Starting phenix.real_space_refine (version: dev) on Fri Jun 3 11:43:54 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xc6_33113/06_2022/7xc6_33113.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xc6_33113/06_2022/7xc6_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_33113/06_2022/7xc6_33113.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xc6_33113/06_2022/7xc6_33113.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xc6_33113/06_2022/7xc6_33113.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xc6_33113/06_2022/7xc6_33113.pdb" } resolution = 2.79 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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-4617/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: 9.25, per 1000 atoms: 0.57 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: 6.94 Conformation dependent library (CDL) restraints added in 2.6 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: 1.03 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: 5.85 Time building geometry restraints manager: 7.44 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 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. 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: 2.170 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: 9.820 Check model and map are aligned: 0.250 Convert atoms to be neutral: 0.150 Process input model: 46.050 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:10.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 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 : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer Outliers : 7.75 % 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: -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 *********************** 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 : 1.786 Fit side-chains revert: symmetry clash outliers start: 140 outliers final: 14 residues processed: 561 average time/residue: 0.9219 time to fit residues: 592.2439 Evaluate side-chains 250 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 236 time to evaluate : 1.901 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 11 residues processed: 3 average time/residue: 0.8013 time to fit residues: 5.4905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 51 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 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: 1.3184 ------------------------------------------------------------------------------- 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 134 HIS A 252 HIS A 360 GLN A 434 ASN B 67 GLN B 252 HIS 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: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.7411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.078 16545 Z= 0.292 Angle : 0.688 10.350 22462 Z= 0.364 Chirality : 0.050 0.252 2514 Planarity : 0.006 0.109 2873 Dihedral : 5.264 26.970 2191 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer Outliers : 5.59 % 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: -1.45 (0.18), residues: 2012 helix: 0.28 (0.17), residues: 838 sheet: -1.52 (0.26), residues: 334 loop : -1.97 (0.20), residues: 840 *********************** 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 356 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 255 time to evaluate : 2.180 Fit side-chains outliers start: 101 outliers final: 29 residues processed: 326 average time/residue: 1.0206 time to fit residues: 377.8391 Evaluate side-chains 189 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 160 time to evaluate : 1.980 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 23 residues processed: 6 average time/residue: 0.4917 time to fit residues: 6.4874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 100 optimal weight: 0.5980 chunk 56 optimal weight: 5.9990 chunk 150 optimal weight: 0.5980 chunk 123 optimal weight: 2.9990 chunk 49 optimal weight: 0.0980 chunk 181 optimal weight: 4.9990 chunk 195 optimal weight: 1.9990 chunk 161 optimal weight: 0.6980 chunk 179 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 145 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 434 ASN B 48 GLN D 67 GLN D 319 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.7804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 16545 Z= 0.150 Angle : 0.496 6.939 22462 Z= 0.267 Chirality : 0.045 0.135 2514 Planarity : 0.004 0.078 2873 Dihedral : 4.448 23.127 2191 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer Outliers : 3.77 % 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: -0.71 (0.18), residues: 2012 helix: 1.02 (0.17), residues: 854 sheet: -1.31 (0.25), residues: 356 loop : -1.70 (0.21), residues: 802 *********************** 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 264 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 196 time to evaluate : 1.970 Fit side-chains outliers start: 68 outliers final: 30 residues processed: 250 average time/residue: 0.9049 time to fit residues: 261.3233 Evaluate side-chains 182 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 152 time to evaluate : 2.017 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 24 residues processed: 7 average time/residue: 0.4691 time to fit residues: 7.1031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 93 optimal weight: 8.9990 chunk 20 optimal weight: 0.0970 chunk 86 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 181 optimal weight: 1.9990 chunk 192 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 64 GLN A 67 GLN B 162 ASN C 162 ASN C 308 ASN C 332 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 moved from start: 0.8716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 16545 Z= 0.232 Angle : 0.546 7.618 22462 Z= 0.291 Chirality : 0.047 0.150 2514 Planarity : 0.004 0.069 2873 Dihedral : 4.672 20.642 2191 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer Outliers : 3.77 % 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: -0.55 (0.19), residues: 2012 helix: 1.20 (0.18), residues: 850 sheet: -1.34 (0.27), residues: 328 loop : -1.59 (0.21), residues: 834 *********************** 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 244 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 176 time to evaluate : 2.028 Fit side-chains outliers start: 68 outliers final: 36 residues processed: 229 average time/residue: 1.0655 time to fit residues: 280.5996 Evaluate side-chains 178 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 142 time to evaluate : 1.849 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 29 residues processed: 7 average time/residue: 0.1943 time to fit residues: 4.7520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 160 optimal weight: 5.9990 chunk 109 optimal weight: 0.9990 chunk 2 optimal weight: 7.9990 chunk 143 optimal weight: 1.9990 chunk 79 optimal weight: 0.2980 chunk 164 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 98 optimal weight: 5.9990 chunk 172 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8947 moved from start: 0.9201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 16545 Z= 0.227 Angle : 0.533 7.646 22462 Z= 0.284 Chirality : 0.046 0.153 2514 Planarity : 0.004 0.067 2873 Dihedral : 4.621 20.776 2191 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer Outliers : 4.04 % 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 (0.19), residues: 2012 helix: 1.29 (0.18), residues: 850 sheet: -1.25 (0.27), residues: 332 loop : -1.50 (0.21), residues: 830 *********************** 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 237 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 164 time to evaluate : 2.003 Fit side-chains outliers start: 73 outliers final: 40 residues processed: 223 average time/residue: 0.8559 time to fit residues: 222.9230 Evaluate side-chains 191 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 151 time to evaluate : 1.950 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 32 residues processed: 8 average time/residue: 0.3869 time to fit residues: 6.8525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 38 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 chunk 47 optimal weight: 7.9990 chunk 192 optimal weight: 4.9990 chunk 159 optimal weight: 4.9990 chunk 89 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 ASN C 29 HIS C 308 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9001 moved from start: 0.9418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.083 16545 Z= 0.330 Angle : 0.589 8.910 22462 Z= 0.313 Chirality : 0.048 0.164 2514 Planarity : 0.004 0.067 2873 Dihedral : 4.920 22.665 2191 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer Outliers : 3.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.49 (0.19), residues: 2012 helix: 1.18 (0.17), residues: 850 sheet: -1.32 (0.27), residues: 334 loop : -1.46 (0.22), residues: 828 *********************** 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 219 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 154 time to evaluate : 2.060 Fit side-chains outliers start: 65 outliers final: 45 residues processed: 205 average time/residue: 0.9417 time to fit residues: 223.1861 Evaluate side-chains 187 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 142 time to evaluate : 1.989 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 38 residues processed: 7 average time/residue: 0.3666 time to fit residues: 6.2174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 185 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 109 optimal weight: 3.9990 chunk 140 optimal weight: 0.2980 chunk 108 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 chunk 107 optimal weight: 0.4980 chunk 191 optimal weight: 0.8980 chunk 120 optimal weight: 0.0980 chunk 116 optimal weight: 1.9990 chunk 88 optimal weight: 8.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 GLN A 359 ASN B 162 ASN C 29 HIS C 228 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.9488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.094 16545 Z= 0.157 Angle : 0.493 7.370 22462 Z= 0.264 Chirality : 0.044 0.266 2514 Planarity : 0.004 0.064 2873 Dihedral : 4.389 20.185 2191 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer Outliers : 3.05 % 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: 1.52 (0.18), residues: 854 sheet: -1.16 (0.27), residues: 332 loop : -1.38 (0.22), residues: 826 *********************** 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 239 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 184 time to evaluate : 2.063 Fit side-chains revert: symmetry clash outliers start: 55 outliers final: 36 residues processed: 230 average time/residue: 0.8810 time to fit residues: 236.9780 Evaluate side-chains 198 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 162 time to evaluate : 2.038 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 31 residues processed: 6 average time/residue: 0.2383 time to fit residues: 4.9130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 118 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 114 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 121 optimal weight: 0.0070 chunk 130 optimal weight: 3.9990 chunk 94 optimal weight: 0.1980 chunk 17 optimal weight: 3.9990 chunk 150 optimal weight: 7.9990 chunk 174 optimal weight: 5.9990 overall best weight: 1.2404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 GLN B 162 ASN C 308 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8952 moved from start: 0.9557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.153 16545 Z= 0.237 Angle : 0.540 11.036 22462 Z= 0.290 Chirality : 0.046 0.204 2514 Planarity : 0.004 0.063 2873 Dihedral : 4.502 19.793 2191 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer Outliers : 2.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.19), residues: 2012 helix: 1.47 (0.18), residues: 858 sheet: -1.16 (0.27), residues: 332 loop : -1.34 (0.22), residues: 822 *********************** 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 215 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 167 time to evaluate : 2.083 Fit side-chains revert: symmetry clash outliers start: 48 outliers final: 37 residues processed: 209 average time/residue: 0.8155 time to fit residues: 200.6445 Evaluate side-chains 193 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 156 time to evaluate : 1.983 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 33 residues processed: 4 average time/residue: 0.2356 time to fit residues: 4.0844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 178 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 161 optimal weight: 0.6980 chunk 169 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 chunk 189 optimal weight: 7.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8979 moved from start: 0.9620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.244 16545 Z= 0.301 Angle : 0.582 15.965 22462 Z= 0.313 Chirality : 0.047 0.184 2514 Planarity : 0.004 0.064 2873 Dihedral : 4.699 21.259 2191 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer Outliers : 2.55 % 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: -0.24 (0.19), residues: 2012 helix: 1.38 (0.17), residues: 854 sheet: -1.19 (0.27), residues: 332 loop : -1.34 (0.22), residues: 826 *********************** 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 206 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 160 time to evaluate : 1.943 Fit side-chains revert: symmetry clash outliers start: 46 outliers final: 42 residues processed: 196 average time/residue: 0.8684 time to fit residues: 198.3356 Evaluate side-chains 200 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 158 time to evaluate : 2.055 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 35 residues processed: 8 average time/residue: 0.4147 time to fit residues: 7.0653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 115 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 198 optimal weight: 0.9990 chunk 182 optimal weight: 2.9990 chunk 157 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 121 optimal weight: 0.5980 chunk 96 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 168 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 ASN C 308 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.9664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.420 16545 Z= 0.308 Angle : 0.574 24.715 22462 Z= 0.312 Chirality : 0.045 0.180 2514 Planarity : 0.004 0.063 2873 Dihedral : 4.448 20.995 2191 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer Outliers : 2.27 % 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: -0.12 (0.19), residues: 2012 helix: 1.52 (0.18), residues: 858 sheet: -1.17 (0.27), residues: 312 loop : -1.32 (0.22), residues: 842 ********************** 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 211 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 170 time to evaluate : 1.883 Fit side-chains revert: symmetry clash outliers start: 41 outliers final: 36 residues processed: 205 average time/residue: 0.8906 time to fit residues: 213.7214 Evaluate side-chains 195 residues out of total 1806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 159 time to evaluate : 2.004 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 33 residues processed: 4 average time/residue: 0.2462 time to fit residues: 4.3633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 48 optimal weight: 5.9990 chunk 145 optimal weight: 0.7980 chunk 23 optimal weight: 0.4980 chunk 43 optimal weight: 6.9990 chunk 158 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 chunk 9 optimal weight: 0.0980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.111675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.092946 restraints weight = 24117.034| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.59 r_work: 0.3084 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 1.40 restraints_weight: 0.2500 r_work: 0.3059 rms_B_bonded: 1.48 restraints_weight: 0.1250 r_work: 0.3044 rms_B_bonded: 1.61 restraints_weight: 0.0625 r_work: 0.3028 rms_B_bonded: 1.80 restraints_weight: 0.0312 r_work: 0.3010 rms_B_bonded: 2.05 restraints_weight: 0.0156 r_work: 0.2989 rms_B_bonded: 2.35 restraints_weight: 0.0078 r_work: 0.2967 rms_B_bonded: 2.73 restraints_weight: 0.0039 r_work: 0.2941 rms_B_bonded: 3.18 restraints_weight: 0.0020 r_work: 0.2911 rms_B_bonded: 3.73 restraints_weight: 0.0010 r_work: 0.2878 rms_B_bonded: 4.38 restraints_weight: 0.0005 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9066 moved from start: 0.9674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.485 16545 Z= 0.396 Angle : 0.729 63.013 22462 Z= 0.352 Chirality : 0.045 0.179 2514 Planarity : 0.004 0.062 2873 Dihedral : 4.406 20.746 2191 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer Outliers : 2.10 % 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: 1.56 (0.18), residues: 858 sheet: -1.15 (0.27), residues: 312 loop : -1.32 (0.22), residues: 842 =============================================================================== Job complete usr+sys time: 4948.90 seconds wall clock time: 90 minutes 56.67 seconds (5456.67 seconds total)