Starting phenix.real_space_refine on Wed Nov 15 00:08:57 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7t_18233/11_2023/8q7t_18233.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7t_18233/11_2023/8q7t_18233.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7t_18233/11_2023/8q7t_18233.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7t_18233/11_2023/8q7t_18233.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7t_18233/11_2023/8q7t_18233.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7t_18233/11_2023/8q7t_18233.pdb" } resolution = 3.0 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= 0.003 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: 5 Type Number sf(0) Gaussians S 9 5.16 5 C 3102 2.51 5 N 903 2.21 5 O 933 1.98 5 H 5136 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ASP 314": "OD1" <-> "OD2" Residue "C GLU 338": "OE1" <-> "OE2" Residue "C PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 348": "OD1" <-> "OD2" Residue "A ASP 358": "OD1" <-> "OD2" Residue "A GLU 372": "OE1" <-> "OE2" Residue "E ASP 314": "OD1" <-> "OD2" Residue "E GLU 338": "OE1" <-> "OE2" Residue "E PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 348": "OD1" <-> "OD2" Residue "G PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 358": "OD1" <-> "OD2" Residue "G GLU 372": "OE1" <-> "OE2" Residue "H ASP 314": "OD1" <-> "OD2" Residue "H GLU 338": "OE1" <-> "OE2" Residue "H PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 348": "OD1" <-> "OD2" Residue "I PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ASP 358": "OD1" <-> "OD2" Residue "I GLU 372": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 10083 Number of models: 1 Model: "" Number of chains: 9 Chain: "B" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1155 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "D" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1155 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "F" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1155 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "C" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1051 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain: "A" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1155 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "E" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1051 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain: "G" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1155 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "H" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1051 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain: "I" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1155 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Time building chain proxies: 4.94, per 1000 atoms: 0.49 Number of scatterers: 10083 At special positions: 0 Unit cell: (161.394, 145.4, 47.982, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 9 16.00 O 933 8.00 N 903 7.00 C 3102 6.00 H 5136 1.00 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: 7.76 Conformation dependent library (CDL) restraints added in 1.1 seconds 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1134 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 25 sheets defined 0.0% alpha, 54.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 306 through 310 removed outlier: 6.488A pdb=" N GLN B 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N TYR D 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL B 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.859A pdb=" N VAL B 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 317 through 325 removed outlier: 6.324A pdb=" N LYS B 317 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N SER D 320 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR B 319 " --> pdb=" O SER D 320 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N CYS D 322 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LYS B 321 " --> pdb=" O CYS D 322 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N SER D 324 " --> pdb=" O LYS B 321 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N GLY B 323 " --> pdb=" O SER D 324 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 328 through 330 removed outlier: 6.603A pdb=" N ILE B 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 337 through 346 removed outlier: 6.569A pdb=" N GLU B 338 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N SER D 341 " --> pdb=" O GLU B 338 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LYS B 340 " --> pdb=" O SER D 341 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N LYS D 343 " --> pdb=" O LYS B 340 " (cutoff:3.500A) removed outlier: 8.811A pdb=" N GLU B 342 " --> pdb=" O LYS D 343 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N ASP D 345 " --> pdb=" O GLU B 342 " (cutoff:3.500A) removed outlier: 9.095A pdb=" N LEU B 344 " --> pdb=" O ASP D 345 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU F 344 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ASP B 345 " --> pdb=" O LEU F 344 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N PHE F 346 " --> pdb=" O ASP B 345 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 350 through 362 removed outlier: 6.899A pdb=" N GLN D 351 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N SER B 352 " --> pdb=" O GLN D 351 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LYS D 353 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ILE B 354 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLY D 355 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N SER B 356 " --> pdb=" O GLY D 355 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N GLN B 351 " --> pdb=" O VAL F 350 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N SER F 352 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LYS B 353 " --> pdb=" O SER F 352 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILE F 354 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N GLY B 355 " --> pdb=" O ILE F 354 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N SER F 356 " --> pdb=" O GLY B 355 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 368 through 377 removed outlier: 6.462A pdb=" N LYS B 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N GLU D 372 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE B 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N HIS D 374 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N THR B 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N LEU D 376 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LYS B 375 " --> pdb=" O LEU D 376 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 309 through 310 removed outlier: 6.542A pdb=" N VAL E 309 " --> pdb=" O TYR H 310 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.796A pdb=" N VAL E 313 " --> pdb=" O ASP H 314 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 317 through 325 removed outlier: 6.468A pdb=" N VAL C 318 " --> pdb=" O THR H 319 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N LYS H 321 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N SER C 320 " --> pdb=" O LYS H 321 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N GLY H 323 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N CYS C 322 " --> pdb=" O GLY H 323 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU H 325 " --> pdb=" O CYS C 322 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N SER C 324 " --> pdb=" O LEU H 325 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LYS E 317 " --> pdb=" O VAL H 318 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N SER H 320 " --> pdb=" O LYS E 317 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N THR E 319 " --> pdb=" O SER H 320 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N CYS H 322 " --> pdb=" O THR E 319 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LYS E 321 " --> pdb=" O CYS H 322 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N SER H 324 " --> pdb=" O LYS E 321 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N GLY E 323 " --> pdb=" O SER H 324 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 328 through 330 removed outlier: 6.461A pdb=" N ILE E 328 " --> pdb=" O HIS H 329 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 337 through 342 removed outlier: 6.576A pdb=" N GLU E 338 " --> pdb=" O VAL H 339 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N SER H 341 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LYS E 340 " --> pdb=" O SER H 341 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 345 through 346 removed outlier: 6.538A pdb=" N ASP E 345 " --> pdb=" O PHE H 346 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 350 through 354 removed outlier: 6.512A pdb=" N GLN E 351 " --> pdb=" O SER H 352 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N ILE H 354 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LYS E 353 " --> pdb=" O ILE H 354 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 359 through 362 removed outlier: 6.523A pdb=" N ASN C 359 " --> pdb=" O ILE H 360 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N HIS H 362 " --> pdb=" O ASN C 359 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N THR C 361 " --> pdb=" O HIS H 362 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 368 through 374 Processing sheet with id=AB8, first strand: chain 'G' and resid 305 through 310 removed outlier: 6.571A pdb=" N VAL A 306 " --> pdb=" O GLN I 307 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N VAL I 309 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE A 308 " --> pdb=" O VAL I 309 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 313 through 314 removed outlier: 6.919A pdb=" N VAL A 313 " --> pdb=" O ASP G 314 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 317 through 325 removed outlier: 6.491A pdb=" N VAL A 318 " --> pdb=" O THR I 319 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N LYS I 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N SER A 320 " --> pdb=" O LYS I 321 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N GLY I 323 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N CYS A 322 " --> pdb=" O GLY I 323 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU I 325 " --> pdb=" O CYS A 322 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N SER A 324 " --> pdb=" O LEU I 325 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 328 through 330 removed outlier: 6.696A pdb=" N ILE A 328 " --> pdb=" O HIS G 329 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 333 through 334 removed outlier: 6.854A pdb=" N GLY A 333 " --> pdb=" O GLY G 334 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 337 through 346 removed outlier: 6.403A pdb=" N GLU A 338 " --> pdb=" O VAL G 339 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N SER G 341 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LYS A 340 " --> pdb=" O SER G 341 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N LYS G 343 " --> pdb=" O LYS A 340 " (cutoff:3.500A) removed outlier: 8.790A pdb=" N GLU A 342 " --> pdb=" O LYS G 343 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N ASP G 345 " --> pdb=" O GLU A 342 " (cutoff:3.500A) removed outlier: 9.079A pdb=" N LEU A 344 " --> pdb=" O ASP G 345 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL A 337 " --> pdb=" O GLU I 338 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N LYS I 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N VAL A 339 " --> pdb=" O LYS I 340 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N GLU I 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N SER A 341 " --> pdb=" O GLU I 342 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU I 344 " --> pdb=" O SER A 341 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N LYS A 343 " --> pdb=" O LEU I 344 " (cutoff:3.500A) removed outlier: 10.382A pdb=" N PHE I 346 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 9.209A pdb=" N ASP A 345 " --> pdb=" O PHE I 346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'G' and resid 350 through 358 removed outlier: 6.406A pdb=" N GLN A 351 " --> pdb=" O SER G 352 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ILE G 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LYS A 353 " --> pdb=" O ILE G 354 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N SER G 356 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 9.380A pdb=" N GLY A 355 " --> pdb=" O SER G 356 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ASP G 358 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 8.771A pdb=" N LEU A 357 " --> pdb=" O ASP G 358 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL A 350 " --> pdb=" O GLN I 351 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N LYS I 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N SER A 352 " --> pdb=" O LYS I 353 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'G' and resid 361 through 362 removed outlier: 6.320A pdb=" N THR A 361 " --> pdb=" O HIS I 362 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 368 through 377 removed outlier: 6.478A pdb=" N LYS A 369 " --> pdb=" O LYS G 370 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N GLU G 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE A 371 " --> pdb=" O GLU G 372 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N HIS G 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N THR A 373 " --> pdb=" O HIS G 374 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N LEU G 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LYS A 375 " --> pdb=" O LEU G 376 " (cutoff:3.500A) 98 hydrogen bonds defined for protein. 294 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: 3.13 Time building geometry restraints manager: 8.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 5127 1.12 - 1.29: 834 1.29 - 1.47: 1711 1.47 - 1.64: 2480 1.64 - 1.82: 9 Bond restraints: 10161 Sorted by residual: bond pdb=" NE2 HIS F 329 " pdb=" HE2 HIS F 329 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" ND2 ASN F 327 " pdb="HD22 ASN F 327 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N LYS D 353 " pdb=" H LYS D 353 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" NE2 HIS D 362 " pdb=" HE2 HIS D 362 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N ASP E 345 " pdb=" H ASP E 345 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 10156 not shown) Histogram of bond angle deviations from ideal: 96.13 - 103.07: 31 103.07 - 110.00: 9630 110.00 - 116.93: 3930 116.93 - 123.86: 4283 123.86 - 130.80: 660 Bond angle restraints: 18534 Sorted by residual: angle pdb=" CA GLY I 355 " pdb=" C GLY I 355 " pdb=" N SER I 356 " ideal model delta sigma weight residual 114.58 119.53 -4.95 8.60e-01 1.35e+00 3.31e+01 angle pdb=" OE1 GLN I 336 " pdb=" CD GLN I 336 " pdb=" NE2 GLN I 336 " ideal model delta sigma weight residual 122.60 117.08 5.52 1.00e+00 1.00e+00 3.05e+01 angle pdb=" OE1 GLN B 336 " pdb=" CD GLN B 336 " pdb=" NE2 GLN B 336 " ideal model delta sigma weight residual 122.60 117.08 5.52 1.00e+00 1.00e+00 3.04e+01 angle pdb=" CA ASP C 358 " pdb=" CB ASP C 358 " pdb=" CG ASP C 358 " ideal model delta sigma weight residual 112.60 117.95 -5.35 1.00e+00 1.00e+00 2.86e+01 angle pdb=" OE1 GLN G 336 " pdb=" CD GLN G 336 " pdb=" NE2 GLN G 336 " ideal model delta sigma weight residual 122.60 117.32 5.28 1.00e+00 1.00e+00 2.79e+01 ... (remaining 18529 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.79: 3531 16.79 - 33.58: 192 33.58 - 50.38: 58 50.38 - 67.17: 110 67.17 - 83.96: 6 Dihedral angle restraints: 3897 sinusoidal: 1890 harmonic: 2007 Sorted by residual: dihedral pdb=" CA PRO C 332 " pdb=" C PRO C 332 " pdb=" N GLY C 333 " pdb=" CA GLY C 333 " ideal model delta harmonic sigma weight residual 180.00 154.19 25.81 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CA GLY C 334 " pdb=" C GLY C 334 " pdb=" N GLY C 335 " pdb=" CA GLY C 335 " ideal model delta harmonic sigma weight residual 180.00 159.38 20.62 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA GLY A 367 " pdb=" C GLY A 367 " pdb=" N ASN A 368 " pdb=" CA ASN A 368 " ideal model delta harmonic sigma weight residual -180.00 -159.83 -20.17 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 3894 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 508 0.081 - 0.161: 213 0.161 - 0.242: 27 0.242 - 0.322: 6 0.322 - 0.402: 2 Chirality restraints: 756 Sorted by residual: chirality pdb=" CA PRO H 332 " pdb=" N PRO H 332 " pdb=" C PRO H 332 " pdb=" CB PRO H 332 " both_signs ideal model delta sigma weight residual False 2.72 2.32 0.40 2.00e-01 2.50e+01 4.05e+00 chirality pdb=" CA PRO C 332 " pdb=" N PRO C 332 " pdb=" C PRO C 332 " pdb=" CB PRO C 332 " both_signs ideal model delta sigma weight residual False 2.72 2.39 0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" CA LYS F 347 " pdb=" N LYS F 347 " pdb=" C LYS F 347 " pdb=" CB LYS F 347 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.19e+00 ... (remaining 753 not shown) Planarity restraints: 1473 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 368 " 0.110 2.00e-02 2.50e+03 1.01e-01 1.53e+02 pdb=" CG ASN A 368 " -0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN A 368 " -0.085 2.00e-02 2.50e+03 pdb=" ND2 ASN A 368 " -0.044 2.00e-02 2.50e+03 pdb="HD21 ASN A 368 " -0.115 2.00e-02 2.50e+03 pdb="HD22 ASN A 368 " 0.161 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 310 " 0.099 2.00e-02 2.50e+03 5.55e-02 9.25e+01 pdb=" CG TYR E 310 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR E 310 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR E 310 " -0.033 2.00e-02 2.50e+03 pdb=" CE1 TYR E 310 " -0.047 2.00e-02 2.50e+03 pdb=" CE2 TYR E 310 " -0.040 2.00e-02 2.50e+03 pdb=" CZ TYR E 310 " -0.018 2.00e-02 2.50e+03 pdb=" OH TYR E 310 " 0.139 2.00e-02 2.50e+03 pdb=" HD1 TYR E 310 " 0.006 2.00e-02 2.50e+03 pdb=" HD2 TYR E 310 " -0.010 2.00e-02 2.50e+03 pdb=" HE1 TYR E 310 " -0.033 2.00e-02 2.50e+03 pdb=" HE2 TYR E 310 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN G 368 " 0.082 2.00e-02 2.50e+03 7.83e-02 9.19e+01 pdb=" CG ASN G 368 " -0.010 2.00e-02 2.50e+03 pdb=" OD1 ASN G 368 " -0.073 2.00e-02 2.50e+03 pdb=" ND2 ASN G 368 " -0.029 2.00e-02 2.50e+03 pdb="HD21 ASN G 368 " -0.094 2.00e-02 2.50e+03 pdb="HD22 ASN G 368 " 0.123 2.00e-02 2.50e+03 ... (remaining 1470 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.14: 599 2.14 - 2.75: 15950 2.75 - 3.37: 26764 3.37 - 3.98: 35994 3.98 - 4.60: 49732 Nonbonded interactions: 129039 Sorted by model distance: nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.520 1.850 nonbonded pdb=" OD1 ASP H 314 " pdb=" HG SER H 316 " model vdw 1.527 1.850 nonbonded pdb=" OD1 ASP F 314 " pdb=" HG SER F 316 " model vdw 1.559 1.850 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.581 1.850 nonbonded pdb=" OD1 ASP I 314 " pdb=" HG SER I 316 " model vdw 1.582 1.850 ... (remaining 129034 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' and resid 308 through 375) selection = (chain 'B' and resid 308 through 375) selection = chain 'C' selection = (chain 'D' and resid 308 through 375) selection = chain 'E' selection = (chain 'F' and resid 308 through 375) selection = (chain 'G' and resid 308 through 375) selection = chain 'H' selection = (chain 'I' and resid 308 through 375) } 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: 2.750 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: 0.150 Extract box with map and model: 12.000 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 34.470 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.030 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:11.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6409 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 : 0.011 0.040 5025 Z= 0.738 Angle : 1.800 6.507 6723 Z= 1.186 Chirality : 0.085 0.402 756 Planarity : 0.009 0.066 855 Dihedral : 12.353 83.957 1920 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 0.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.18 % Allowed : 3.17 % Favored : 96.65 % 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: -1.65 (0.27), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.25 (0.21), residues: 636 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 166 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 2 residues processed: 167 average time/residue: 2.4280 time to fit residues: 420.9441 Evaluate side-chains 83 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 81 time to evaluate : 0.762 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 1 average time/residue: 0.1741 time to fit residues: 1.2093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 336 GLN G 327 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6525 moved from start: 0.4545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 5025 Z= 0.328 Angle : 0.643 4.788 6723 Z= 0.333 Chirality : 0.049 0.144 756 Planarity : 0.004 0.027 855 Dihedral : 6.357 20.668 663 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.53 % Allowed : 15.34 % Favored : 81.13 % 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: -1.24 (0.29), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.93 (0.22), residues: 636 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 99 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 111 average time/residue: 2.1788 time to fit residues: 253.1570 Evaluate side-chains 88 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 77 time to evaluate : 0.901 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 2 average time/residue: 1.3427 time to fit residues: 4.0631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 15 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 58 optimal weight: 0.0870 chunk 48 optimal weight: 10.0000 chunk 18 optimal weight: 20.0000 chunk 43 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 overall best weight: 2.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 330 HIS F 327 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6518 moved from start: 0.5313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5025 Z= 0.195 Angle : 0.557 4.827 6723 Z= 0.278 Chirality : 0.051 0.137 756 Planarity : 0.003 0.024 855 Dihedral : 5.564 18.873 663 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.88 % Allowed : 17.64 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.28), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.02 (0.22), residues: 636 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 86 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 12 residues processed: 102 average time/residue: 2.1042 time to fit residues: 224.8616 Evaluate side-chains 85 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 73 time to evaluate : 0.788 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 12 residues processed: 1 average time/residue: 0.1650 time to fit residues: 1.2279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 6 optimal weight: 20.0000 chunk 26 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 57 optimal weight: 0.4980 chunk 51 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6540 moved from start: 0.5703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 5025 Z= 0.225 Angle : 0.547 6.566 6723 Z= 0.273 Chirality : 0.050 0.147 756 Planarity : 0.003 0.050 855 Dihedral : 5.345 19.000 663 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.41 % Allowed : 18.87 % Favored : 76.72 % 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: -1.42 (0.28), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.07 (0.22), residues: 636 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 75 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 13 residues processed: 95 average time/residue: 2.0934 time to fit residues: 208.5016 Evaluate side-chains 86 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 73 time to evaluate : 0.878 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 13 residues processed: 0 time to fit residues: 1.0806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 40.0000 chunk 43 optimal weight: 0.0050 chunk 23 optimal weight: 0.3980 chunk 49 optimal weight: 4.9990 chunk 40 optimal weight: 0.0570 chunk 29 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 19 optimal weight: 20.0000 chunk 11 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 overall best weight: 1.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 336 GLN F 327 ASN ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6534 moved from start: 0.5847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5025 Z= 0.170 Angle : 0.511 5.527 6723 Z= 0.254 Chirality : 0.050 0.156 756 Planarity : 0.003 0.037 855 Dihedral : 5.009 17.980 663 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.53 % Allowed : 18.52 % Favored : 77.95 % 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: -1.41 (0.28), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.06 (0.22), residues: 636 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 79 time to evaluate : 0.894 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 13 residues processed: 96 average time/residue: 2.1825 time to fit residues: 219.0598 Evaluate side-chains 85 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 72 time to evaluate : 0.772 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 12 residues processed: 1 average time/residue: 2.3933 time to fit residues: 3.4475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 4 optimal weight: 20.0000 chunk 19 optimal weight: 30.0000 chunk 30 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 6 optimal weight: 20.0000 chunk 33 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6553 moved from start: 0.6081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5025 Z= 0.225 Angle : 0.524 6.035 6723 Z= 0.262 Chirality : 0.049 0.151 756 Planarity : 0.003 0.031 855 Dihedral : 5.047 18.933 663 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.53 % Allowed : 18.34 % Favored : 78.13 % 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 (0.28), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.09 (0.22), residues: 636 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 76 time to evaluate : 0.785 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 14 residues processed: 93 average time/residue: 2.0486 time to fit residues: 199.4812 Evaluate side-chains 85 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 71 time to evaluate : 0.783 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 13 residues processed: 1 average time/residue: 0.1696 time to fit residues: 1.3816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 6.9990 chunk 48 optimal weight: 9.9990 chunk 57 optimal weight: 3.9990 chunk 36 optimal weight: 0.3980 chunk 35 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 336 GLN F 327 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6537 moved from start: 0.6250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5025 Z= 0.162 Angle : 0.495 4.919 6723 Z= 0.245 Chirality : 0.050 0.149 756 Planarity : 0.003 0.030 855 Dihedral : 4.771 17.491 663 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.35 % Allowed : 18.87 % Favored : 77.78 % 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 (0.28), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.09 (0.22), residues: 636 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 77 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 12 residues processed: 93 average time/residue: 2.1932 time to fit residues: 213.4026 Evaluate side-chains 83 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 71 time to evaluate : 0.861 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 11 residues processed: 1 average time/residue: 0.1816 time to fit residues: 1.3178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 6.9990 chunk 5 optimal weight: 0.6980 chunk 45 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 55 optimal weight: 0.6980 chunk 50 optimal weight: 9.9990 chunk 53 optimal weight: 0.4980 chunk 32 optimal weight: 1.9990 chunk 23 optimal weight: 0.2980 chunk 42 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 336 GLN E 374 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6530 moved from start: 0.6427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5025 Z= 0.151 Angle : 0.482 4.394 6723 Z= 0.237 Chirality : 0.050 0.146 756 Planarity : 0.003 0.031 855 Dihedral : 4.475 15.865 663 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.29 % Allowed : 20.46 % Favored : 77.25 % 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: -1.43 (0.28), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.08 (0.22), residues: 636 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 74 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 11 residues processed: 87 average time/residue: 2.2484 time to fit residues: 204.4171 Evaluate side-chains 80 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 69 time to evaluate : 0.900 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 11 residues processed: 0 time to fit residues: 1.1786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 7.9990 chunk 50 optimal weight: 8.9990 chunk 53 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6545 moved from start: 0.6583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5025 Z= 0.190 Angle : 0.504 5.269 6723 Z= 0.248 Chirality : 0.049 0.145 756 Planarity : 0.003 0.031 855 Dihedral : 4.573 16.447 663 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.82 % Allowed : 19.75 % Favored : 77.43 % 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: -1.42 (0.29), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.07 (0.22), residues: 636 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 65 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 11 residues processed: 79 average time/residue: 2.2308 time to fit residues: 184.5988 Evaluate side-chains 76 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 65 time to evaluate : 0.887 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 11 residues processed: 0 time to fit residues: 1.0890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 20.0000 chunk 36 optimal weight: 0.8980 chunk 29 optimal weight: 0.4980 chunk 37 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 13 optimal weight: 0.0070 chunk 47 optimal weight: 9.9990 chunk 19 optimal weight: 20.0000 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6525 moved from start: 0.6640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5025 Z= 0.151 Angle : 0.491 5.938 6723 Z= 0.241 Chirality : 0.051 0.146 756 Planarity : 0.003 0.032 855 Dihedral : 4.304 15.325 663 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.12 % Allowed : 20.28 % Favored : 77.60 % 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: -1.40 (0.29), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.06 (0.22), residues: 636 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 69 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 11 residues processed: 80 average time/residue: 2.2734 time to fit residues: 190.3136 Evaluate side-chains 79 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 68 time to evaluate : 0.883 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 11 residues processed: 0 time to fit residues: 1.0686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 8.9990 chunk 6 optimal weight: 6.9990 chunk 8 optimal weight: 8.9990 chunk 41 optimal weight: 2.9990 chunk 2 optimal weight: 20.0000 chunk 34 optimal weight: 0.0770 chunk 54 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 overall best weight: 3.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.199783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.143843 restraints weight = 17161.575| |-----------------------------------------------------------------------------| r_work (start): 0.4082 rms_B_bonded: 1.78 r_work: 0.4002 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3922 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.6751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5025 Z= 0.224 Angle : 0.511 5.740 6723 Z= 0.255 Chirality : 0.049 0.147 756 Planarity : 0.003 0.030 855 Dihedral : 4.626 17.069 663 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.29 % Allowed : 19.58 % Favored : 78.13 % 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: -1.43 (0.29), residues: 636 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.08 (0.22), residues: 636 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5125.11 seconds wall clock time: 90 minutes 12.27 seconds (5412.27 seconds total)