Starting phenix.real_space_refine on Fri Feb 16 18:51:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xc6_33113/02_2024/7xc6_33113.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xc6_33113/02_2024/7xc6_33113.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xc6_33113/02_2024/7xc6_33113.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xc6_33113/02_2024/7xc6_33113.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xc6_33113/02_2024/7xc6_33113.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xc6_33113/02_2024/7xc6_33113.pdb" } resolution = 2.79 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= 0.004 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 68 5.16 5 C 10316 2.51 5 N 2691 2.21 5 O 3101 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E GLU 34": "OE1" <-> "OE2" Residue "E GLU 45": "OE1" <-> "OE2" Residue "E GLU 55": "OE1" <-> "OE2" Residue "E ASP 67": "OD1" <-> "OD2" Residue "E ASP 318": "OD1" <-> "OD2" Residue "E ASP 331": "OD1" <-> "OD2" Residue "E ASP 351": "OD1" <-> "OD2" Residue "A ARG 24": "NH1" <-> "NH2" Residue "A GLU 28": "OE1" <-> "OE2" Residue "A GLU 52": "OE1" <-> "OE2" Residue "A GLU 108": "OE1" <-> "OE2" Residue "A ASP 124": "OD1" <-> "OD2" Residue "A ASP 137": "OD1" <-> "OD2" Residue "A ASP 223": "OD1" <-> "OD2" Residue "A ASP 235": "OD1" <-> "OD2" Residue "A ASP 258": "OD1" <-> "OD2" Residue "A ASP 307": "OD1" <-> "OD2" Residue "A GLU 315": "OE1" <-> "OE2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "A GLU 355": "OE1" <-> "OE2" Residue "A ASP 358": "OD1" <-> "OD2" Residue "A TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 467": "OD1" <-> "OD2" Residue "A ARG 476": "NH1" <-> "NH2" Residue "B ARG 24": "NH1" <-> "NH2" Residue "B GLU 28": "OE1" <-> "OE2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B GLU 108": "OE1" <-> "OE2" Residue "B ASP 124": "OD1" <-> "OD2" Residue "B ASP 137": "OD1" <-> "OD2" Residue "B ASP 223": "OD1" <-> "OD2" Residue "B ASP 235": "OD1" <-> "OD2" Residue "B ASP 258": "OD1" <-> "OD2" Residue "B ASP 307": "OD1" <-> "OD2" Residue "B GLU 315": "OE1" <-> "OE2" Residue "B GLU 318": "OE1" <-> "OE2" Residue "B GLU 355": "OE1" <-> "OE2" Residue "B ASP 358": "OD1" <-> "OD2" Residue "B TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 467": "OD1" <-> "OD2" Residue "B ARG 476": "NH1" <-> "NH2" Residue "C ARG 24": "NH1" <-> "NH2" Residue "C GLU 28": "OE1" <-> "OE2" Residue "C GLU 52": "OE1" <-> "OE2" Residue "C GLU 108": "OE1" <-> "OE2" Residue "C ASP 124": "OD1" <-> "OD2" Residue "C ASP 137": "OD1" <-> "OD2" Residue "C ASP 223": "OD1" <-> "OD2" Residue "C ASP 235": "OD1" <-> "OD2" Residue "C ASP 258": "OD1" <-> "OD2" Residue "C ASP 307": "OD1" <-> "OD2" Residue "C GLU 315": "OE1" <-> "OE2" Residue "C GLU 318": "OE1" <-> "OE2" Residue "C GLU 355": "OE1" <-> "OE2" Residue "C ASP 358": "OD1" <-> "OD2" Residue "C TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 467": "OD1" <-> "OD2" Residue "C ARG 476": "NH1" <-> "NH2" Residue "D ARG 24": "NH1" <-> "NH2" Residue "D GLU 28": "OE1" <-> "OE2" Residue "D GLU 52": "OE1" <-> "OE2" Residue "D GLU 108": "OE1" <-> "OE2" Residue "D ASP 124": "OD1" <-> "OD2" Residue "D ASP 137": "OD1" <-> "OD2" Residue "D ASP 223": "OD1" <-> "OD2" Residue "D ASP 235": "OD1" <-> "OD2" Residue "D ASP 258": "OD1" <-> "OD2" Residue "D ASP 307": "OD1" <-> "OD2" Residue "D GLU 315": "OE1" <-> "OE2" Residue "D GLU 318": "OE1" <-> "OE2" Residue "D GLU 355": "OE1" <-> "OE2" Residue "D ASP 358": "OD1" <-> "OD2" Residue "D TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 467": "OD1" <-> "OD2" Residue "D ARG 476": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16176 Number of models: 1 Model: "" Number of chains: 5 Chain: "E" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 956 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 7, 'TRANS': 110} Chain breaks: 2 Chain: "A" Number of atoms: 3805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3805 Classifications: {'peptide': 477} Link IDs: {'PTRANS': 20, 'TRANS': 456} Chain: "B" Number of atoms: 3805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3805 Classifications: {'peptide': 477} Link IDs: {'PTRANS': 20, 'TRANS': 456} Chain: "C" Number of atoms: 3805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3805 Classifications: {'peptide': 477} Link IDs: {'PTRANS': 20, 'TRANS': 456} Chain: "D" Number of atoms: 3805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3805 Classifications: {'peptide': 477} Link IDs: {'PTRANS': 20, 'TRANS': 456} Time building chain proxies: 8.68, per 1000 atoms: 0.54 Number of scatterers: 16176 At special positions: 0 Unit cell: (120.785, 128.282, 157.437, 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 68 16.00 O 3101 8.00 N 2691 7.00 C 10316 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: 6.41 Conformation dependent library (CDL) restraints added in 2.9 seconds 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3860 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 19 sheets defined 45.7% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.96 Creating SS restraints... Processing helix chain 'E' and resid 33 through 54 Processing helix chain 'E' and resid 54 through 63 Processing helix chain 'E' and resid 82 through 87 removed outlier: 3.811A pdb=" N TYR E 86 " --> pdb=" O SER E 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 56 Processing helix chain 'A' and resid 64 through 81 removed outlier: 3.779A pdb=" N SER A 81 " --> pdb=" O GLN A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 98 Processing helix chain 'A' and resid 101 through 118 Processing helix chain 'A' and resid 118 through 131 Processing helix chain 'A' and resid 163 through 177 removed outlier: 3.939A pdb=" N GLY A 167 " --> pdb=" O VAL A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 204 Processing helix chain 'A' and resid 209 through 211 No H-bonds generated for 'chain 'A' and resid 209 through 211' Processing helix chain 'A' and resid 224 through 233 removed outlier: 3.850A pdb=" N CYS A 233 " --> pdb=" O GLN A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 252 Processing helix chain 'A' and resid 276 through 290 removed outlier: 3.588A pdb=" N SER A 280 " --> pdb=" O ASP A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 294 Processing helix chain 'A' and resid 308 through 327 removed outlier: 3.683A pdb=" N ASP A 325 " --> pdb=" O ASN A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 349 Processing helix chain 'A' and resid 388 through 396 removed outlier: 4.070A pdb=" N THR A 393 " --> pdb=" O SER A 390 " (cutoff:3.500A) Proline residue: A 394 - end of helix Processing helix chain 'A' and resid 408 through 414 Processing helix chain 'A' and resid 415 through 422 Processing helix chain 'A' and resid 446 through 450 Processing helix chain 'A' and resid 473 through 481 Processing helix chain 'B' and resid 47 through 56 Processing helix chain 'B' and resid 64 through 81 removed outlier: 3.778A pdb=" N SER B 81 " --> pdb=" O GLN B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 98 Processing helix chain 'B' and resid 101 through 118 Processing helix chain 'B' and resid 118 through 131 Processing helix chain 'B' and resid 163 through 177 removed outlier: 3.940A pdb=" N GLY B 167 " --> pdb=" O VAL B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 204 Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'B' and resid 224 through 233 removed outlier: 3.850A pdb=" N CYS B 233 " --> pdb=" O GLN B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 252 Processing helix chain 'B' and resid 276 through 290 removed outlier: 3.588A pdb=" N SER B 280 " --> pdb=" O ASP B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 294 Processing helix chain 'B' and resid 308 through 327 removed outlier: 3.683A pdb=" N ASP B 325 " --> pdb=" O ASN B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 349 Processing helix chain 'B' and resid 388 through 396 removed outlier: 4.069A pdb=" N THR B 393 " --> pdb=" O SER B 390 " (cutoff:3.500A) Proline residue: B 394 - end of helix Processing helix chain 'B' and resid 408 through 414 Processing helix chain 'B' and resid 415 through 422 Processing helix chain 'B' and resid 446 through 450 Processing helix chain 'B' and resid 473 through 481 Processing helix chain 'C' and resid 47 through 56 Processing helix chain 'C' and resid 64 through 81 removed outlier: 3.778A pdb=" N SER C 81 " --> pdb=" O GLN C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 98 Processing helix chain 'C' and resid 101 through 118 Processing helix chain 'C' and resid 118 through 131 Processing helix chain 'C' and resid 163 through 177 removed outlier: 3.939A pdb=" N GLY C 167 " --> pdb=" O VAL C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 204 Processing helix chain 'C' and resid 209 through 211 No H-bonds generated for 'chain 'C' and resid 209 through 211' Processing helix chain 'C' and resid 224 through 233 removed outlier: 3.850A pdb=" N CYS C 233 " --> pdb=" O GLN C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 252 Processing helix chain 'C' and resid 276 through 290 removed outlier: 3.588A pdb=" N SER C 280 " --> pdb=" O ASP C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 294 Processing helix chain 'C' and resid 308 through 327 removed outlier: 3.683A pdb=" N ASP C 325 " --> pdb=" O ASN C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 349 Processing helix chain 'C' and resid 388 through 396 removed outlier: 4.069A pdb=" N THR C 393 " --> pdb=" O SER C 390 " (cutoff:3.500A) Proline residue: C 394 - end of helix Processing helix chain 'C' and resid 408 through 414 Processing helix chain 'C' and resid 415 through 422 Processing helix chain 'C' and resid 446 through 450 Processing helix chain 'C' and resid 473 through 481 Processing helix chain 'D' and resid 47 through 56 Processing helix chain 'D' and resid 64 through 81 removed outlier: 3.778A pdb=" N SER D 81 " --> pdb=" O GLN D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 98 Processing helix chain 'D' and resid 101 through 118 Processing helix chain 'D' and resid 118 through 131 Processing helix chain 'D' and resid 163 through 177 removed outlier: 3.940A pdb=" N GLY D 167 " --> pdb=" O VAL D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 204 Processing helix chain 'D' and resid 209 through 211 No H-bonds generated for 'chain 'D' and resid 209 through 211' Processing helix chain 'D' and resid 224 through 233 removed outlier: 3.851A pdb=" N CYS D 233 " --> pdb=" O GLN D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 252 Processing helix chain 'D' and resid 276 through 290 removed outlier: 3.588A pdb=" N SER D 280 " --> pdb=" O ASP D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 294 Processing helix chain 'D' and resid 308 through 327 removed outlier: 3.683A pdb=" N ASP D 325 " --> pdb=" O ASN D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 349 Processing helix chain 'D' and resid 388 through 396 removed outlier: 4.070A pdb=" N THR D 393 " --> pdb=" O SER D 390 " (cutoff:3.500A) Proline residue: D 394 - end of helix Processing helix chain 'D' and resid 408 through 414 Processing helix chain 'D' and resid 415 through 422 Processing helix chain 'D' and resid 446 through 450 Processing helix chain 'D' and resid 473 through 481 Processing sheet with id=AA1, first strand: chain 'E' and resid 79 through 80 removed outlier: 6.944A pdb=" N PHE E 79 " --> pdb=" O VAL E 329 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N ASP E 331 " --> pdb=" O PHE E 79 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N ILE E 314 " --> pdb=" O THR E 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 79 through 80 removed outlier: 6.944A pdb=" N PHE E 79 " --> pdb=" O VAL E 329 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N ASP E 331 " --> pdb=" O PHE E 79 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG E 354 " --> pdb=" O ILE E 333 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 336 through 337 Processing sheet with id=AA4, first strand: chain 'A' and resid 13 through 14 removed outlier: 6.354A pdb=" N LYS A 13 " --> pdb=" O SER A 42 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 145 through 151 Processing sheet with id=AA6, first strand: chain 'A' and resid 213 through 216 removed outlier: 6.617A pdb=" N CYS A 181 " --> pdb=" O SER A 214 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N MET A 216 " --> pdb=" O CYS A 181 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ILE A 183 " --> pdb=" O MET A 216 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N SER A 155 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N LYS A 184 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N HIS A 157 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL A 156 " --> pdb=" O VAL A 238 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL A 237 " --> pdb=" O LEU A 260 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 356 removed outlier: 6.422A pdb=" N LEU A 363 " --> pdb=" O ALA A 381 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ILE A 383 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL A 365 " --> pdb=" O ILE A 383 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N HIS A 385 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N GLN A 300 " --> pdb=" O SER A 380 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N SER A 267 " --> pdb=" O GLN A 300 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE A 302 " --> pdb=" O SER A 267 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ALA A 269 " --> pdb=" O ILE A 302 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N TYR A 304 " --> pdb=" O ALA A 269 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL A 271 " --> pdb=" O TYR A 304 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 426 through 427 removed outlier: 6.322A pdb=" N ILE A 427 " --> pdb=" O GLU B 458 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 13 through 14 removed outlier: 6.354A pdb=" N LYS B 13 " --> pdb=" O SER B 42 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 213 through 216 removed outlier: 6.617A pdb=" N CYS B 181 " --> pdb=" O SER B 214 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N MET B 216 " --> pdb=" O CYS B 181 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ILE B 183 " --> pdb=" O MET B 216 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N SER B 155 " --> pdb=" O ILE B 182 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N LYS B 184 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N HIS B 157 " --> pdb=" O LYS B 184 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL B 156 " --> pdb=" O VAL B 238 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL B 237 " --> pdb=" O LEU B 260 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 354 through 356 removed outlier: 6.421A pdb=" N LEU B 363 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ILE B 383 " --> pdb=" O LEU B 363 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL B 365 " --> pdb=" O ILE B 383 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N HIS B 385 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N GLN B 300 " --> pdb=" O SER B 380 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N SER B 267 " --> pdb=" O GLN B 300 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE B 302 " --> pdb=" O SER B 267 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ALA B 269 " --> pdb=" O ILE B 302 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N TYR B 304 " --> pdb=" O ALA B 269 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL B 271 " --> pdb=" O TYR B 304 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.354A pdb=" N LYS C 13 " --> pdb=" O SER C 42 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 145 through 151 Processing sheet with id=AB5, first strand: chain 'C' and resid 213 through 216 removed outlier: 6.617A pdb=" N CYS C 181 " --> pdb=" O SER C 214 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N MET C 216 " --> pdb=" O CYS C 181 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ILE C 183 " --> pdb=" O MET C 216 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N SER C 155 " --> pdb=" O ILE C 182 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N LYS C 184 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N HIS C 157 " --> pdb=" O LYS C 184 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL C 156 " --> pdb=" O VAL C 238 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL C 237 " --> pdb=" O LEU C 260 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 354 through 356 removed outlier: 6.422A pdb=" N LEU C 363 " --> pdb=" O ALA C 381 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ILE C 383 " --> pdb=" O LEU C 363 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N VAL C 365 " --> pdb=" O ILE C 383 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N HIS C 385 " --> pdb=" O VAL C 365 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N GLN C 300 " --> pdb=" O SER C 380 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N SER C 267 " --> pdb=" O GLN C 300 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE C 302 " --> pdb=" O SER C 267 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ALA C 269 " --> pdb=" O ILE C 302 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N TYR C 304 " --> pdb=" O ALA C 269 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL C 271 " --> pdb=" O TYR C 304 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 426 through 427 removed outlier: 6.423A pdb=" N ILE C 427 " --> pdb=" O GLU D 458 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 13 through 14 removed outlier: 6.354A pdb=" N LYS D 13 " --> pdb=" O SER D 42 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 213 through 216 removed outlier: 6.618A pdb=" N CYS D 181 " --> pdb=" O SER D 214 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N MET D 216 " --> pdb=" O CYS D 181 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ILE D 183 " --> pdb=" O MET D 216 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N SER D 155 " --> pdb=" O ILE D 182 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N LYS D 184 " --> pdb=" O SER D 155 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N HIS D 157 " --> pdb=" O LYS D 184 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL D 156 " --> pdb=" O VAL D 238 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL D 237 " --> pdb=" O LEU D 260 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'D' and resid 354 through 356 removed outlier: 6.422A pdb=" N LEU D 363 " --> pdb=" O ALA D 381 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ILE D 383 " --> pdb=" O LEU D 363 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N VAL D 365 " --> pdb=" O ILE D 383 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N HIS D 385 " --> pdb=" O VAL D 365 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N GLN D 300 " --> pdb=" O SER D 380 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N SER D 267 " --> pdb=" O GLN D 300 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE D 302 " --> pdb=" O SER D 267 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ALA D 269 " --> pdb=" O ILE D 302 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N TYR D 304 " --> pdb=" O ALA D 269 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL D 271 " --> pdb=" O TYR D 304 " (cutoff:3.500A) 669 hydrogen bonds defined for protein. 1890 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: 5.22 Time building geometry restraints manager: 6.88 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: 5197 1.34 - 1.45: 2407 1.45 - 1.57: 8831 1.57 - 1.69: 0 1.69 - 1.81: 110 Bond restraints: 16545 Sorted by residual: bond pdb=" CB THR A 407 " pdb=" CG2 THR A 407 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.66e+00 bond pdb=" CB THR D 407 " pdb=" CG2 THR D 407 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.60e+00 bond pdb=" CB THR C 407 " pdb=" CG2 THR C 407 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.59e+00 bond pdb=" CB GLU C 28 " pdb=" CG GLU C 28 " ideal model delta sigma weight residual 1.520 1.568 -0.048 3.00e-02 1.11e+03 2.54e+00 bond pdb=" CB THR B 407 " pdb=" CG2 THR B 407 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.51e+00 ... (remaining 16540 not shown) Histogram of bond angle deviations from ideal: 99.45 - 106.36: 423 106.36 - 113.28: 9093 113.28 - 120.20: 6006 120.20 - 127.11: 6734 127.11 - 134.03: 206 Bond angle restraints: 22462 Sorted by residual: angle pdb=" CA LYS B 351 " pdb=" CB LYS B 351 " pdb=" CG LYS B 351 " ideal model delta sigma weight residual 114.10 125.27 -11.17 2.00e+00 2.50e-01 3.12e+01 angle pdb=" CA LYS A 351 " pdb=" CB LYS A 351 " pdb=" CG LYS A 351 " ideal model delta sigma weight residual 114.10 125.26 -11.16 2.00e+00 2.50e-01 3.11e+01 angle pdb=" CA LYS C 351 " pdb=" CB LYS C 351 " pdb=" CG LYS C 351 " ideal model delta sigma weight residual 114.10 125.24 -11.14 2.00e+00 2.50e-01 3.10e+01 angle pdb=" CA LYS D 351 " pdb=" CB LYS D 351 " pdb=" CG LYS D 351 " ideal model delta sigma weight residual 114.10 125.21 -11.11 2.00e+00 2.50e-01 3.09e+01 angle pdb=" N GLY D 431 " pdb=" CA GLY D 431 " pdb=" C GLY D 431 " ideal model delta sigma weight residual 115.80 107.39 8.41 1.74e+00 3.30e-01 2.34e+01 ... (remaining 22457 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 8560 17.82 - 35.64: 1011 35.64 - 53.46: 267 53.46 - 71.28: 66 71.28 - 89.10: 40 Dihedral angle restraints: 9944 sinusoidal: 3970 harmonic: 5974 Sorted by residual: dihedral pdb=" CA ALA C 378 " pdb=" C ALA C 378 " pdb=" N ARG C 379 " pdb=" CA ARG C 379 " ideal model delta harmonic sigma weight residual 180.00 157.25 22.75 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA ALA B 378 " pdb=" C ALA B 378 " pdb=" N ARG B 379 " pdb=" CA ARG B 379 " ideal model delta harmonic sigma weight residual 180.00 157.25 22.75 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA ALA D 378 " pdb=" C ALA D 378 " pdb=" N ARG D 379 " pdb=" CA ARG D 379 " ideal model delta harmonic sigma weight residual 180.00 157.30 22.70 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 9941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1482 0.038 - 0.076: 700 0.076 - 0.114: 254 0.114 - 0.152: 68 0.152 - 0.190: 10 Chirality restraints: 2514 Sorted by residual: chirality pdb=" CA THR B 407 " pdb=" N THR B 407 " pdb=" C THR B 407 " pdb=" CB THR B 407 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 9.04e-01 chirality pdb=" CA THR D 407 " pdb=" N THR D 407 " pdb=" C THR D 407 " pdb=" CB THR D 407 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 9.01e-01 chirality pdb=" CA THR A 407 " pdb=" N THR A 407 " pdb=" C THR A 407 " pdb=" CB THR A 407 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 8.83e-01 ... (remaining 2511 not shown) Planarity restraints: 2873 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 299 " 0.038 5.00e-02 4.00e+02 5.72e-02 5.24e+00 pdb=" N PRO E 300 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO E 300 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 300 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 28 " 0.009 2.00e-02 2.50e+03 1.85e-02 3.42e+00 pdb=" CD GLU A 28 " -0.032 2.00e-02 2.50e+03 pdb=" OE1 GLU A 28 " 0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU A 28 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 28 " -0.009 2.00e-02 2.50e+03 1.84e-02 3.38e+00 pdb=" CD GLU B 28 " 0.032 2.00e-02 2.50e+03 pdb=" OE1 GLU B 28 " -0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU B 28 " -0.011 2.00e-02 2.50e+03 ... (remaining 2870 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 189 2.58 - 3.16: 13325 3.16 - 3.74: 26027 3.74 - 4.32: 38918 4.32 - 4.90: 62508 Nonbonded interactions: 140967 Sorted by model distance: nonbonded pdb=" O PRO E 300 " pdb=" OG SER C 341 " model vdw 2.003 2.440 nonbonded pdb=" O TRP D 409 " pdb=" OG SER D 412 " model vdw 2.030 2.440 nonbonded pdb=" O TRP A 409 " pdb=" OG SER A 412 " model vdw 2.030 2.440 nonbonded pdb=" O TRP B 409 " pdb=" OG SER B 412 " model vdw 2.030 2.440 nonbonded pdb=" O TRP C 409 " pdb=" OG SER C 412 " model vdw 2.030 2.440 ... (remaining 140962 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' selection = chain 'D' } 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 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: 3.330 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: 0.020 Extract box with map and model: 14.730 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 43.330 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6467 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 0.054 16545 Z= 0.370 Angle : 0.717 11.169 22462 Z= 0.405 Chirality : 0.050 0.190 2514 Planarity : 0.004 0.057 2873 Dihedral : 17.666 89.098 6084 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 7.75 % Allowed : 12.96 % Favored : 79.29 % 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: -2.40 (0.17), residues: 2012 helix: -0.71 (0.15), residues: 814 sheet: -1.87 (0.27), residues: 296 loop : -2.30 (0.19), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 292 HIS 0.003 0.001 HIS C 220 PHE 0.013 0.002 PHE B 372 TYR 0.021 0.001 TYR E 86 ARG 0.003 0.000 ARG D 437 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 456 time to evaluate : 1.885 Fit side-chains revert: symmetry clash REVERT: E 85 LYS cc_start: 0.5792 (OUTLIER) cc_final: 0.5437 (mmtt) REVERT: E 299 ASP cc_start: 0.7491 (t70) cc_final: 0.7206 (t0) REVERT: A 310 ASP cc_start: 0.7136 (m-30) cc_final: 0.6553 (p0) REVERT: A 351 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7781 (mtmm) REVERT: A 388 ASP cc_start: 0.7017 (OUTLIER) cc_final: 0.6559 (t0) REVERT: D 351 LYS cc_start: 0.6578 (OUTLIER) cc_final: 0.6308 (mmpt) REVERT: D 361 SER cc_start: 0.5197 (OUTLIER) cc_final: 0.4990 (m) outliers start: 140 outliers final: 14 residues processed: 561 average time/residue: 0.9339 time to fit residues: 597.6545 Evaluate side-chains 259 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 240 time to evaluate : 1.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain B residue 221 ASN Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 372 PHE Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 351 LYS Chi-restraints excluded: chain D residue 361 SER Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 452 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 168 optimal weight: 0.7980 chunk 150 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 180 optimal weight: 7.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 GLN A 77 GLN A 134 HIS A 252 HIS A 360 GLN A 434 ASN B 48 GLN B 67 GLN C 29 HIS C 67 GLN C 162 ASN C 252 HIS C 360 GLN C 385 HIS D 48 GLN D 83 ASN D 229 GLN D 252 HIS D 385 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.6646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 16545 Z= 0.276 Angle : 0.657 10.047 22462 Z= 0.350 Chirality : 0.049 0.189 2514 Planarity : 0.005 0.047 2873 Dihedral : 6.569 122.003 2225 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 5.09 % Allowed : 21.26 % Favored : 73.64 % 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: -1.44 (0.17), residues: 2012 helix: 0.41 (0.17), residues: 818 sheet: -1.60 (0.24), residues: 354 loop : -2.02 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 218 HIS 0.005 0.001 HIS A 134 PHE 0.016 0.002 PHE C 313 TYR 0.014 0.002 TYR B 382 ARG 0.006 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 265 time to evaluate : 1.870 Fit side-chains REVERT: A 54 ILE cc_start: 0.9080 (OUTLIER) cc_final: 0.8791 (mt) REVERT: A 345 LYS cc_start: 0.7640 (mmpt) cc_final: 0.7411 (pptt) REVERT: C 339 SER cc_start: 0.8575 (t) cc_final: 0.8341 (t) REVERT: C 358 ASP cc_start: 0.8070 (OUTLIER) cc_final: 0.7827 (m-30) REVERT: D 250 THR cc_start: 0.8864 (OUTLIER) cc_final: 0.8598 (m) outliers start: 92 outliers final: 30 residues processed: 330 average time/residue: 1.0529 time to fit residues: 392.0180 Evaluate side-chains 193 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 160 time to evaluate : 1.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 357 ASN Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 308 ASN Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain B residue 29 HIS Chi-restraints excluded: chain B residue 221 ASN Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 456 SER Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 371 SER Chi-restraints excluded: chain D residue 452 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 100 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 181 optimal weight: 2.9990 chunk 195 optimal weight: 3.9990 chunk 161 optimal weight: 0.8980 chunk 179 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 145 optimal weight: 0.8980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 64 GLN E 357 ASN A 66 ASN A 273 ASN A 434 ASN B 442 HIS C 374 ASN D 67 GLN D 319 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.8846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 16545 Z= 0.323 Angle : 0.628 9.479 22462 Z= 0.333 Chirality : 0.050 0.184 2514 Planarity : 0.004 0.054 2873 Dihedral : 5.307 47.556 2198 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 4.98 % Allowed : 23.09 % Favored : 71.93 % 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: -0.91 (0.18), residues: 2012 helix: 0.80 (0.17), residues: 846 sheet: -1.32 (0.26), residues: 358 loop : -1.75 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 362 HIS 0.005 0.001 HIS D 207 PHE 0.013 0.002 PHE C 334 TYR 0.020 0.002 TYR D 323 ARG 0.005 0.001 ARG B 459 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 194 time to evaluate : 1.931 Fit side-chains REVERT: E 53 ASN cc_start: 0.7607 (OUTLIER) cc_final: 0.7259 (t0) REVERT: A 106 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8480 (ttpp) REVERT: A 290 PHE cc_start: 0.8667 (OUTLIER) cc_final: 0.8347 (t80) REVERT: A 308 ASN cc_start: 0.7487 (OUTLIER) cc_final: 0.7252 (m-40) REVERT: A 319 GLN cc_start: 0.9043 (OUTLIER) cc_final: 0.7702 (mp10) REVERT: B 30 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.6944 (mp0) REVERT: B 334 PHE cc_start: 0.8033 (t80) cc_final: 0.7795 (t80) REVERT: B 458 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.7987 (mt-10) REVERT: C 258 ASP cc_start: 0.7386 (t0) cc_final: 0.7048 (t70) outliers start: 90 outliers final: 26 residues processed: 265 average time/residue: 0.9280 time to fit residues: 282.6855 Evaluate side-chains 176 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 143 time to evaluate : 1.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 53 ASN Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 308 ASN Chi-restraints excluded: chain A residue 319 GLN Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 221 ASN Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain C residue 29 HIS Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain C residue 290 PHE Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 452 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 178 optimal weight: 5.9990 chunk 136 optimal weight: 0.0670 chunk 93 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 86 optimal weight: 8.9990 chunk 121 optimal weight: 0.9980 chunk 181 optimal weight: 2.9990 chunk 192 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 172 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 overall best weight: 0.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 52 ASN C 162 ASN C 308 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.9052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16545 Z= 0.178 Angle : 0.516 8.323 22462 Z= 0.275 Chirality : 0.046 0.149 2514 Planarity : 0.004 0.043 2873 Dihedral : 4.865 44.560 2196 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 3.49 % Allowed : 24.42 % Favored : 72.09 % 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: -0.52 (0.19), residues: 2012 helix: 1.21 (0.18), residues: 850 sheet: -1.32 (0.27), residues: 330 loop : -1.56 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 218 HIS 0.006 0.001 HIS E 40 PHE 0.024 0.001 PHE A 334 TYR 0.020 0.001 TYR D 243 ARG 0.003 0.000 ARG B 437 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 173 time to evaluate : 2.102 Fit side-chains REVERT: E 70 ILE cc_start: 0.6856 (OUTLIER) cc_final: 0.6537 (pp) REVERT: E 351 ASP cc_start: 0.6932 (m-30) cc_final: 0.6417 (m-30) REVERT: E 354 ARG cc_start: 0.7559 (ptt90) cc_final: 0.7352 (ptt180) REVERT: A 266 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8489 (tmtp) REVERT: A 345 LYS cc_start: 0.7840 (mmpt) cc_final: 0.7455 (pptt) REVERT: B 30 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6821 (mp0) REVERT: B 334 PHE cc_start: 0.8076 (t80) cc_final: 0.7855 (t80) REVERT: B 397 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6757 (mp0) REVERT: B 432 MET cc_start: 0.7520 (OUTLIER) cc_final: 0.5999 (mmm) REVERT: B 458 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.7819 (mt-10) outliers start: 63 outliers final: 23 residues processed: 219 average time/residue: 0.9963 time to fit residues: 249.3223 Evaluate side-chains 172 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 143 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 290 PHE Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 452 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 160 optimal weight: 0.0370 chunk 109 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 143 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 164 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 98 optimal weight: 0.8980 chunk 172 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 overall best weight: 0.9460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 52 ASN A 228 GLN C 29 HIS C 308 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.9202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16545 Z= 0.178 Angle : 0.505 7.971 22462 Z= 0.269 Chirality : 0.045 0.142 2514 Planarity : 0.004 0.041 2873 Dihedral : 4.668 43.124 2194 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 3.27 % Allowed : 24.75 % Favored : 71.98 % 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 (0.19), residues: 2012 helix: 1.41 (0.18), residues: 858 sheet: -1.18 (0.27), residues: 332 loop : -1.44 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 218 HIS 0.006 0.001 HIS E 40 PHE 0.012 0.001 PHE C 334 TYR 0.009 0.001 TYR D 323 ARG 0.002 0.000 ARG B 437 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 161 time to evaluate : 2.144 Fit side-chains revert: symmetry clash REVERT: E 58 LYS cc_start: 0.7621 (tttt) cc_final: 0.7272 (tmmm) REVERT: E 351 ASP cc_start: 0.6957 (OUTLIER) cc_final: 0.6448 (m-30) REVERT: E 354 ARG cc_start: 0.7531 (ptt90) cc_final: 0.7327 (ptt180) REVERT: A 266 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8539 (tmtp) REVERT: A 345 LYS cc_start: 0.7850 (mmpt) cc_final: 0.7460 (pptt) REVERT: B 30 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6879 (mp0) REVERT: B 334 PHE cc_start: 0.8074 (t80) cc_final: 0.7869 (t80) REVERT: B 432 MET cc_start: 0.7510 (OUTLIER) cc_final: 0.6056 (mmm) REVERT: D 343 ILE cc_start: 0.8784 (OUTLIER) cc_final: 0.8422 (mt) outliers start: 59 outliers final: 27 residues processed: 203 average time/residue: 0.9544 time to fit residues: 222.4367 Evaluate side-chains 177 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 145 time to evaluate : 1.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 351 ASP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 221 ASN Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 290 PHE Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 290 PHE Chi-restraints excluded: chain C residue 372 PHE Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 452 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 64 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 112 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 192 optimal weight: 4.9990 chunk 159 optimal weight: 4.9990 chunk 89 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.9399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16545 Z= 0.278 Angle : 0.562 8.691 22462 Z= 0.299 Chirality : 0.048 0.160 2514 Planarity : 0.004 0.041 2873 Dihedral : 5.063 46.033 2194 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 3.65 % Allowed : 24.09 % Favored : 72.26 % 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: -0.35 (0.19), residues: 2012 helix: 1.31 (0.18), residues: 850 sheet: -1.26 (0.27), residues: 334 loop : -1.42 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 240 HIS 0.004 0.001 HIS E 40 PHE 0.022 0.001 PHE A 334 TYR 0.020 0.001 TYR D 243 ARG 0.003 0.000 ARG B 437 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 159 time to evaluate : 1.939 Fit side-chains REVERT: E 58 LYS cc_start: 0.7780 (tttt) cc_final: 0.7310 (tmmm) REVERT: E 351 ASP cc_start: 0.7033 (OUTLIER) cc_final: 0.6545 (m-30) REVERT: E 354 ARG cc_start: 0.7638 (ptt90) cc_final: 0.7404 (ptt180) REVERT: A 266 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8538 (tmtp) REVERT: A 290 PHE cc_start: 0.8685 (OUTLIER) cc_final: 0.8383 (t80) REVERT: A 345 LYS cc_start: 0.7786 (OUTLIER) cc_final: 0.7436 (pptt) REVERT: B 278 THR cc_start: 0.8322 (OUTLIER) cc_final: 0.8014 (t) REVERT: B 458 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.7841 (mt-10) REVERT: C 359 ASN cc_start: 0.8763 (m110) cc_final: 0.8561 (m110) REVERT: D 343 ILE cc_start: 0.8810 (OUTLIER) cc_final: 0.8438 (mt) outliers start: 66 outliers final: 33 residues processed: 211 average time/residue: 0.9743 time to fit residues: 235.8088 Evaluate side-chains 184 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 144 time to evaluate : 1.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 351 ASP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 290 PHE Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 290 PHE Chi-restraints excluded: chain C residue 372 PHE Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 290 PHE Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 452 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 185 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 109 optimal weight: 4.9990 chunk 140 optimal weight: 4.9990 chunk 108 optimal weight: 0.7980 chunk 162 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 191 optimal weight: 1.9990 chunk 120 optimal weight: 0.5980 chunk 116 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN C 308 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.9489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16545 Z= 0.169 Angle : 0.502 8.074 22462 Z= 0.268 Chirality : 0.045 0.256 2514 Planarity : 0.003 0.039 2873 Dihedral : 4.687 42.753 2194 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 3.05 % Allowed : 24.70 % Favored : 72.26 % 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: -0.15 (0.19), residues: 2012 helix: 1.51 (0.18), residues: 854 sheet: -1.12 (0.28), residues: 312 loop : -1.38 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 409 HIS 0.006 0.001 HIS E 40 PHE 0.011 0.001 PHE C 334 TYR 0.007 0.001 TYR D 323 ARG 0.003 0.000 ARG E 37 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 168 time to evaluate : 2.068 Fit side-chains REVERT: E 58 LYS cc_start: 0.7858 (tttt) cc_final: 0.7362 (tmmm) REVERT: E 71 SER cc_start: 0.6301 (OUTLIER) cc_final: 0.5655 (p) REVERT: E 85 LYS cc_start: 0.7069 (OUTLIER) cc_final: 0.6334 (mmmt) REVERT: E 332 ASP cc_start: 0.6144 (m-30) cc_final: 0.5924 (p0) REVERT: E 351 ASP cc_start: 0.7013 (m-30) cc_final: 0.6618 (m-30) REVERT: A 266 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8619 (tmtp) REVERT: A 290 PHE cc_start: 0.8627 (OUTLIER) cc_final: 0.8301 (t80) REVERT: A 345 LYS cc_start: 0.7763 (OUTLIER) cc_final: 0.7424 (pptt) REVERT: B 12 ILE cc_start: 0.5609 (OUTLIER) cc_final: 0.5266 (pp) REVERT: B 351 LYS cc_start: 0.8482 (mmtp) cc_final: 0.8239 (mmmt) REVERT: B 374 ASN cc_start: 0.7984 (m-40) cc_final: 0.7710 (m-40) REVERT: C 359 ASN cc_start: 0.8749 (m110) cc_final: 0.8532 (m110) outliers start: 55 outliers final: 30 residues processed: 213 average time/residue: 0.9028 time to fit residues: 222.7720 Evaluate side-chains 191 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 155 time to evaluate : 1.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 290 PHE Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 290 PHE Chi-restraints excluded: chain C residue 372 PHE Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 452 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 118 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 114 optimal weight: 0.6980 chunk 57 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 94 optimal weight: 0.0060 chunk 17 optimal weight: 3.9990 chunk 150 optimal weight: 6.9990 chunk 174 optimal weight: 5.9990 overall best weight: 1.3402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN B 348 GLN C 308 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.9545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16545 Z= 0.212 Angle : 0.526 10.032 22462 Z= 0.279 Chirality : 0.046 0.163 2514 Planarity : 0.004 0.038 2873 Dihedral : 4.785 44.802 2194 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 3.16 % Allowed : 25.03 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.19), residues: 2012 helix: 1.51 (0.18), residues: 850 sheet: -1.15 (0.27), residues: 332 loop : -1.35 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 218 HIS 0.003 0.001 HIS C 286 PHE 0.027 0.001 PHE A 334 TYR 0.010 0.001 TYR D 323 ARG 0.003 0.000 ARG B 437 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 159 time to evaluate : 1.925 Fit side-chains REVERT: E 58 LYS cc_start: 0.7893 (tttt) cc_final: 0.7379 (tmmm) REVERT: E 71 SER cc_start: 0.6303 (OUTLIER) cc_final: 0.5639 (p) REVERT: E 85 LYS cc_start: 0.7080 (OUTLIER) cc_final: 0.6351 (mmmt) REVERT: E 332 ASP cc_start: 0.6179 (m-30) cc_final: 0.5880 (p0) REVERT: E 351 ASP cc_start: 0.7083 (m-30) cc_final: 0.6695 (m-30) REVERT: A 290 PHE cc_start: 0.8654 (OUTLIER) cc_final: 0.8358 (t80) REVERT: A 342 LEU cc_start: 0.8690 (mt) cc_final: 0.8363 (tt) REVERT: A 345 LYS cc_start: 0.7730 (OUTLIER) cc_final: 0.7392 (pptt) REVERT: A 432 MET cc_start: 0.7472 (OUTLIER) cc_final: 0.5951 (mmm) REVERT: B 351 LYS cc_start: 0.8467 (mmtp) cc_final: 0.8236 (mmmt) REVERT: B 397 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6502 (mp0) REVERT: B 458 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.7760 (mt-10) REVERT: C 359 ASN cc_start: 0.8750 (m110) cc_final: 0.8535 (m110) outliers start: 57 outliers final: 34 residues processed: 204 average time/residue: 0.9181 time to fit residues: 217.2382 Evaluate side-chains 196 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 155 time to evaluate : 2.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 432 MET Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 290 PHE Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 290 PHE Chi-restraints excluded: chain C residue 372 PHE Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 452 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 183 optimal weight: 4.9990 chunk 167 optimal weight: 0.9980 chunk 178 optimal weight: 3.9990 chunk 107 optimal weight: 0.1980 chunk 77 optimal weight: 0.3980 chunk 140 optimal weight: 0.2980 chunk 54 optimal weight: 1.9990 chunk 161 optimal weight: 0.5980 chunk 169 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 chunk 189 optimal weight: 6.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 228 GLN C 374 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.9619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 16545 Z= 0.135 Angle : 0.483 8.584 22462 Z= 0.258 Chirality : 0.044 0.184 2514 Planarity : 0.003 0.037 2873 Dihedral : 4.406 39.372 2194 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.27 % Allowed : 25.58 % Favored : 72.15 % 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: 0.04 (0.19), residues: 2012 helix: 1.72 (0.18), residues: 854 sheet: -1.04 (0.28), residues: 312 loop : -1.33 (0.22), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 218 HIS 0.003 0.001 HIS C 286 PHE 0.010 0.001 PHE C 334 TYR 0.006 0.001 TYR B 323 ARG 0.003 0.000 ARG E 48 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 177 time to evaluate : 1.954 Fit side-chains REVERT: E 58 LYS cc_start: 0.7896 (tttt) cc_final: 0.7383 (tmmm) REVERT: E 85 LYS cc_start: 0.7141 (OUTLIER) cc_final: 0.6356 (mmmt) REVERT: E 351 ASP cc_start: 0.7009 (m-30) cc_final: 0.6654 (m-30) REVERT: A 290 PHE cc_start: 0.8554 (OUTLIER) cc_final: 0.8211 (t80) REVERT: A 345 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.7399 (pptt) REVERT: A 374 ASN cc_start: 0.7751 (m-40) cc_final: 0.7539 (m-40) REVERT: B 315 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7561 (mm-30) REVERT: B 351 LYS cc_start: 0.8369 (mmtp) cc_final: 0.8166 (mmmt) REVERT: B 374 ASN cc_start: 0.7870 (m-40) cc_final: 0.7606 (m-40) REVERT: C 125 ILE cc_start: 0.8455 (mt) cc_final: 0.8083 (mt) REVERT: C 359 ASN cc_start: 0.8742 (m110) cc_final: 0.8528 (m110) outliers start: 41 outliers final: 24 residues processed: 207 average time/residue: 0.9663 time to fit residues: 232.2854 Evaluate side-chains 194 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 167 time to evaluate : 1.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 290 PHE Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 371 SER Chi-restraints excluded: chain D residue 452 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 115 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 198 optimal weight: 0.9980 chunk 182 optimal weight: 5.9990 chunk 157 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 121 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 125 optimal weight: 0.0670 chunk 168 optimal weight: 0.8980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 GLN C 308 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.9635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16545 Z= 0.156 Angle : 0.493 9.042 22462 Z= 0.262 Chirality : 0.045 0.185 2514 Planarity : 0.003 0.036 2873 Dihedral : 4.414 40.251 2194 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 1.99 % Allowed : 26.08 % Favored : 71.93 % 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: 0.08 (0.19), residues: 2012 helix: 1.77 (0.18), residues: 858 sheet: -1.07 (0.27), residues: 332 loop : -1.32 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 218 HIS 0.003 0.001 HIS B 286 PHE 0.028 0.001 PHE A 334 TYR 0.018 0.001 TYR C 243 ARG 0.005 0.000 ARG E 48 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 164 time to evaluate : 1.909 Fit side-chains REVERT: E 58 LYS cc_start: 0.7906 (tttt) cc_final: 0.7384 (tmmm) REVERT: E 351 ASP cc_start: 0.6984 (m-30) cc_final: 0.6615 (m-30) REVERT: A 290 PHE cc_start: 0.8571 (OUTLIER) cc_final: 0.8230 (t80) REVERT: A 345 LYS cc_start: 0.7719 (OUTLIER) cc_final: 0.7394 (pptt) REVERT: A 374 ASN cc_start: 0.7784 (m-40) cc_final: 0.7564 (m-40) REVERT: B 290 PHE cc_start: 0.8737 (OUTLIER) cc_final: 0.8141 (t80) REVERT: B 374 ASN cc_start: 0.7856 (m-40) cc_final: 0.7602 (m-40) REVERT: C 125 ILE cc_start: 0.8515 (mt) cc_final: 0.8098 (mt) REVERT: C 359 ASN cc_start: 0.8755 (m110) cc_final: 0.8538 (m110) outliers start: 36 outliers final: 26 residues processed: 193 average time/residue: 0.9333 time to fit residues: 207.4230 Evaluate side-chains 187 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 158 time to evaluate : 1.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 33 ASP Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 290 PHE Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 290 PHE Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 452 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 48 optimal weight: 0.8980 chunk 145 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 158 optimal weight: 0.4980 chunk 66 optimal weight: 2.9990 chunk 162 optimal weight: 0.9990 chunk 20 optimal weight: 7.9990 chunk 29 optimal weight: 0.5980 chunk 138 optimal weight: 4.9990 chunk 9 optimal weight: 0.0870 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 402 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.114008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.095442 restraints weight = 24140.675| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.60 r_work: 0.3052 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.9666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 16545 Z= 0.143 Angle : 0.487 8.617 22462 Z= 0.259 Chirality : 0.044 0.181 2514 Planarity : 0.003 0.037 2873 Dihedral : 4.319 37.964 2193 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 1.77 % Allowed : 26.52 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.19 (0.19), residues: 2012 helix: 2.00 (0.18), residues: 834 sheet: -0.99 (0.27), residues: 340 loop : -1.34 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 218 HIS 0.003 0.001 HIS B 286 PHE 0.010 0.001 PHE C 334 TYR 0.006 0.001 TYR A 243 ARG 0.008 0.000 ARG E 48 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5372.14 seconds wall clock time: 97 minutes 4.49 seconds (5824.49 seconds total)