Starting phenix.real_space_refine on Fri Jan 19 21:03:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vfe_31950/01_2024/7vfe_31950.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vfe_31950/01_2024/7vfe_31950.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vfe_31950/01_2024/7vfe_31950.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vfe_31950/01_2024/7vfe_31950.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vfe_31950/01_2024/7vfe_31950.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vfe_31950/01_2024/7vfe_31950.pdb" } resolution = 2.63 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= 0.000 sd= 1.000 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 36 5.16 5 C 8079 2.51 5 N 2052 2.21 5 O 2463 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 57": "OE1" <-> "OE2" Residue "A GLU 74": "OE1" <-> "OE2" Residue "A TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 113": "OE1" <-> "OE2" Residue "A ASP 137": "OD1" <-> "OD2" Residue "A TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 165": "OE1" <-> "OE2" Residue "A GLU 230": "OE1" <-> "OE2" Residue "A GLU 248": "OE1" <-> "OE2" Residue "A TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 293": "OD1" <-> "OD2" Residue "A ASP 318": "OD1" <-> "OD2" Residue "A TYR 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 333": "OD1" <-> "OD2" Residue "A TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 444": "OE1" <-> "OE2" Residue "A PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 531": "OD1" <-> "OD2" Residue "B PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 57": "OE1" <-> "OE2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "B TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 113": "OE1" <-> "OE2" Residue "B ASP 137": "OD1" <-> "OD2" Residue "B TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 165": "OE1" <-> "OE2" Residue "B GLU 230": "OE1" <-> "OE2" Residue "B GLU 248": "OE1" <-> "OE2" Residue "B TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 293": "OD1" <-> "OD2" Residue "B ASP 318": "OD1" <-> "OD2" Residue "B TYR 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 333": "OD1" <-> "OD2" Residue "B TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 444": "OE1" <-> "OE2" Residue "B PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 531": "OD1" <-> "OD2" Residue "C PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 57": "OE1" <-> "OE2" Residue "C GLU 74": "OE1" <-> "OE2" Residue "C TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 113": "OE1" <-> "OE2" Residue "C ASP 137": "OD1" <-> "OD2" Residue "C TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 165": "OE1" <-> "OE2" Residue "C GLU 230": "OE1" <-> "OE2" Residue "C GLU 248": "OE1" <-> "OE2" Residue "C TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 293": "OD1" <-> "OD2" Residue "C ASP 318": "OD1" <-> "OD2" Residue "C TYR 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 333": "OD1" <-> "OD2" Residue "C TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 444": "OE1" <-> "OE2" Residue "C PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 531": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 12630 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4210 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 25, 'TRANS': 503} Chain breaks: 1 Chain: "B" Number of atoms: 4210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4210 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 25, 'TRANS': 503} Chain breaks: 1 Chain: "C" Number of atoms: 4210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4210 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 25, 'TRANS': 503} Chain breaks: 1 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N ARG A 83 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG A 83 " occ=0.50 residue: pdb=" N ARG B 83 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG B 83 " occ=0.50 residue: pdb=" N ARG C 83 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG C 83 " occ=0.50 Time building chain proxies: 6.93, per 1000 atoms: 0.55 Number of scatterers: 12630 At special positions: 0 Unit cell: (99.456, 102.564, 111.888, 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 36 16.00 O 2463 8.00 N 2052 7.00 C 8079 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 Time building additional restraints: 4.37 Conformation dependent library (CDL) restraints added in 2.6 seconds 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3024 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 36 sheets defined 19.8% alpha, 42.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.92 Creating SS restraints... Processing helix chain 'A' and resid 89 through 94 Processing helix chain 'A' and resid 112 through 120 Processing helix chain 'A' and resid 122 through 129 Processing helix chain 'A' and resid 132 through 137 Processing helix chain 'A' and resid 160 through 164 removed outlier: 3.800A pdb=" N VAL A 164 " --> pdb=" O PRO A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 169 Processing helix chain 'A' and resid 186 through 189 Processing helix chain 'A' and resid 198 through 206 Processing helix chain 'A' and resid 279 through 295 removed outlier: 4.127A pdb=" N ASP A 293 " --> pdb=" O SER A 289 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ASP A 294 " --> pdb=" O ARG A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 394 removed outlier: 3.590A pdb=" N THR A 393 " --> pdb=" O ASN A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 401 removed outlier: 3.777A pdb=" N TRP A 400 " --> pdb=" O PRO A 396 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR A 401 " --> pdb=" O VAL A 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 396 through 401' Processing helix chain 'A' and resid 413 through 418 Processing helix chain 'A' and resid 458 through 469 Processing helix chain 'A' and resid 516 through 521 Processing helix chain 'B' and resid 89 through 94 Processing helix chain 'B' and resid 112 through 120 Processing helix chain 'B' and resid 122 through 129 Processing helix chain 'B' and resid 132 through 137 Processing helix chain 'B' and resid 160 through 164 removed outlier: 3.801A pdb=" N VAL B 164 " --> pdb=" O PRO B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 169 Processing helix chain 'B' and resid 186 through 189 Processing helix chain 'B' and resid 198 through 206 Processing helix chain 'B' and resid 279 through 295 removed outlier: 4.127A pdb=" N ASP B 293 " --> pdb=" O SER B 289 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ASP B 294 " --> pdb=" O ARG B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 394 removed outlier: 3.591A pdb=" N THR B 393 " --> pdb=" O ASN B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 401 removed outlier: 3.778A pdb=" N TRP B 400 " --> pdb=" O PRO B 396 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR B 401 " --> pdb=" O VAL B 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 396 through 401' Processing helix chain 'B' and resid 413 through 418 Processing helix chain 'B' and resid 458 through 469 Processing helix chain 'B' and resid 516 through 521 Processing helix chain 'C' and resid 89 through 94 Processing helix chain 'C' and resid 112 through 120 Processing helix chain 'C' and resid 122 through 129 Processing helix chain 'C' and resid 132 through 137 Processing helix chain 'C' and resid 160 through 164 removed outlier: 3.801A pdb=" N VAL C 164 " --> pdb=" O PRO C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 169 Processing helix chain 'C' and resid 186 through 189 Processing helix chain 'C' and resid 198 through 206 Processing helix chain 'C' and resid 279 through 295 removed outlier: 4.127A pdb=" N ASP C 293 " --> pdb=" O SER C 289 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ASP C 294 " --> pdb=" O ARG C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 394 removed outlier: 3.592A pdb=" N THR C 393 " --> pdb=" O ASN C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 401 removed outlier: 3.777A pdb=" N TRP C 400 " --> pdb=" O PRO C 396 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR C 401 " --> pdb=" O VAL C 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 396 through 401' Processing helix chain 'C' and resid 413 through 418 Processing helix chain 'C' and resid 458 through 469 Processing helix chain 'C' and resid 516 through 521 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 40 removed outlier: 3.918A pdb=" N ILE A 215 " --> pdb=" O HIS A 68 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N HIS A 68 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N TYR A 217 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N LEU A 66 " --> pdb=" O TYR A 217 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU A 69 " --> pdb=" O ILE A 158 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 40 removed outlier: 3.918A pdb=" N ILE A 215 " --> pdb=" O HIS A 68 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N HIS A 68 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N TYR A 217 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N LEU A 66 " --> pdb=" O TYR A 217 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 44 removed outlier: 6.656A pdb=" N THR A 179 " --> pdb=" O ILE A 100 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ILE A 100 " --> pdb=" O THR A 179 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR A 181 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL A 98 " --> pdb=" O THR A 181 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THR A 183 " --> pdb=" O ASN A 96 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ASN A 96 " --> pdb=" O GLU A 111 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N GLU A 111 " --> pdb=" O ASN A 96 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL A 98 " --> pdb=" O GLU A 109 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLU A 109 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE A 100 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY A 105 " --> pdb=" O SER A 102 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 78 through 79 removed outlier: 6.607A pdb=" N VAL A 78 " --> pdb=" O ILE A 148 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 139 through 141 Processing sheet with id=AA6, first strand: chain 'A' and resid 227 through 236 removed outlier: 3.968A pdb=" N GLN A 522 " --> pdb=" O TYR A 262 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N SER A 254 " --> pdb=" O ASN A 530 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU A 532 " --> pdb=" O ALA A 252 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ALA A 252 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA A 252 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 475 through 478 removed outlier: 3.663A pdb=" N ARG A 475 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ALA A 252 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU A 532 " --> pdb=" O ALA A 252 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N SER A 254 " --> pdb=" O ASN A 530 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLN A 522 " --> pdb=" O TYR A 262 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 243 through 247 removed outlier: 6.426A pdb=" N LYS A 502 " --> pdb=" O PHE A 447 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N PHE A 447 " --> pdb=" O LYS A 502 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N SER A 504 " --> pdb=" O VAL A 445 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N VAL A 445 " --> pdb=" O SER A 504 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ARG A 506 " --> pdb=" O LEU A 443 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N LEU A 443 " --> pdb=" O ARG A 506 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL A 508 " --> pdb=" O SER A 441 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N PHE A 447 " --> pdb=" O VAL A 451 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N VAL A 451 " --> pdb=" O PHE A 447 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 269 through 270 Processing sheet with id=AB1, first strand: chain 'A' and resid 296 through 299 Processing sheet with id=AB2, first strand: chain 'A' and resid 320 through 322 removed outlier: 6.779A pdb=" N ASP A 327 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N ILE A 368 " --> pdb=" O ASP A 327 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N TYR A 329 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N GLY A 370 " --> pdb=" O TYR A 329 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LYS A 331 " --> pdb=" O GLY A 370 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N TYR A 372 " --> pdb=" O LYS A 331 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ASP A 333 " --> pdb=" O TYR A 372 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N PHE A 365 " --> pdb=" O HIS A 386 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N HIS A 386 " --> pdb=" O PHE A 365 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA A 367 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ILE A 384 " --> pdb=" O ALA A 367 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N THR A 369 " --> pdb=" O ALA A 382 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 349 through 350 Processing sheet with id=AB4, first strand: chain 'B' and resid 32 through 40 removed outlier: 3.917A pdb=" N ILE B 215 " --> pdb=" O HIS B 68 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N HIS B 68 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N TYR B 217 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N LEU B 66 " --> pdb=" O TYR B 217 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU B 69 " --> pdb=" O ILE B 158 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 32 through 40 removed outlier: 3.917A pdb=" N ILE B 215 " --> pdb=" O HIS B 68 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N HIS B 68 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N TYR B 217 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N LEU B 66 " --> pdb=" O TYR B 217 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 42 through 44 removed outlier: 6.656A pdb=" N THR B 179 " --> pdb=" O ILE B 100 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ILE B 100 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N THR B 181 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL B 98 " --> pdb=" O THR B 181 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THR B 183 " --> pdb=" O ASN B 96 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ASN B 96 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N GLU B 111 " --> pdb=" O ASN B 96 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL B 98 " --> pdb=" O GLU B 109 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLU B 109 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE B 100 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY B 105 " --> pdb=" O SER B 102 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 78 through 79 removed outlier: 6.608A pdb=" N VAL B 78 " --> pdb=" O ILE B 148 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 139 through 141 Processing sheet with id=AB9, first strand: chain 'B' and resid 227 through 236 removed outlier: 3.968A pdb=" N GLN B 522 " --> pdb=" O TYR B 262 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N SER B 254 " --> pdb=" O ASN B 530 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU B 532 " --> pdb=" O ALA B 252 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ALA B 252 " --> pdb=" O LEU B 532 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA B 252 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 475 through 478 removed outlier: 3.663A pdb=" N ARG B 475 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ALA B 252 " --> pdb=" O LEU B 532 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU B 532 " --> pdb=" O ALA B 252 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N SER B 254 " --> pdb=" O ASN B 530 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLN B 522 " --> pdb=" O TYR B 262 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 243 through 247 removed outlier: 6.426A pdb=" N LYS B 502 " --> pdb=" O PHE B 447 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N PHE B 447 " --> pdb=" O LYS B 502 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N SER B 504 " --> pdb=" O VAL B 445 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N VAL B 445 " --> pdb=" O SER B 504 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ARG B 506 " --> pdb=" O LEU B 443 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N LEU B 443 " --> pdb=" O ARG B 506 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL B 508 " --> pdb=" O SER B 441 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N PHE B 447 " --> pdb=" O VAL B 451 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N VAL B 451 " --> pdb=" O PHE B 447 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 269 through 270 Processing sheet with id=AC4, first strand: chain 'B' and resid 296 through 299 Processing sheet with id=AC5, first strand: chain 'B' and resid 320 through 322 removed outlier: 6.779A pdb=" N ASP B 327 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N ILE B 368 " --> pdb=" O ASP B 327 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N TYR B 329 " --> pdb=" O ILE B 368 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N GLY B 370 " --> pdb=" O TYR B 329 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LYS B 331 " --> pdb=" O GLY B 370 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N TYR B 372 " --> pdb=" O LYS B 331 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ASP B 333 " --> pdb=" O TYR B 372 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N PHE B 365 " --> pdb=" O HIS B 386 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N HIS B 386 " --> pdb=" O PHE B 365 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ALA B 367 " --> pdb=" O ILE B 384 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ILE B 384 " --> pdb=" O ALA B 367 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N THR B 369 " --> pdb=" O ALA B 382 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 349 through 350 Processing sheet with id=AC7, first strand: chain 'C' and resid 32 through 40 removed outlier: 3.916A pdb=" N ILE C 215 " --> pdb=" O HIS C 68 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N HIS C 68 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N TYR C 217 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N LEU C 66 " --> pdb=" O TYR C 217 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU C 69 " --> pdb=" O ILE C 158 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 32 through 40 removed outlier: 3.916A pdb=" N ILE C 215 " --> pdb=" O HIS C 68 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N HIS C 68 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N TYR C 217 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N LEU C 66 " --> pdb=" O TYR C 217 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 42 through 44 removed outlier: 6.657A pdb=" N THR C 179 " --> pdb=" O ILE C 100 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ILE C 100 " --> pdb=" O THR C 179 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR C 181 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N VAL C 98 " --> pdb=" O THR C 181 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THR C 183 " --> pdb=" O ASN C 96 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ASN C 96 " --> pdb=" O GLU C 111 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N GLU C 111 " --> pdb=" O ASN C 96 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL C 98 " --> pdb=" O GLU C 109 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLU C 109 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE C 100 " --> pdb=" O ILE C 107 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY C 105 " --> pdb=" O SER C 102 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 78 through 79 removed outlier: 6.607A pdb=" N VAL C 78 " --> pdb=" O ILE C 148 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 139 through 141 Processing sheet with id=AD3, first strand: chain 'C' and resid 227 through 236 removed outlier: 3.968A pdb=" N GLN C 522 " --> pdb=" O TYR C 262 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N SER C 254 " --> pdb=" O ASN C 530 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU C 532 " --> pdb=" O ALA C 252 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ALA C 252 " --> pdb=" O LEU C 532 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA C 252 " --> pdb=" O ILE C 492 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 475 through 478 removed outlier: 3.662A pdb=" N ARG C 475 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ALA C 252 " --> pdb=" O LEU C 532 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU C 532 " --> pdb=" O ALA C 252 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N SER C 254 " --> pdb=" O ASN C 530 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLN C 522 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 243 through 247 removed outlier: 6.427A pdb=" N LYS C 502 " --> pdb=" O PHE C 447 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N PHE C 447 " --> pdb=" O LYS C 502 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N SER C 504 " --> pdb=" O VAL C 445 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N VAL C 445 " --> pdb=" O SER C 504 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ARG C 506 " --> pdb=" O LEU C 443 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N LEU C 443 " --> pdb=" O ARG C 506 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL C 508 " --> pdb=" O SER C 441 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N PHE C 447 " --> pdb=" O VAL C 451 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N VAL C 451 " --> pdb=" O PHE C 447 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 269 through 270 Processing sheet with id=AD7, first strand: chain 'C' and resid 296 through 299 Processing sheet with id=AD8, first strand: chain 'C' and resid 320 through 322 removed outlier: 6.779A pdb=" N ASP C 327 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N ILE C 368 " --> pdb=" O ASP C 327 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N TYR C 329 " --> pdb=" O ILE C 368 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N GLY C 370 " --> pdb=" O TYR C 329 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LYS C 331 " --> pdb=" O GLY C 370 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N TYR C 372 " --> pdb=" O LYS C 331 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ASP C 333 " --> pdb=" O TYR C 372 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N PHE C 365 " --> pdb=" O HIS C 386 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N HIS C 386 " --> pdb=" O PHE C 365 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA C 367 " --> pdb=" O ILE C 384 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ILE C 384 " --> pdb=" O ALA C 367 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR C 369 " --> pdb=" O ALA C 382 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 349 through 350 480 hydrogen bonds defined for protein. 1251 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: 4.89 Time building geometry restraints manager: 4.77 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: 4026 1.34 - 1.45: 2308 1.45 - 1.57: 6512 1.57 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 12906 Sorted by residual: bond pdb=" CB CYS C 94 " pdb=" SG CYS C 94 " ideal model delta sigma weight residual 1.808 1.749 0.059 3.30e-02 9.18e+02 3.21e+00 bond pdb=" CB CYS B 94 " pdb=" SG CYS B 94 " ideal model delta sigma weight residual 1.808 1.749 0.059 3.30e-02 9.18e+02 3.20e+00 bond pdb=" CB CYS A 94 " pdb=" SG CYS A 94 " ideal model delta sigma weight residual 1.808 1.750 0.058 3.30e-02 9.18e+02 3.09e+00 bond pdb=" CA ASN C 45 " pdb=" CB ASN C 45 " ideal model delta sigma weight residual 1.530 1.497 0.033 2.00e-02 2.50e+03 2.72e+00 bond pdb=" CA ASN A 45 " pdb=" CB ASN A 45 " ideal model delta sigma weight residual 1.530 1.497 0.033 2.00e-02 2.50e+03 2.68e+00 ... (remaining 12901 not shown) Histogram of bond angle deviations from ideal: 100.26 - 107.01: 365 107.01 - 113.77: 7310 113.77 - 120.52: 4796 120.52 - 127.28: 4999 127.28 - 134.03: 86 Bond angle restraints: 17556 Sorted by residual: angle pdb=" N ILE A 395 " pdb=" CA ILE A 395 " pdb=" C ILE A 395 " ideal model delta sigma weight residual 108.95 113.29 -4.34 9.80e-01 1.04e+00 1.96e+01 angle pdb=" N ILE C 395 " pdb=" CA ILE C 395 " pdb=" C ILE C 395 " ideal model delta sigma weight residual 108.95 113.29 -4.34 9.80e-01 1.04e+00 1.96e+01 angle pdb=" N ILE B 395 " pdb=" CA ILE B 395 " pdb=" C ILE B 395 " ideal model delta sigma weight residual 108.95 113.27 -4.32 9.80e-01 1.04e+00 1.94e+01 angle pdb=" CA LYS A 93 " pdb=" CB LYS A 93 " pdb=" CG LYS A 93 " ideal model delta sigma weight residual 114.10 110.11 3.99 2.00e+00 2.50e-01 3.98e+00 angle pdb=" CA LYS C 93 " pdb=" CB LYS C 93 " pdb=" CG LYS C 93 " ideal model delta sigma weight residual 114.10 110.12 3.98 2.00e+00 2.50e-01 3.96e+00 ... (remaining 17551 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 7144 17.99 - 35.98: 455 35.98 - 53.98: 123 53.98 - 71.97: 22 71.97 - 89.96: 11 Dihedral angle restraints: 7755 sinusoidal: 3054 harmonic: 4701 Sorted by residual: dihedral pdb=" CA PRO B 483 " pdb=" C PRO B 483 " pdb=" N LYS B 484 " pdb=" CA LYS B 484 " ideal model delta harmonic sigma weight residual -180.00 -160.77 -19.23 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA PRO A 483 " pdb=" C PRO A 483 " pdb=" N LYS A 484 " pdb=" CA LYS A 484 " ideal model delta harmonic sigma weight residual -180.00 -160.79 -19.21 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA TYR B 407 " pdb=" C TYR B 407 " pdb=" N ASN B 408 " pdb=" CA ASN B 408 " ideal model delta harmonic sigma weight residual 180.00 160.80 19.20 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 7752 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 817 0.028 - 0.056: 598 0.056 - 0.084: 350 0.084 - 0.112: 209 0.112 - 0.140: 51 Chirality restraints: 2025 Sorted by residual: chirality pdb=" CA LYS B 93 " pdb=" N LYS B 93 " pdb=" C LYS B 93 " pdb=" CB LYS B 93 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.91e-01 chirality pdb=" CA LYS C 93 " pdb=" N LYS C 93 " pdb=" C LYS C 93 " pdb=" CB LYS C 93 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.89e-01 chirality pdb=" CA LYS A 93 " pdb=" N LYS A 93 " pdb=" C LYS A 93 " pdb=" CB LYS A 93 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.70e-01 ... (remaining 2022 not shown) Planarity restraints: 2241 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 209 " 0.037 5.00e-02 4.00e+02 5.59e-02 5.01e+00 pdb=" N PRO A 210 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 210 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 210 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 209 " -0.037 5.00e-02 4.00e+02 5.56e-02 4.94e+00 pdb=" N PRO B 210 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 210 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 210 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 209 " 0.037 5.00e-02 4.00e+02 5.55e-02 4.94e+00 pdb=" N PRO C 210 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO C 210 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 210 " 0.031 5.00e-02 4.00e+02 ... (remaining 2238 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 3531 2.81 - 3.33: 10626 3.33 - 3.85: 22044 3.85 - 4.38: 25568 4.38 - 4.90: 43320 Nonbonded interactions: 105089 Sorted by model distance: nonbonded pdb=" OG SER A 322 " pdb=" OD1 ASP A 327 " model vdw 2.285 2.440 nonbonded pdb=" OG SER B 322 " pdb=" OD1 ASP B 327 " model vdw 2.285 2.440 nonbonded pdb=" OG SER C 322 " pdb=" OD1 ASP C 327 " model vdw 2.286 2.440 nonbonded pdb=" OG1 THR C 352 " pdb=" OD1 ASN C 515 " model vdw 2.391 2.440 nonbonded pdb=" OG1 THR B 352 " pdb=" OD1 ASN B 515 " model vdw 2.392 2.440 ... (remaining 105084 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.730 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: 4.050 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 36.900 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.060 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:13.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 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 : 0.008 0.059 12906 Z= 0.505 Angle : 0.582 6.768 17556 Z= 0.322 Chirality : 0.053 0.140 2025 Planarity : 0.005 0.056 2241 Dihedral : 13.518 89.962 4731 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.08 % Allowed : 8.83 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.19), residues: 1575 helix: -1.39 (0.29), residues: 228 sheet: 0.34 (0.23), residues: 468 loop : -0.71 (0.19), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 108 HIS 0.004 0.001 HIS C 97 PHE 0.016 0.002 PHE A 84 TYR 0.014 0.002 TYR A 463 ARG 0.004 0.001 ARG C 475 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 184 time to evaluate : 1.566 Fit side-chains revert: symmetry clash REVERT: A 547 MET cc_start: 0.7797 (mmt) cc_final: 0.7338 (mmt) REVERT: C 33 MET cc_start: 0.8670 (tpt) cc_final: 0.8375 (tpp) REVERT: C 62 TYR cc_start: 0.7645 (m-80) cc_final: 0.7321 (m-80) REVERT: C 471 ASN cc_start: 0.8197 (m-40) cc_final: 0.7894 (m-40) outliers start: 45 outliers final: 22 residues processed: 223 average time/residue: 1.2234 time to fit residues: 296.9672 Evaluate side-chains 139 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 117 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 454 SER Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain C residue 538 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.8980 chunk 118 optimal weight: 0.0670 chunk 65 optimal weight: 0.6980 chunk 40 optimal weight: 0.3980 chunk 79 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 141 optimal weight: 0.8980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN B 61 GLN B 403 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 12906 Z= 0.142 Angle : 0.461 7.883 17556 Z= 0.247 Chirality : 0.047 0.166 2025 Planarity : 0.004 0.044 2241 Dihedral : 5.577 92.306 1754 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.33 % Allowed : 13.42 % Favored : 84.26 % 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: -0.06 (0.20), residues: 1575 helix: -0.13 (0.35), residues: 228 sheet: 0.62 (0.23), residues: 468 loop : -0.32 (0.20), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 108 HIS 0.003 0.001 HIS C 383 PHE 0.012 0.001 PHE C 199 TYR 0.012 0.001 TYR C 520 ARG 0.003 0.000 ARG A 234 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 138 time to evaluate : 1.415 Fit side-chains revert: symmetry clash REVERT: A 113 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.7452 (tp30) REVERT: A 538 ASP cc_start: 0.6982 (OUTLIER) cc_final: 0.6765 (p0) REVERT: A 547 MET cc_start: 0.7827 (mmt) cc_final: 0.7309 (mmt) REVERT: B 471 ASN cc_start: 0.8045 (m-40) cc_final: 0.7839 (m-40) REVERT: C 220 LYS cc_start: 0.7992 (mppt) cc_final: 0.7641 (mmtp) REVERT: C 471 ASN cc_start: 0.8063 (m-40) cc_final: 0.7775 (m-40) REVERT: C 524 GLN cc_start: 0.8814 (mt0) cc_final: 0.8509 (mt0) outliers start: 34 outliers final: 13 residues processed: 166 average time/residue: 1.2213 time to fit residues: 221.8827 Evaluate side-chains 138 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 123 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 502 LYS Chi-restraints excluded: chain B residue 538 ASP Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain C residue 538 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 117 optimal weight: 0.0970 chunk 96 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 chunk 153 optimal weight: 0.8980 chunk 126 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 overall best weight: 2.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 334 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 12906 Z= 0.445 Angle : 0.584 7.689 17556 Z= 0.309 Chirality : 0.052 0.171 2025 Planarity : 0.005 0.052 2241 Dihedral : 5.437 73.072 1740 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.81 % Allowed : 14.10 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.20), residues: 1575 helix: -0.11 (0.35), residues: 228 sheet: 0.88 (0.24), residues: 438 loop : -0.24 (0.19), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 108 HIS 0.008 0.002 HIS A 516 PHE 0.016 0.002 PHE B 199 TYR 0.017 0.002 TYR A 520 ARG 0.005 0.001 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 119 time to evaluate : 1.426 Fit side-chains revert: symmetry clash REVERT: A 74 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7662 (mt-10) REVERT: A 113 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.7481 (tp30) REVERT: A 547 MET cc_start: 0.7900 (mmt) cc_final: 0.7568 (mmt) REVERT: B 33 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.8006 (tpt) REVERT: B 113 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8165 (tp30) REVERT: B 325 ASP cc_start: 0.7130 (p0) cc_final: 0.6836 (p0) REVERT: B 471 ASN cc_start: 0.8271 (m-40) cc_final: 0.7996 (m-40) REVERT: C 74 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7534 (mt-10) REVERT: C 220 LYS cc_start: 0.8137 (mppt) cc_final: 0.7709 (mmtp) outliers start: 41 outliers final: 24 residues processed: 149 average time/residue: 1.2649 time to fit residues: 206.3473 Evaluate side-chains 144 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 115 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain B residue 33 MET Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 378 ARG Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 502 LYS Chi-restraints excluded: chain B residue 538 ASP Chi-restraints excluded: chain C residue 74 GLU Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 374 ASP Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain C residue 502 LYS Chi-restraints excluded: chain C residue 538 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 150 optimal weight: 0.1980 chunk 74 optimal weight: 3.9990 chunk 134 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 334 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12906 Z= 0.212 Angle : 0.483 9.036 17556 Z= 0.254 Chirality : 0.047 0.164 2025 Planarity : 0.004 0.052 2241 Dihedral : 4.997 56.686 1740 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.92 % Allowed : 15.13 % Favored : 82.96 % 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: 0.22 (0.21), residues: 1575 helix: 0.19 (0.36), residues: 228 sheet: 0.81 (0.24), residues: 465 loop : -0.17 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 108 HIS 0.003 0.001 HIS A 516 PHE 0.013 0.001 PHE C 199 TYR 0.013 0.001 TYR A 520 ARG 0.002 0.000 ARG A 234 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 121 time to evaluate : 1.505 Fit side-chains revert: symmetry clash REVERT: A 74 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7620 (mt-10) REVERT: A 113 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.7466 (tp30) REVERT: A 547 MET cc_start: 0.7893 (mmt) cc_final: 0.7523 (mmt) REVERT: B 471 ASN cc_start: 0.8224 (m-40) cc_final: 0.7933 (m-40) REVERT: C 74 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7486 (mt-10) REVERT: C 220 LYS cc_start: 0.8132 (mppt) cc_final: 0.7724 (mmtp) outliers start: 28 outliers final: 17 residues processed: 142 average time/residue: 1.2387 time to fit residues: 192.4816 Evaluate side-chains 139 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 119 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 378 ARG Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 502 LYS Chi-restraints excluded: chain B residue 538 ASP Chi-restraints excluded: chain C residue 74 GLU Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain C residue 502 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 chunk 2 optimal weight: 0.8980 chunk 112 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 128 optimal weight: 0.0570 chunk 104 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 135 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 overall best weight: 1.1902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12906 Z= 0.209 Angle : 0.477 9.171 17556 Z= 0.249 Chirality : 0.047 0.131 2025 Planarity : 0.004 0.051 2241 Dihedral : 4.602 56.276 1735 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.60 % Allowed : 14.51 % Favored : 82.89 % 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: 0.32 (0.21), residues: 1575 helix: 0.33 (0.36), residues: 228 sheet: 0.81 (0.24), residues: 468 loop : -0.07 (0.20), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 108 HIS 0.002 0.001 HIS C 516 PHE 0.012 0.001 PHE C 199 TYR 0.012 0.001 TYR A 520 ARG 0.002 0.000 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 119 time to evaluate : 1.392 Fit side-chains revert: symmetry clash REVERT: A 35 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.7390 (tm-30) REVERT: A 74 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7604 (mt-10) REVERT: A 113 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.7472 (tp30) REVERT: A 547 MET cc_start: 0.7790 (mmt) cc_final: 0.7450 (mmt) REVERT: B 113 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8079 (tt0) REVERT: B 325 ASP cc_start: 0.7480 (p0) cc_final: 0.7107 (p0) REVERT: B 471 ASN cc_start: 0.8216 (m-40) cc_final: 0.7933 (m-40) REVERT: C 74 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7569 (mt-10) REVERT: C 220 LYS cc_start: 0.8159 (mppt) cc_final: 0.7780 (mmtp) outliers start: 38 outliers final: 22 residues processed: 152 average time/residue: 1.1712 time to fit residues: 195.6541 Evaluate side-chains 145 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 118 time to evaluate : 1.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 378 ARG Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 502 LYS Chi-restraints excluded: chain B residue 538 ASP Chi-restraints excluded: chain C residue 74 GLU Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain C residue 502 LYS Chi-restraints excluded: chain C residue 538 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 3.9990 chunk 135 optimal weight: 0.3980 chunk 29 optimal weight: 4.9990 chunk 88 optimal weight: 0.4980 chunk 37 optimal weight: 0.9990 chunk 150 optimal weight: 0.5980 chunk 125 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 12 optimal weight: 0.0980 chunk 49 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12906 Z= 0.122 Angle : 0.437 10.128 17556 Z= 0.226 Chirality : 0.046 0.126 2025 Planarity : 0.004 0.051 2241 Dihedral : 4.317 58.971 1735 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.26 % Allowed : 14.99 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.21), residues: 1575 helix: 0.35 (0.36), residues: 234 sheet: 0.85 (0.24), residues: 468 loop : 0.05 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 108 HIS 0.001 0.000 HIS A 97 PHE 0.009 0.001 PHE A 199 TYR 0.010 0.001 TYR B 520 ARG 0.004 0.000 ARG C 378 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 121 time to evaluate : 1.597 Fit side-chains REVERT: A 74 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7594 (mt-10) REVERT: A 245 THR cc_start: 0.9126 (OUTLIER) cc_final: 0.8696 (m) REVERT: A 547 MET cc_start: 0.7759 (mmt) cc_final: 0.7412 (mmt) REVERT: B 113 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.7975 (tt0) REVERT: B 325 ASP cc_start: 0.7473 (OUTLIER) cc_final: 0.7215 (p0) REVERT: B 471 ASN cc_start: 0.8130 (m-40) cc_final: 0.7844 (m-40) REVERT: C 74 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7563 (mt-10) REVERT: C 220 LYS cc_start: 0.8139 (mppt) cc_final: 0.7790 (mmtp) outliers start: 33 outliers final: 20 residues processed: 148 average time/residue: 1.2435 time to fit residues: 201.9312 Evaluate side-chains 141 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 116 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 378 ARG Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 502 LYS Chi-restraints excluded: chain B residue 538 ASP Chi-restraints excluded: chain C residue 74 GLU Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain C residue 538 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 chunk 110 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 150 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 12906 Z= 0.379 Angle : 0.544 9.927 17556 Z= 0.283 Chirality : 0.050 0.139 2025 Planarity : 0.004 0.053 2241 Dihedral : 4.816 57.498 1735 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.35 % Allowed : 14.17 % Favored : 82.48 % 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: 0.32 (0.21), residues: 1575 helix: 0.26 (0.36), residues: 228 sheet: 0.87 (0.23), residues: 480 loop : -0.10 (0.20), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 108 HIS 0.005 0.001 HIS A 516 PHE 0.014 0.002 PHE C 199 TYR 0.016 0.002 TYR A 520 ARG 0.004 0.001 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 116 time to evaluate : 1.606 Fit side-chains REVERT: A 35 GLN cc_start: 0.7894 (OUTLIER) cc_final: 0.7346 (tm-30) REVERT: A 74 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7678 (mt-10) REVERT: A 113 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.7475 (tp30) REVERT: A 547 MET cc_start: 0.7849 (mmt) cc_final: 0.7601 (mmt) REVERT: B 113 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8157 (tp30) REVERT: B 325 ASP cc_start: 0.7683 (p0) cc_final: 0.7392 (p0) REVERT: C 74 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7522 (mt-10) REVERT: C 220 LYS cc_start: 0.8175 (mppt) cc_final: 0.7783 (mmtp) outliers start: 49 outliers final: 32 residues processed: 156 average time/residue: 1.1646 time to fit residues: 199.6194 Evaluate side-chains 151 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 114 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 502 LYS Chi-restraints excluded: chain B residue 538 ASP Chi-restraints excluded: chain C residue 74 GLU Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 374 ASP Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain C residue 502 LYS Chi-restraints excluded: chain C residue 538 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 118 optimal weight: 0.5980 chunk 136 optimal weight: 2.9990 chunk 144 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN C 334 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12906 Z= 0.187 Angle : 0.477 10.746 17556 Z= 0.248 Chirality : 0.047 0.135 2025 Planarity : 0.004 0.052 2241 Dihedral : 4.565 58.956 1735 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.46 % Allowed : 15.06 % Favored : 82.48 % 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: 0.41 (0.21), residues: 1575 helix: 0.39 (0.36), residues: 228 sheet: 0.83 (0.24), residues: 468 loop : 0.02 (0.20), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 108 HIS 0.002 0.001 HIS A 97 PHE 0.011 0.001 PHE C 199 TYR 0.015 0.001 TYR C 520 ARG 0.006 0.000 ARG C 404 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 120 time to evaluate : 1.484 Fit side-chains REVERT: A 35 GLN cc_start: 0.7862 (OUTLIER) cc_final: 0.7362 (tm-30) REVERT: A 74 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7616 (mt-10) REVERT: A 218 MET cc_start: 0.7543 (mpt) cc_final: 0.7310 (mmt) REVERT: A 547 MET cc_start: 0.7742 (mmt) cc_final: 0.7425 (mmt) REVERT: B 113 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8067 (tt0) REVERT: B 325 ASP cc_start: 0.7503 (OUTLIER) cc_final: 0.7241 (p0) REVERT: B 471 ASN cc_start: 0.8099 (m-40) cc_final: 0.7856 (m-40) REVERT: C 74 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7567 (mt-10) REVERT: C 220 LYS cc_start: 0.8160 (mppt) cc_final: 0.7787 (mmtp) outliers start: 36 outliers final: 25 residues processed: 151 average time/residue: 1.1565 time to fit residues: 191.5170 Evaluate side-chains 147 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 117 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 502 LYS Chi-restraints excluded: chain B residue 538 ASP Chi-restraints excluded: chain C residue 74 GLU Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 374 ASP Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain C residue 538 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 4.9990 chunk 140 optimal weight: 0.2980 chunk 144 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 132 optimal weight: 0.0570 chunk 139 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 overall best weight: 0.8704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12906 Z= 0.166 Angle : 0.471 11.064 17556 Z= 0.244 Chirality : 0.046 0.132 2025 Planarity : 0.004 0.051 2241 Dihedral : 4.442 58.646 1735 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.33 % Allowed : 15.40 % Favored : 82.27 % 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: 0.43 (0.21), residues: 1575 helix: 0.27 (0.36), residues: 237 sheet: 0.86 (0.24), residues: 468 loop : 0.07 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 108 HIS 0.002 0.001 HIS A 97 PHE 0.011 0.001 PHE A 199 TYR 0.014 0.001 TYR C 520 ARG 0.011 0.000 ARG C 404 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 117 time to evaluate : 1.626 Fit side-chains REVERT: A 35 GLN cc_start: 0.7851 (OUTLIER) cc_final: 0.7374 (tm-30) REVERT: A 74 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7602 (mt-10) REVERT: A 218 MET cc_start: 0.7539 (mpt) cc_final: 0.7288 (mmt) REVERT: A 245 THR cc_start: 0.9152 (OUTLIER) cc_final: 0.8728 (m) REVERT: A 547 MET cc_start: 0.7749 (mmt) cc_final: 0.7483 (mmt) REVERT: B 113 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8021 (tt0) REVERT: B 325 ASP cc_start: 0.7540 (OUTLIER) cc_final: 0.7312 (p0) REVERT: B 471 ASN cc_start: 0.8116 (m-40) cc_final: 0.7856 (m-40) REVERT: C 74 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7556 (mt-10) REVERT: C 220 LYS cc_start: 0.8159 (mppt) cc_final: 0.7798 (mmtp) outliers start: 34 outliers final: 22 residues processed: 148 average time/residue: 1.1908 time to fit residues: 193.5929 Evaluate side-chains 146 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 118 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 502 LYS Chi-restraints excluded: chain B residue 538 ASP Chi-restraints excluded: chain C residue 74 GLU Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 374 ASP Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain C residue 538 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 102 optimal weight: 0.5980 chunk 155 optimal weight: 4.9990 chunk 143 optimal weight: 6.9990 chunk 123 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12906 Z= 0.224 Angle : 0.498 10.905 17556 Z= 0.258 Chirality : 0.047 0.137 2025 Planarity : 0.004 0.052 2241 Dihedral : 4.573 58.715 1735 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.19 % Allowed : 15.33 % Favored : 82.48 % 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: 0.42 (0.21), residues: 1575 helix: 0.35 (0.36), residues: 231 sheet: 0.86 (0.24), residues: 468 loop : 0.02 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 108 HIS 0.002 0.001 HIS A 250 PHE 0.012 0.001 PHE C 199 TYR 0.016 0.001 TYR C 520 ARG 0.010 0.000 ARG C 404 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 115 time to evaluate : 1.401 Fit side-chains REVERT: A 35 GLN cc_start: 0.7876 (OUTLIER) cc_final: 0.7369 (tm-30) REVERT: A 74 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7609 (mt-10) REVERT: A 113 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.7462 (tp30) REVERT: A 245 THR cc_start: 0.9157 (OUTLIER) cc_final: 0.8738 (m) REVERT: A 547 MET cc_start: 0.7746 (mmt) cc_final: 0.7487 (mmt) REVERT: B 113 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8112 (tt0) REVERT: B 325 ASP cc_start: 0.7568 (OUTLIER) cc_final: 0.7318 (p0) REVERT: B 471 ASN cc_start: 0.8156 (m-40) cc_final: 0.7914 (m-40) REVERT: C 74 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7556 (mt-10) REVERT: C 220 LYS cc_start: 0.8163 (mppt) cc_final: 0.7799 (mmtp) outliers start: 32 outliers final: 24 residues processed: 145 average time/residue: 1.2114 time to fit residues: 192.1495 Evaluate side-chains 145 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 114 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 502 LYS Chi-restraints excluded: chain B residue 538 ASP Chi-restraints excluded: chain C residue 74 GLU Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 374 ASP Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain C residue 502 LYS Chi-restraints excluded: chain C residue 538 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 127 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 22 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.107742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.089178 restraints weight = 15436.227| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 1.87 r_work: 0.2825 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2710 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2706 r_free = 0.2706 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2706 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12906 Z= 0.283 Angle : 0.525 10.849 17556 Z= 0.274 Chirality : 0.048 0.141 2025 Planarity : 0.004 0.052 2241 Dihedral : 4.735 58.741 1735 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.26 % Allowed : 15.26 % Favored : 82.48 % 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: 0.39 (0.21), residues: 1575 helix: 0.27 (0.36), residues: 231 sheet: 0.85 (0.24), residues: 468 loop : 0.01 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 108 HIS 0.003 0.001 HIS A 516 PHE 0.013 0.002 PHE C 199 TYR 0.017 0.002 TYR C 520 ARG 0.009 0.000 ARG C 404 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4060.40 seconds wall clock time: 73 minutes 20.75 seconds (4400.75 seconds total)