cc_start: 0.7934 (mmm) cc_final: 0.7475 (mmm) REVERT: B 473 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8384 (tm-30) REVERT: B 477 LEU cc_start: 0.9630 (mt) cc_final: 0.9137 (mt) REVERT: C 149 LEU cc_start: 0.9276 (tp) cc_final: 0.9010 (tt) REVERT: C 282 MET cc_start: 0.9038 (tpt) cc_final: 0.8635 (tpt) REVERT: C 360 MET cc_start: 0.9376 (mmm) cc_final: 0.9130 (tpp) REVERT: C 363 CYS cc_start: 0.8833 (m) cc_final: 0.8498 (m) REVERT: C 387 MET cc_start: 0.7653 (mmm) cc_final: 0.7401 (mmm) outliers start: 70 outliers final: 34 residues processed: 321 average time/residue: 0.1885 time to fit residues: 87.0151 Evaluate side-chains 277 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 242 time to evaluate : 0.859 ------------------------------------------------------------------------------- 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 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 409 LEU Chi-restraints excluded: chain A residue 467 CYS Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 362 LYS Chi-restraints excluded: chain B residue 475 ASP 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 268 VAL Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 470 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 13 optimal weight: 0.0970 chunk 57 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.4770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10116 Z= 0.224 Angle : 0.744 10.809 13788 Z= 0.343 Chirality : 0.042 0.311 1728 Planarity : 0.004 0.030 1719 Dihedral : 4.596 50.874 1476 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 7.11 % Allowed : 23.92 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.23), residues: 1332 helix: 0.68 (0.17), residues: 897 sheet: None (None), residues: 0 loop : -2.88 (0.26), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 461 HIS 0.004 0.001 HIS A 313 PHE 0.034 0.001 PHE C 192 TYR 0.024 0.002 TYR C 485 ARG 0.003 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 340 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 266 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 TRP cc_start: 0.8013 (m100) cc_final: 0.7621 (m-10) REVERT: A 217 ARG cc_start: 0.6185 (ttt90) cc_final: 0.4437 (ptt90) REVERT: A 282 MET cc_start: 0.8269 (ttm) cc_final: 0.7682 (tmm) REVERT: A 302 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8245 (pp) REVERT: A 413 LYS cc_start: 0.9090 (mttt) cc_final: 0.8820 (mmmt) REVERT: A 464 ASP cc_start: 0.8883 (t70) cc_final: 0.8446 (t70) REVERT: B 130 TRP cc_start: 0.7980 (m100) cc_final: 0.7086 (m100) REVERT: B 182 ASP cc_start: 0.8527 (t0) cc_final: 0.8048 (t0) REVERT: B 338 TRP cc_start: 0.8305 (t60) cc_final: 0.8014 (t60) REVERT: B 352 SER cc_start: 0.9212 (t) cc_final: 0.8956 (t) REVERT: B 363 CYS cc_start: 0.8895 (m) cc_final: 0.8535 (m) REVERT: B 366 GLU cc_start: 0.7995 (tm-30) cc_final: 0.7692 (tm-30) REVERT: B 387 MET cc_start: 0.8062 (mmm) cc_final: 0.7530 (mmm) REVERT: B 473 GLU cc_start: 0.8818 (tm-30) cc_final: 0.8512 (tm-30) REVERT: C 149 LEU cc_start: 0.9302 (tp) cc_final: 0.9040 (tt) REVERT: C 363 CYS cc_start: 0.8763 (m) cc_final: 0.8474 (m) outliers start: 74 outliers final: 45 residues processed: 310 average time/residue: 0.1871 time to fit residues: 83.7838 Evaluate side-chains 287 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 241 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 196 LEU 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 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 409 LEU Chi-restraints excluded: chain A residue 467 CYS Chi-restraints excluded: chain A residue 475 ASP 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 203 SER Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 475 ASP 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 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 268 VAL 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 401 ILE Chi-restraints excluded: chain C residue 437 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- 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 394 GLN ** B 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 367 ASN B 403 GLN B 483 GLN C 394 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.5062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10116 Z= 0.235 Angle : 0.747 10.793 13788 Z= 0.344 Chirality : 0.042 0.309 1728 Planarity : 0.003 0.029 1719 Dihedral : 4.564 50.873 1476 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 7.49 % Allowed : 25.65 % Favored : 66.86 % 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: -0.16 (0.23), residues: 1332 helix: 1.07 (0.18), residues: 897 sheet: None (None), residues: 0 loop : -2.73 (0.27), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 461 HIS 0.003 0.001 HIS B 316 PHE 0.034 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 337 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 259 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ILE cc_start: 0.9219 (pt) cc_final: 0.8710 (mt) REVERT: A 154 GLN cc_start: 0.9224 (mp10) cc_final: 0.9007 (mp10) REVERT: A 217 ARG cc_start: 0.6211 (ttt90) cc_final: 0.4359 (ptt90) REVERT: A 247 LYS cc_start: 0.9148 (tppt) cc_final: 0.8586 (tmtt) REVERT: A 282 MET cc_start: 0.8251 (ttm) cc_final: 0.7703 (tmm) REVERT: A 301 ARG cc_start: 0.6847 (OUTLIER) cc_final: 0.6539 (ttp-110) REVERT: A 413 LYS cc_start: 0.9141 (mttt) cc_final: 0.8834 (mmmt) REVERT: A 464 ASP cc_start: 0.8922 (t70) cc_final: 0.8453 (t70) REVERT: B 130 TRP cc_start: 0.7974 (m100) cc_final: 0.7020 (m100) REVERT: B 141 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8845 (tt) REVERT: B 182 ASP cc_start: 0.8475 (t0) cc_final: 0.8055 (t0) REVERT: B 338 TRP cc_start: 0.8351 (t60) cc_final: 0.8128 (t60) REVERT: B 352 SER cc_start: 0.9204 (t) cc_final: 0.8734 (p) REVERT: B 363 CYS cc_start: 0.8891 (m) cc_final: 0.8548 (m) REVERT: B 366 GLU cc_start: 0.8011 (tm-30) cc_final: 0.7782 (tm-30) REVERT: B 387 MET cc_start: 0.8097 (mmm) cc_final: 0.7474 (mmm) REVERT: B 473 GLU cc_start: 0.8849 (tm-30) cc_final: 0.8580 (tm-30) REVERT: C 149 LEU cc_start: 0.9331 (tp) cc_final: 0.8987 (tt) REVERT: C 186 ASP cc_start: 0.8720 (t0) cc_final: 0.8347 (t70) REVERT: C 284 LEU cc_start: 0.9634 (OUTLIER) cc_final: 0.9340 (mm) REVERT: C 313 HIS cc_start: 0.9366 (OUTLIER) cc_final: 0.8849 (m-70) REVERT: C 362 LYS cc_start: 0.8896 (tppp) cc_final: 0.8430 (tppp) REVERT: C 363 CYS cc_start: 0.8764 (m) cc_final: 0.8492 (m) outliers start: 78 outliers final: 53 residues processed: 303 average time/residue: 0.1885 time to fit residues: 82.3333 Evaluate side-chains 299 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 242 time to evaluate : 1.019 ------------------------------------------------------------------------------- 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 186 ASP Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 301 ARG 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 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 A residue 475 ASP Chi-restraints excluded: chain A residue 482 LEU 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 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 203 SER Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 475 ASP 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 109 VAL 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 284 LEU Chi-restraints excluded: chain C residue 313 HIS 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 395 CYS Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 425 SER 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 114 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 74 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 123 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 GLN A 483 GLN ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.5298 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= 0.189 Angle : 0.729 9.982 13788 Z= 0.333 Chirality : 0.042 0.278 1728 Planarity : 0.003 0.028 1719 Dihedral : 4.455 50.848 1476 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 6.53 % Allowed : 27.19 % Favored : 66.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.24), residues: 1332 helix: 1.35 (0.18), residues: 885 sheet: None (None), residues: 0 loop : -2.83 (0.26), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 461 HIS 0.002 0.001 HIS B 316 PHE 0.027 0.001 PHE C 192 TYR 0.026 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 330 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 262 time to evaluate : 1.133 Fit side-chains REVERT: A 104 ILE cc_start: 0.9208 (pt) cc_final: 0.8792 (mt) REVERT: A 154 GLN cc_start: 0.9251 (mp10) cc_final: 0.9008 (mp10) REVERT: A 184 PHE cc_start: 0.8309 (m-80) cc_final: 0.8108 (m-80) REVERT: A 217 ARG cc_start: 0.6143 (ttt90) cc_final: 0.4332 (ptt90) REVERT: A 247 LYS cc_start: 0.9153 (tppt) cc_final: 0.8582 (tmtt) REVERT: A 282 MET cc_start: 0.8231 (ttm) cc_final: 0.7760 (tmm) REVERT: A 291 GLU cc_start: 0.8505 (tm-30) cc_final: 0.8246 (tm-30) REVERT: A 301 ARG cc_start: 0.6967 (OUTLIER) cc_final: 0.6582 (ttp-110) REVERT: A 388 ASP cc_start: 0.8608 (p0) cc_final: 0.8320 (p0) REVERT: A 413 LYS cc_start: 0.9082 (mttt) cc_final: 0.8829 (mmmt) REVERT: A 464 ASP cc_start: 0.8835 (t70) cc_final: 0.8369 (t70) REVERT: B 130 TRP cc_start: 0.7970 (m100) cc_final: 0.7016 (m100) REVERT: B 141 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8827 (tt) REVERT: B 182 ASP cc_start: 0.8429 (t0) cc_final: 0.8000 (t0) REVERT: B 275 TRP cc_start: 0.8835 (m100) cc_final: 0.8211 (m-10) REVERT: B 338 TRP cc_start: 0.8289 (t60) cc_final: 0.8063 (t60) REVERT: B 352 SER cc_start: 0.9171 (t) cc_final: 0.8890 (t) REVERT: B 363 CYS cc_start: 0.8918 (m) cc_final: 0.8562 (m) REVERT: B 366 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7783 (tm-30) REVERT: B 387 MET cc_start: 0.7811 (mmm) cc_final: 0.7352 (mmm) REVERT: C 81 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8681 (tp) REVERT: C 149 LEU cc_start: 0.9263 (tp) cc_final: 0.8967 (tt) REVERT: C 186 ASP cc_start: 0.8766 (t0) cc_final: 0.8535 (t0) REVERT: C 282 MET cc_start: 0.9024 (tpt) cc_final: 0.8611 (tpt) REVERT: C 284 LEU cc_start: 0.9651 (OUTLIER) cc_final: 0.9343 (mm) REVERT: C 363 CYS cc_start: 0.8739 (m) cc_final: 0.8486 (m) outliers start: 68 outliers final: 39 residues processed: 302 average time/residue: 0.1893 time to fit residues: 82.0229 Evaluate side-chains 287 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 244 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU 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 186 ASP Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 301 ARG Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 467 CYS Chi-restraints excluded: chain A residue 475 ASP 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 119 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 384 THR 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 475 ASP 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 132 LEU Chi-restraints excluded: chain C residue 153 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 404 LEU Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 467 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 50 optimal weight: 0.2980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 ASN ** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.5485 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= 0.189 Angle : 0.749 12.297 13788 Z= 0.336 Chirality : 0.042 0.276 1728 Planarity : 0.003 0.032 1719 Dihedral : 4.407 51.104 1476 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 6.24 % Allowed : 28.82 % Favored : 64.94 % 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: 0.20 (0.24), residues: 1332 helix: 1.48 (0.18), residues: 885 sheet: None (None), residues: 0 loop : -2.79 (0.26), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 461 HIS 0.003 0.001 HIS A 373 PHE 0.023 0.001 PHE C 192 TYR 0.024 0.002 TYR C 485 ARG 0.006 0.000 ARG A 376 *********************** 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 324 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 259 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ILE cc_start: 0.9170 (pt) cc_final: 0.8853 (mt) REVERT: A 154 GLN cc_start: 0.9276 (mp10) cc_final: 0.9039 (mp10) REVERT: A 217 ARG cc_start: 0.6144 (ttt90) cc_final: 0.4342 (ptt90) REVERT: A 247 LYS cc_start: 0.9149 (tppt) cc_final: 0.8570 (tmtt) REVERT: A 282 MET cc_start: 0.8249 (ttm) cc_final: 0.7747 (tmm) REVERT: A 388 ASP cc_start: 0.8629 (p0) cc_final: 0.8337 (p0) REVERT: A 413 LYS cc_start: 0.9083 (mttt) cc_final: 0.8813 (mmmt) REVERT: A 464 ASP cc_start: 0.8859 (t70) cc_final: 0.8385 (t70) REVERT: B 92 PRO cc_start: 0.9030 (Cg_exo) cc_final: 0.8823 (Cg_endo) REVERT: B 130 TRP cc_start: 0.7930 (m100) cc_final: 0.7012 (m100) REVERT: B 141 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8823 (tt) REVERT: B 182 ASP cc_start: 0.8391 (t0) cc_final: 0.8004 (t0) REVERT: B 275 TRP cc_start: 0.8768 (m100) cc_final: 0.8139 (m-10) REVERT: B 338 TRP cc_start: 0.8206 (t60) cc_final: 0.8000 (t60) REVERT: B 352 SER cc_start: 0.9138 (t) cc_final: 0.8860 (t) REVERT: B 363 CYS cc_start: 0.8925 (m) cc_final: 0.8550 (m) REVERT: B 366 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7751 (tm-30) REVERT: B 387 MET cc_start: 0.7840 (mmm) cc_final: 0.7316 (mmm) REVERT: B 473 GLU cc_start: 0.8875 (tm-30) cc_final: 0.8609 (tm-30) REVERT: C 145 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8853 (tp) REVERT: C 186 ASP cc_start: 0.8778 (t0) cc_final: 0.8523 (t0) REVERT: C 282 MET cc_start: 0.9056 (tpt) cc_final: 0.8659 (tpt) REVERT: C 284 LEU cc_start: 0.9652 (OUTLIER) cc_final: 0.9328 (mm) REVERT: C 313 HIS cc_start: 0.9366 (OUTLIER) cc_final: 0.9047 (m-70) REVERT: C 363 CYS cc_start: 0.8721 (m) cc_final: 0.8483 (m) outliers start: 65 outliers final: 43 residues processed: 298 average time/residue: 0.1916 time to fit residues: 82.0988 Evaluate side-chains 291 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 244 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 CYS 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 186 ASP Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 301 ARG Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 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 A residue 475 ASP Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 328 PHE Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 384 THR 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 475 ASP Chi-restraints excluded: chain B residue 485 TYR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 313 HIS Chi-restraints excluded: chain C residue 328 PHE Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 467 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 121 optimal weight: 0.2980 chunk 111 optimal weight: 0.8980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 GLN ** B 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 403 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.5576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10116 Z= 0.224 Angle : 0.765 13.780 13788 Z= 0.348 Chirality : 0.042 0.292 1728 Planarity : 0.003 0.031 1719 Dihedral : 4.468 51.252 1476 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 6.24 % Allowed : 29.39 % Favored : 64.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.24), residues: 1332 helix: 1.45 (0.18), residues: 888 sheet: -0.34 (0.95), residues: 30 loop : -2.75 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 461 HIS 0.002 0.001 HIS B 316 PHE 0.021 0.001 PHE C 192 TYR 0.024 0.002 TYR C 485 ARG 0.003 0.000 ARG A 376 *********************** 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 314 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 249 time to evaluate : 1.063 Fit side-chains REVERT: A 104 ILE cc_start: 0.9154 (pt) cc_final: 0.8851 (mt) REVERT: A 154 GLN cc_start: 0.9301 (mp10) cc_final: 0.9085 (mp10) REVERT: A 184 PHE cc_start: 0.8100 (OUTLIER) cc_final: 0.7556 (t80) REVERT: A 217 ARG cc_start: 0.6214 (ttt90) cc_final: 0.4396 (ptt90) REVERT: A 247 LYS cc_start: 0.9162 (tppt) cc_final: 0.8580 (tmtt) REVERT: A 282 MET cc_start: 0.8315 (ttm) cc_final: 0.7805 (tmm) REVERT: A 388 ASP cc_start: 0.8555 (p0) cc_final: 0.8293 (p0) REVERT: A 413 LYS cc_start: 0.9107 (mttt) cc_final: 0.8830 (mmmt) REVERT: A 464 ASP cc_start: 0.8882 (t70) cc_final: 0.8430 (t70) REVERT: B 130 TRP cc_start: 0.7977 (m100) cc_final: 0.6991 (m100) REVERT: B 182 ASP cc_start: 0.8432 (t0) cc_final: 0.8029 (t0) REVERT: B 275 TRP cc_start: 0.8801 (m100) cc_final: 0.8149 (m-10) REVERT: B 331 LYS cc_start: 0.8396 (tptt) cc_final: 0.8178 (tptp) REVERT: B 352 SER cc_start: 0.9096 (t) cc_final: 0.8636 (p) REVERT: B 366 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7781 (tm-30) REVERT: B 387 MET cc_start: 0.7910 (mmm) cc_final: 0.7335 (mmm) REVERT: C 145 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8864 (tp) REVERT: C 186 ASP cc_start: 0.8731 (t0) cc_final: 0.8463 (t0) REVERT: C 282 MET cc_start: 0.9033 (tpt) cc_final: 0.8638 (tpt) REVERT: C 284 LEU cc_start: 0.9663 (OUTLIER) cc_final: 0.9359 (mm) REVERT: C 313 HIS cc_start: 0.9402 (OUTLIER) cc_final: 0.9046 (m-70) REVERT: C 363 CYS cc_start: 0.8715 (m) cc_final: 0.8475 (m) outliers start: 65 outliers final: 45 residues processed: 286 average time/residue: 0.1866 time to fit residues: 76.7616 Evaluate side-chains 286 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 237 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 CYS Chi-restraints excluded: chain A residue 57 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 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 A residue 475 ASP Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain B residue 48 CYS 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 180 VAL Chi-restraints excluded: chain B residue 203 SER 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 384 THR 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 475 ASP Chi-restraints excluded: chain B residue 485 TYR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 313 HIS Chi-restraints excluded: chain C residue 328 PHE Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 346 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 3.9990 chunk 121 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 107 optimal weight: 0.6980 chunk 112 optimal weight: 0.9990 chunk 77 optimal weight: 0.0010 chunk 125 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 GLN B 483 GLN C 403 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.5771 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= 0.185 Angle : 0.773 12.316 13788 Z= 0.345 Chirality : 0.042 0.266 1728 Planarity : 0.003 0.035 1719 Dihedral : 4.399 51.205 1476 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 5.28 % Allowed : 30.84 % Favored : 63.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.24), residues: 1332 helix: 1.50 (0.18), residues: 891 sheet: -0.31 (0.95), residues: 30 loop : -2.84 (0.27), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 461 HIS 0.001 0.001 HIS A 313 PHE 0.021 0.001 PHE C 192 TYR 0.025 0.002 TYR C 485 ARG 0.002 0.000 ARG A 376 *********************** 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 309 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 254 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ILE cc_start: 0.9114 (pt) cc_final: 0.8898 (mt) REVERT: A 184 PHE cc_start: 0.8134 (OUTLIER) cc_final: 0.7616 (t80) REVERT: A 217 ARG cc_start: 0.6129 (ttt90) cc_final: 0.4367 (ptt90) REVERT: A 247 LYS cc_start: 0.9145 (tppt) cc_final: 0.8569 (tmtt) REVERT: A 282 MET cc_start: 0.8344 (ttm) cc_final: 0.7829 (tmm) REVERT: A 362 LYS cc_start: 0.9291 (ttpp) cc_final: 0.8935 (tmmt) REVERT: A 376 ARG cc_start: 0.8035 (mmt90) cc_final: 0.7760 (mmt90) REVERT: A 388 ASP cc_start: 0.8531 (p0) cc_final: 0.8279 (p0) REVERT: A 413 LYS cc_start: 0.9058 (mttt) cc_final: 0.8792 (mmmt) REVERT: A 464 ASP cc_start: 0.8849 (t70) cc_final: 0.8388 (t70) REVERT: B 130 TRP cc_start: 0.7908 (m100) cc_final: 0.7131 (m100) REVERT: B 154 GLN cc_start: 0.9136 (mm110) cc_final: 0.8916 (mm110) REVERT: B 182 ASP cc_start: 0.8402 (t0) cc_final: 0.8014 (t0) REVERT: B 275 TRP cc_start: 0.8708 (m100) cc_final: 0.8072 (m-10) REVERT: B 331 LYS cc_start: 0.8317 (tptt) cc_final: 0.8071 (tptp) REVERT: B 352 SER cc_start: 0.9095 (t) cc_final: 0.8795 (t) REVERT: B 366 GLU cc_start: 0.7965 (tm-30) cc_final: 0.7737 (tm-30) REVERT: B 387 MET cc_start: 0.7787 (mmm) cc_final: 0.7232 (mmm) REVERT: C 145 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8736 (tp) REVERT: C 186 ASP cc_start: 0.8719 (t0) cc_final: 0.8440 (t0) REVERT: C 284 LEU cc_start: 0.9659 (OUTLIER) cc_final: 0.9355 (mm) REVERT: C 313 HIS cc_start: 0.9399 (OUTLIER) cc_final: 0.9112 (m-70) REVERT: C 362 LYS cc_start: 0.8960 (tppt) cc_final: 0.8545 (tppt) REVERT: C 363 CYS cc_start: 0.8824 (m) cc_final: 0.8541 (m) outliers start: 55 outliers final: 47 residues processed: 284 average time/residue: 0.1950 time to fit residues: 79.0787 Evaluate side-chains 292 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 241 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 CYS Chi-restraints excluded: chain A residue 57 LEU 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 301 ARG 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 467 CYS Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain B residue 48 CYS 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 180 VAL Chi-restraints excluded: chain B residue 203 SER 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 337 LEU Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 384 THR 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 470 LEU Chi-restraints excluded: chain B residue 475 ASP Chi-restraints excluded: chain B residue 485 TYR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 313 HIS Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 328 PHE Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 404 LEU 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 59 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 121 optimal weight: 0.0070 chunk 104 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 80 optimal weight: 0.4980 chunk 64 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 111 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.5798 ------------------------------------------------------------------------------- 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 ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.5900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10116 Z= 0.178 Angle : 0.772 13.683 13788 Z= 0.343 Chirality : 0.041 0.256 1728 Planarity : 0.003 0.032 1719 Dihedral : 4.330 51.447 1476 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 4.90 % Allowed : 30.93 % Favored : 64.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.24), residues: 1332 helix: 1.56 (0.18), residues: 891 sheet: None (None), residues: 0 loop : -2.77 (0.26), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 461 HIS 0.002 0.001 HIS B 316 PHE 0.020 0.001 PHE C 192 TYR 0.024 0.001 TYR C 485 ARG 0.007 0.000 ARG C 50 ********************** 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 311 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 260 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 PHE cc_start: 0.8114 (OUTLIER) cc_final: 0.7583 (t80) REVERT: A 217 ARG cc_start: 0.6137 (ttt90) cc_final: 0.4376 (ptt90) REVERT: A 247 LYS cc_start: 0.9125 (tppt) cc_final: 0.8558 (tmtt) REVERT: A 267 MET cc_start: 0.8731 (mmm) cc_final: 0.8074 (mmm) REVERT: A 282 MET cc_start: 0.8333 (ttm) cc_final: 0.7819 (tmm) REVERT: A 362 LYS cc_start: 0.9240 (ttpp) cc_final: 0.8907 (tmmt) REVERT: A 388 ASP cc_start: 0.8440 (p0) cc_final: 0.8167 (p0) REVERT: A 413 LYS cc_start: 0.9036 (mttt) cc_final: 0.8814 (mmmt) REVERT: A 464 ASP cc_start: 0.8834 (t70) cc_final: 0.8382 (t70) REVERT: B 130 TRP cc_start: 0.7884 (m100) cc_final: 0.7120 (m100) REVERT: B 182 ASP cc_start: 0.8333 (t0) cc_final: 0.7981 (t0) REVERT: B 208 TYR cc_start: 0.7681 (m-80) cc_final: 0.7371 (m-80) REVERT: B 275 TRP cc_start: 0.8682 (m100) cc_final: 0.8067 (m-10) REVERT: B 352 SER cc_start: 0.9112 (t) cc_final: 0.8841 (t) REVERT: B 366 GLU cc_start: 0.7940 (tm-30) cc_final: 0.7727 (tm-30) REVERT: B 387 MET cc_start: 0.7795 (mmm) cc_final: 0.7270 (mmm) REVERT: C 145 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8753 (tp) REVERT: C 179 GLU cc_start: 0.7565 (mp0) cc_final: 0.7207 (mp0) REVERT: C 186 ASP cc_start: 0.8728 (t0) cc_final: 0.8444 (t0) REVERT: C 267 MET cc_start: 0.9031 (tpp) cc_final: 0.8812 (mmm) REVERT: C 273 ILE cc_start: 0.9572 (mm) cc_final: 0.9319 (mp) REVERT: C 284 LEU cc_start: 0.9661 (OUTLIER) cc_final: 0.9354 (mm) REVERT: C 313 HIS cc_start: 0.9353 (OUTLIER) cc_final: 0.9107 (m-70) REVERT: C 363 CYS cc_start: 0.8802 (m) cc_final: 0.8546 (m) outliers start: 51 outliers final: 45 residues processed: 288 average time/residue: 0.1904 time to fit residues: 79.2962 Evaluate side-chains 293 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 244 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 CYS Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 100 LEU 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 301 ARG 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 467 CYS Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 328 PHE Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 384 THR 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 470 LEU Chi-restraints excluded: chain B residue 485 TYR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 313 HIS Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 328 PHE Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 404 LEU 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 96 optimal weight: 0.9990 chunk 15 optimal weight: 0.2980 chunk 29 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 19 optimal weight: 0.6980 chunk 92 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.101077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.078824 restraints weight = 24011.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.081385 restraints weight = 12531.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.083097 restraints weight = 8291.015| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.5952 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 : 0.777 11.364 13788 Z= 0.346 Chirality : 0.042 0.259 1728 Planarity : 0.003 0.032 1719 Dihedral : 4.339 51.623 1476 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 5.48 % Allowed : 30.16 % Favored : 64.36 % 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: 0.45 (0.24), residues: 1332 helix: 1.58 (0.18), residues: 891 sheet: -0.21 (0.95), residues: 30 loop : -2.69 (0.28), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 461 HIS 0.002 0.001 HIS A 313 PHE 0.051 0.001 PHE C 192 TYR 0.024 0.001 TYR C 485 ARG 0.007 0.000 ARG C 50 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2337.52 seconds wall clock time: 42 minutes 30.04 seconds (2550.04 seconds total)