Starting phenix.real_space_refine on Mon Jun 24 23:22:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ero_19928/06_2024/9ero_19928.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ero_19928/06_2024/9ero_19928.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ero_19928/06_2024/9ero_19928.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ero_19928/06_2024/9ero_19928.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ero_19928/06_2024/9ero_19928.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ero_19928/06_2024/9ero_19928.pdb" } resolution = 2.9 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 10 5.16 5 C 3625 2.51 5 N 1070 2.21 5 O 1070 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 349": "NH1" <-> "NH2" Residue "A GLU 372": "OE1" <-> "OE2" Residue "A ARG 379": "NH1" <-> "NH2" Residue "B TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 314": "OD1" <-> "OD2" Residue "B PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 372": "OE1" <-> "OE2" Residue "B PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 379": "NH1" <-> "NH2" Residue "C TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 349": "NH1" <-> "NH2" Residue "C GLU 372": "OE1" <-> "OE2" Residue "C ARG 379": "NH1" <-> "NH2" Residue "D TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 314": "OD1" <-> "OD2" Residue "D PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 372": "OE1" <-> "OE2" Residue "D PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 379": "NH1" <-> "NH2" Residue "E TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 349": "NH1" <-> "NH2" Residue "E GLU 372": "OE1" <-> "OE2" Residue "E ARG 379": "NH1" <-> "NH2" Residue "F TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 314": "OD1" <-> "OD2" Residue "F PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 372": "OE1" <-> "OE2" Residue "F PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 379": "NH1" <-> "NH2" Residue "G TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 349": "NH1" <-> "NH2" Residue "G GLU 372": "OE1" <-> "OE2" Residue "G ARG 379": "NH1" <-> "NH2" Residue "H TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 314": "OD1" <-> "OD2" Residue "H PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 372": "OE1" <-> "OE2" Residue "H PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 379": "NH1" <-> "NH2" Residue "I TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 349": "NH1" <-> "NH2" Residue "I GLU 372": "OE1" <-> "OE2" Residue "I ARG 379": "NH1" <-> "NH2" Residue "J TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 314": "OD1" <-> "OD2" Residue "J PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 372": "OE1" <-> "OE2" Residue "J PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 379": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 5775 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 581 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Conformer: "B" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} bond proxies already assigned to first conformer: 574 Chain: "B" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "C" Number of atoms: 581 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Conformer: "B" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} bond proxies already assigned to first conformer: 574 Chain: "D" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "E" Number of atoms: 581 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Conformer: "B" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} bond proxies already assigned to first conformer: 574 Chain: "F" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "G" Number of atoms: 581 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Conformer: "B" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} bond proxies already assigned to first conformer: 574 Chain: "H" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "I" Number of atoms: 581 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Conformer: "B" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} bond proxies already assigned to first conformer: 574 Chain: "J" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Time building chain proxies: 6.48, per 1000 atoms: 1.12 Number of scatterers: 5775 At special positions: 0 Unit cell: (121.952, 131.84, 45.32, 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 10 16.00 O 1070 8.00 N 1070 7.00 C 3625 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: 2.06 Conformation dependent library (CDL) restraints added in 2.1 seconds 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1330 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 18 sheets defined 0.0% alpha, 47.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'G' and resid 306 through 310 removed outlier: 6.299A pdb=" N GLN E 307 " --> pdb=" O ILE G 308 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N TYR G 310 " --> pdb=" O GLN E 307 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL E 309 " --> pdb=" O TYR G 310 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLN A 307 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N TYR E 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL A 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 313 through 314 removed outlier: 6.725A pdb=" N VAL E 313 " --> pdb=" O ASP G 314 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL A 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 317 through 318 removed outlier: 6.345A pdb=" N LYS E 317 " --> pdb=" O VAL G 318 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LYS A 317 " --> pdb=" O VAL E 318 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 321 through 330 removed outlier: 6.453A pdb=" N LYS E 321 " --> pdb=" O CYS G 322 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N SER G 324 " --> pdb=" O LYS E 321 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N GLY E 323 " --> pdb=" O SER G 324 " (cutoff:3.500A) removed outlier: 10.047A pdb=" N GLY G 326 " --> pdb=" O GLY E 323 " (cutoff:3.500A) removed outlier: 8.862A pdb=" N LEU E 325 " --> pdb=" O GLY G 326 " (cutoff:3.500A) removed outlier: 9.392A pdb=" N ILE G 328 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ASN E 327 " --> pdb=" O ILE G 328 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N HIS G 330 " --> pdb=" O ASN E 327 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N HIS E 329 " --> pdb=" O HIS G 330 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LYS A 321 " --> pdb=" O CYS E 322 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N SER E 324 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N GLY A 323 " --> pdb=" O SER E 324 " (cutoff:3.500A) removed outlier: 10.047A pdb=" N GLY E 326 " --> pdb=" O GLY A 323 " (cutoff:3.500A) removed outlier: 8.863A pdb=" N LEU A 325 " --> pdb=" O GLY E 326 " (cutoff:3.500A) removed outlier: 9.392A pdb=" N ILE E 328 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ASN A 327 " --> pdb=" O ILE E 328 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N HIS E 330 " --> pdb=" O ASN A 327 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N HIS A 329 " --> pdb=" O HIS E 330 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N SER A 324 " --> pdb=" O GLY C 323 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LEU C 325 " --> pdb=" O SER A 324 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLY A 326 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASN C 327 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N SER C 324 " --> pdb=" O GLY I 323 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LEU I 325 " --> pdb=" O SER C 324 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLY C 326 " --> pdb=" O LEU I 325 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASN I 327 " --> pdb=" O GLY C 326 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 337 through 346 removed outlier: 6.826A pdb=" N LEU E 344 " --> pdb=" O LYS G 343 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ASP G 345 " --> pdb=" O LEU E 344 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N PHE E 346 " --> pdb=" O ASP G 345 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU A 344 " --> pdb=" O LYS E 343 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ASP E 345 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N PHE A 346 " --> pdb=" O ASP E 345 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL A 337 " --> pdb=" O GLU C 338 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N LYS C 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL A 339 " --> pdb=" O LYS C 340 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N GLU C 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N SER A 341 " --> pdb=" O GLU C 342 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU C 344 " --> pdb=" O SER A 341 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LYS A 343 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 9.995A pdb=" N PHE C 346 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 9.317A pdb=" N ASP A 345 " --> pdb=" O PHE C 346 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL C 337 " --> pdb=" O GLU I 338 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N LYS I 340 " --> pdb=" O VAL C 337 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL C 339 " --> pdb=" O LYS I 340 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N GLU I 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N SER C 341 " --> pdb=" O GLU I 342 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU I 344 " --> pdb=" O SER C 341 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LYS C 343 " --> pdb=" O LEU I 344 " (cutoff:3.500A) removed outlier: 9.995A pdb=" N PHE I 346 " --> pdb=" O LYS C 343 " (cutoff:3.500A) removed outlier: 9.318A pdb=" N ASP C 345 " --> pdb=" O PHE I 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 350 through 351 removed outlier: 6.299A pdb=" N VAL A 350 " --> pdb=" O GLN C 351 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL C 350 " --> pdb=" O GLN I 351 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 354 through 357 removed outlier: 6.020A pdb=" N ILE A 354 " --> pdb=" O GLY C 355 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N LEU C 357 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N SER A 356 " --> pdb=" O LEU C 357 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ILE C 354 " --> pdb=" O GLY I 355 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N LEU I 357 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N SER C 356 " --> pdb=" O LEU I 357 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 360 through 362 removed outlier: 6.421A pdb=" N THR A 361 " --> pdb=" O HIS C 362 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N THR C 361 " --> pdb=" O HIS I 362 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 371 through 378 removed outlier: 6.568A pdb=" N GLU A 372 " --> pdb=" O THR C 373 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N LYS C 375 " --> pdb=" O GLU A 372 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N HIS A 374 " --> pdb=" O LYS C 375 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N THR C 377 " --> pdb=" O HIS A 374 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU A 376 " --> pdb=" O THR C 377 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLU C 372 " --> pdb=" O THR I 373 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N LYS I 375 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N HIS C 374 " --> pdb=" O LYS I 375 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N THR I 377 " --> pdb=" O HIS C 374 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU C 376 " --> pdb=" O THR I 377 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 306 through 310 removed outlier: 6.392A pdb=" N GLN B 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N TYR D 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL B 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N GLN D 307 " --> pdb=" O ILE J 308 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N TYR J 310 " --> pdb=" O GLN D 307 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL D 309 " --> pdb=" O TYR J 310 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 313 through 314 removed outlier: 6.784A pdb=" N VAL B 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL D 313 " --> pdb=" O ASP J 314 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 317 through 325 removed outlier: 6.858A pdb=" N VAL H 318 " --> pdb=" O LYS F 317 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N THR F 319 " --> pdb=" O VAL H 318 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N SER H 320 " --> pdb=" O THR F 319 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LYS F 321 " --> pdb=" O SER H 320 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N CYS H 322 " --> pdb=" O LYS F 321 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N GLY F 323 " --> pdb=" O CYS H 322 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL F 318 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N THR B 319 " --> pdb=" O VAL F 318 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N SER F 320 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LYS B 321 " --> pdb=" O SER F 320 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N CYS F 322 " --> pdb=" O LYS B 321 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N GLY B 323 " --> pdb=" O CYS F 322 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N VAL B 318 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 10.692A pdb=" N LYS D 321 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 9.227A pdb=" N SER B 320 " --> pdb=" O LYS D 321 " (cutoff:3.500A) removed outlier: 10.212A pdb=" N GLY D 323 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N CYS B 322 " --> pdb=" O GLY D 323 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N LEU D 325 " --> pdb=" O CYS B 322 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N SER B 324 " --> pdb=" O LEU D 325 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N VAL D 318 " --> pdb=" O THR J 319 " (cutoff:3.500A) removed outlier: 10.692A pdb=" N LYS J 321 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 9.228A pdb=" N SER D 320 " --> pdb=" O LYS J 321 " (cutoff:3.500A) removed outlier: 10.212A pdb=" N GLY J 323 " --> pdb=" O SER D 320 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N CYS D 322 " --> pdb=" O GLY J 323 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N LEU J 325 " --> pdb=" O CYS D 322 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N SER D 324 " --> pdb=" O LEU J 325 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 337 through 342 removed outlier: 6.516A pdb=" N VAL F 337 " --> pdb=" O GLU H 338 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N LYS H 340 " --> pdb=" O VAL F 337 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL F 339 " --> pdb=" O LYS H 340 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N GLU H 342 " --> pdb=" O VAL F 339 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N SER F 341 " --> pdb=" O GLU H 342 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL B 337 " --> pdb=" O GLU F 338 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N LYS F 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL B 339 " --> pdb=" O LYS F 340 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N GLU F 342 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N SER B 341 " --> pdb=" O GLU F 342 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 345 through 346 removed outlier: 6.405A pdb=" N ASP B 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ASP D 345 " --> pdb=" O PHE J 346 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 350 through 351 removed outlier: 6.368A pdb=" N VAL F 350 " --> pdb=" O GLN H 351 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N VAL B 350 " --> pdb=" O GLN F 351 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 354 through 357 removed outlier: 6.014A pdb=" N ILE F 354 " --> pdb=" O GLY H 355 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LEU H 357 " --> pdb=" O ILE F 354 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N SER F 356 " --> pdb=" O LEU H 357 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ILE B 354 " --> pdb=" O GLY F 355 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LEU F 357 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N SER B 356 " --> pdb=" O LEU F 357 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 360 through 362 removed outlier: 6.451A pdb=" N THR F 361 " --> pdb=" O HIS H 362 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N THR B 361 " --> pdb=" O HIS F 362 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 369 through 378 removed outlier: 6.373A pdb=" N LYS F 370 " --> pdb=" O ILE H 371 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N THR H 373 " --> pdb=" O LYS F 370 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N GLU F 372 " --> pdb=" O THR H 373 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N LYS H 375 " --> pdb=" O GLU F 372 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N HIS F 374 " --> pdb=" O LYS H 375 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N THR H 377 " --> pdb=" O HIS F 374 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU F 376 " --> pdb=" O THR H 377 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LYS B 370 " --> pdb=" O ILE F 371 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N THR F 373 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N GLU B 372 " --> pdb=" O THR F 373 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N LYS F 375 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N HIS B 374 " --> pdb=" O LYS F 375 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N THR F 377 " --> pdb=" O HIS B 374 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU B 376 " --> pdb=" O THR F 377 " (cutoff:3.500A) 116 hydrogen bonds defined for protein. 346 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: 1.64 Time building geometry restraints manager: 2.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1382 1.33 - 1.45: 1330 1.45 - 1.57: 3153 1.57 - 1.70: 0 1.70 - 1.82: 10 Bond restraints: 5875 Sorted by residual: bond pdb=" CG HIS I 330 " pdb=" CD2 HIS I 330 " ideal model delta sigma weight residual 1.354 1.296 0.058 1.10e-02 8.26e+03 2.75e+01 bond pdb=" CG HIS A 330 " pdb=" CD2 HIS A 330 " ideal model delta sigma weight residual 1.354 1.297 0.057 1.10e-02 8.26e+03 2.72e+01 bond pdb=" CG HIS C 330 " pdb=" CD2 HIS C 330 " ideal model delta sigma weight residual 1.354 1.297 0.057 1.10e-02 8.26e+03 2.72e+01 bond pdb=" CG HIS G 330 " pdb=" CD2 HIS G 330 " ideal model delta sigma weight residual 1.354 1.297 0.057 1.10e-02 8.26e+03 2.70e+01 bond pdb=" CG HIS E 330 " pdb=" CD2 HIS E 330 " ideal model delta sigma weight residual 1.354 1.297 0.057 1.10e-02 8.26e+03 2.68e+01 ... (remaining 5870 not shown) Histogram of bond angle deviations from ideal: 100.94 - 107.71: 446 107.71 - 114.47: 3129 114.47 - 121.23: 2599 121.23 - 128.00: 1656 128.00 - 134.76: 40 Bond angle restraints: 7870 Sorted by residual: angle pdb=" CA HIS H 330 " pdb=" CB HIS H 330 " pdb=" CG HIS H 330 " ideal model delta sigma weight residual 113.80 120.13 -6.33 1.00e+00 1.00e+00 4.00e+01 angle pdb=" CA HIS B 330 " pdb=" CB HIS B 330 " pdb=" CG HIS B 330 " ideal model delta sigma weight residual 113.80 120.12 -6.32 1.00e+00 1.00e+00 4.00e+01 angle pdb=" CA HIS F 330 " pdb=" CB HIS F 330 " pdb=" CG HIS F 330 " ideal model delta sigma weight residual 113.80 120.12 -6.32 1.00e+00 1.00e+00 3.99e+01 angle pdb=" CA HIS J 330 " pdb=" CB HIS J 330 " pdb=" CG HIS J 330 " ideal model delta sigma weight residual 113.80 120.11 -6.31 1.00e+00 1.00e+00 3.99e+01 angle pdb=" CA HIS D 330 " pdb=" CB HIS D 330 " pdb=" CG HIS D 330 " ideal model delta sigma weight residual 113.80 120.09 -6.29 1.00e+00 1.00e+00 3.96e+01 ... (remaining 7865 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.60: 2835 10.60 - 21.20: 540 21.20 - 31.80: 155 31.80 - 42.40: 25 42.40 - 53.00: 35 Dihedral angle restraints: 3590 sinusoidal: 1500 harmonic: 2090 Sorted by residual: dihedral pdb=" CA PRO D 332 " pdb=" C PRO D 332 " pdb=" N GLY D 333 " pdb=" CA GLY D 333 " ideal model delta harmonic sigma weight residual -180.00 -140.16 -39.84 0 5.00e+00 4.00e-02 6.35e+01 dihedral pdb=" CA PRO J 332 " pdb=" C PRO J 332 " pdb=" N GLY J 333 " pdb=" CA GLY J 333 " ideal model delta harmonic sigma weight residual -180.00 -140.17 -39.83 0 5.00e+00 4.00e-02 6.34e+01 dihedral pdb=" CA PRO B 332 " pdb=" C PRO B 332 " pdb=" N GLY B 333 " pdb=" CA GLY B 333 " ideal model delta harmonic sigma weight residual -180.00 -140.18 -39.82 0 5.00e+00 4.00e-02 6.34e+01 ... (remaining 3587 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.054: 342 0.054 - 0.107: 343 0.107 - 0.159: 139 0.159 - 0.212: 41 0.212 - 0.264: 20 Chirality restraints: 885 Sorted by residual: chirality pdb=" CB ILE C 328 " pdb=" CA ILE C 328 " pdb=" CG1 ILE C 328 " pdb=" CG2 ILE C 328 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CB ILE A 328 " pdb=" CA ILE A 328 " pdb=" CG1 ILE A 328 " pdb=" CG2 ILE A 328 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CB ILE E 328 " pdb=" CA ILE E 328 " pdb=" CG1 ILE E 328 " pdb=" CG2 ILE E 328 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 882 not shown) Planarity restraints: 1000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS C 362 " -0.027 2.00e-02 2.50e+03 2.16e-02 7.00e+00 pdb=" CG HIS C 362 " 0.041 2.00e-02 2.50e+03 pdb=" ND1 HIS C 362 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 HIS C 362 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 HIS C 362 " -0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS C 362 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 362 " -0.026 2.00e-02 2.50e+03 2.15e-02 6.93e+00 pdb=" CG HIS A 362 " 0.041 2.00e-02 2.50e+03 pdb=" ND1 HIS A 362 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 HIS A 362 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 HIS A 362 " -0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS A 362 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS G 362 " -0.026 2.00e-02 2.50e+03 2.15e-02 6.93e+00 pdb=" CG HIS G 362 " 0.041 2.00e-02 2.50e+03 pdb=" ND1 HIS G 362 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 HIS G 362 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 HIS G 362 " -0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS G 362 " -0.019 2.00e-02 2.50e+03 ... (remaining 997 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.92: 2165 2.92 - 3.42: 5189 3.42 - 3.91: 9284 3.91 - 4.41: 9861 4.41 - 4.90: 20275 Nonbonded interactions: 46774 Sorted by model distance: nonbonded pdb=" OD1 ASP I 314 " pdb=" OG SER I 316 " model vdw 2.427 2.440 nonbonded pdb=" OD1 ASP G 314 " pdb=" OG SER G 316 " model vdw 2.427 2.440 nonbonded pdb=" OD1 ASP C 314 " pdb=" OG SER C 316 " model vdw 2.427 2.440 nonbonded pdb=" OD1 ASP A 314 " pdb=" OG SER A 316 " model vdw 2.427 2.440 nonbonded pdb=" OD1 ASP E 314 " pdb=" OG SER E 316 " model vdw 2.428 2.440 ... (remaining 46769 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 305 through 328 or resid 330 through 379)) selection = (chain 'B' and (resid 305 through 328 or resid 330 through 379)) selection = (chain 'C' and (resid 305 through 328 or resid 330 through 379)) selection = (chain 'D' and (resid 305 through 328 or resid 330 through 379)) selection = (chain 'E' and (resid 305 through 328 or resid 330 through 379)) selection = (chain 'F' and (resid 305 through 328 or resid 330 through 379)) selection = (chain 'G' and (resid 305 through 328 or resid 330 through 379)) selection = (chain 'H' and (resid 305 through 328 or resid 330 through 379)) selection = (chain 'I' and (resid 305 through 328 or resid 330 through 379)) selection = (chain 'J' and (resid 305 through 328 or resid 330 through 379)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 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: 4.100 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: 0.000 Extract box with map and model: 12.780 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 24.000 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.020 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:12.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 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 : 0.010 0.069 5875 Z= 0.643 Angle : 1.675 8.271 7870 Z= 1.070 Chirality : 0.091 0.264 885 Planarity : 0.011 0.046 1000 Dihedral : 13.222 53.002 2260 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 5.26 % Allowed : 6.02 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.39 % 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: -4.12 (0.17), residues: 735 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.13 (0.13), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.015 0.007 HIS C 374 PHE 0.026 0.006 PHE G 346 TYR 0.021 0.007 TYR H 310 ARG 0.009 0.002 ARG J 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 123 time to evaluate : 0.774 Fit side-chains revert: symmetry clash REVERT: B 317 LYS cc_start: 0.7966 (pttt) cc_final: 0.7500 (ptpt) REVERT: B 338 GLU cc_start: 0.8554 (tt0) cc_final: 0.8222 (tm-30) REVERT: B 340 LYS cc_start: 0.8127 (mttt) cc_final: 0.7402 (tppp) REVERT: D 338 GLU cc_start: 0.8491 (tt0) cc_final: 0.8059 (tm-30) REVERT: D 340 LYS cc_start: 0.8215 (mttt) cc_final: 0.7386 (tppp) REVERT: F 317 LYS cc_start: 0.8005 (pttt) cc_final: 0.7742 (ptmm) REVERT: F 338 GLU cc_start: 0.8522 (tt0) cc_final: 0.8209 (tm-30) REVERT: F 340 LYS cc_start: 0.8083 (mttt) cc_final: 0.7378 (tppp) REVERT: G 340 LYS cc_start: 0.8769 (mttt) cc_final: 0.8470 (mmtp) REVERT: G 378 PHE cc_start: 0.7443 (t80) cc_final: 0.7233 (t80) REVERT: H 329 HIS cc_start: 0.7875 (OUTLIER) cc_final: 0.7649 (t-90) REVERT: H 338 GLU cc_start: 0.8643 (tt0) cc_final: 0.8401 (tm-30) REVERT: H 349 ARG cc_start: 0.7450 (OUTLIER) cc_final: 0.5542 (mmm160) REVERT: I 349 ARG cc_start: 0.8401 (mtt180) cc_final: 0.7063 (mmp-170) REVERT: J 317 LYS cc_start: 0.8516 (pttt) cc_final: 0.8248 (ptmt) REVERT: J 338 GLU cc_start: 0.8659 (tt0) cc_final: 0.8449 (tm-30) REVERT: J 340 LYS cc_start: 0.8468 (mttt) cc_final: 0.7789 (tppp) REVERT: J 349 ARG cc_start: 0.7719 (OUTLIER) cc_final: 0.7491 (ptp-170) REVERT: J 375 LYS cc_start: 0.8597 (tttt) cc_final: 0.8293 (tttm) outliers start: 35 outliers final: 8 residues processed: 157 average time/residue: 1.4128 time to fit residues: 229.9215 Evaluate side-chains 110 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 99 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain D residue 331 LYS Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain H residue 329 HIS Chi-restraints excluded: chain H residue 349 ARG Chi-restraints excluded: chain H residue 350 VAL Chi-restraints excluded: chain J residue 325 LEU Chi-restraints excluded: chain J residue 349 ARG Chi-restraints excluded: chain J residue 350 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 29 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 54 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 63 optimal weight: 0.0570 overall best weight: 3.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 368 ASN ** I 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** J 368 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 5875 Z= 0.317 Angle : 0.732 6.742 7870 Z= 0.367 Chirality : 0.051 0.129 885 Planarity : 0.004 0.025 1000 Dihedral : 8.047 58.982 803 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 3.46 % Allowed : 16.39 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.23), residues: 735 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.92 (0.18), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS I 330 PHE 0.015 0.002 PHE A 378 TYR 0.019 0.004 TYR F 310 ARG 0.001 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 80 time to evaluate : 0.681 Fit side-chains REVERT: C 340 LYS cc_start: 0.8508 (mttt) cc_final: 0.8295 (mttp) REVERT: E 378 PHE cc_start: 0.7443 (t80) cc_final: 0.7034 (t80) REVERT: G 340 LYS cc_start: 0.8878 (mttt) cc_final: 0.8548 (mtpp) REVERT: G 342 GLU cc_start: 0.9093 (mt-10) cc_final: 0.8705 (mp0) REVERT: G 378 PHE cc_start: 0.7257 (t80) cc_final: 0.6828 (t80) REVERT: H 317 LYS cc_start: 0.8313 (pttt) cc_final: 0.8051 (ptmt) REVERT: H 340 LYS cc_start: 0.7903 (mttt) cc_final: 0.7118 (tptm) REVERT: I 318 VAL cc_start: 0.8796 (t) cc_final: 0.8584 (m) REVERT: I 349 ARG cc_start: 0.8458 (mtt180) cc_final: 0.6918 (mmm160) outliers start: 23 outliers final: 5 residues processed: 100 average time/residue: 1.1383 time to fit residues: 119.2944 Evaluate side-chains 69 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 64 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain H residue 350 VAL Chi-restraints excluded: chain J residue 350 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 17 optimal weight: 9.9990 chunk 63 optimal weight: 7.9990 chunk 68 optimal weight: 9.9990 chunk 56 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 chunk 62 optimal weight: 0.0570 overall best weight: 1.7704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5875 Z= 0.199 Angle : 0.642 7.340 7870 Z= 0.313 Chirality : 0.049 0.125 885 Planarity : 0.002 0.019 1000 Dihedral : 5.632 34.053 785 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 4.36 % Allowed : 16.99 % Favored : 78.65 % 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: -1.88 (0.25), residues: 735 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.43 (0.19), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS I 330 PHE 0.016 0.001 PHE C 378 TYR 0.014 0.003 TYR F 310 ARG 0.001 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 66 time to evaluate : 0.690 Fit side-chains REVERT: B 324 SER cc_start: 0.8234 (OUTLIER) cc_final: 0.7844 (m) REVERT: E 378 PHE cc_start: 0.7411 (t80) cc_final: 0.6996 (t80) REVERT: G 318 VAL cc_start: 0.8537 (OUTLIER) cc_final: 0.8073 (m) REVERT: G 340 LYS cc_start: 0.8841 (mttt) cc_final: 0.8528 (mtpp) REVERT: G 342 GLU cc_start: 0.9102 (mt-10) cc_final: 0.8694 (mp0) REVERT: I 349 ARG cc_start: 0.8449 (mtt180) cc_final: 0.6878 (mmm160) outliers start: 29 outliers final: 10 residues processed: 87 average time/residue: 1.2017 time to fit residues: 110.2126 Evaluate side-chains 73 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 61 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain H residue 348 ASP Chi-restraints excluded: chain H residue 350 VAL Chi-restraints excluded: chain J residue 320 SER Chi-restraints excluded: chain J residue 350 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 7 optimal weight: 10.0000 chunk 30 optimal weight: 8.9990 chunk 42 optimal weight: 0.0980 chunk 63 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 56 optimal weight: 0.0170 chunk 38 optimal weight: 4.9990 overall best weight: 1.6224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5875 Z= 0.180 Angle : 0.622 7.717 7870 Z= 0.299 Chirality : 0.048 0.124 885 Planarity : 0.002 0.017 1000 Dihedral : 5.258 29.616 785 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 3.31 % Allowed : 19.40 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.26), residues: 735 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.24 (0.20), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 330 PHE 0.014 0.001 PHE A 378 TYR 0.016 0.003 TYR F 310 ARG 0.001 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 75 time to evaluate : 0.689 Fit side-chains REVERT: B 348 ASP cc_start: 0.8916 (OUTLIER) cc_final: 0.8581 (t0) REVERT: D 379 ARG cc_start: 0.6706 (mmt90) cc_final: 0.6496 (mmt90) REVERT: E 340 LYS cc_start: 0.8382 (mttt) cc_final: 0.8021 (mtpp) REVERT: G 318 VAL cc_start: 0.8568 (OUTLIER) cc_final: 0.8124 (m) REVERT: G 340 LYS cc_start: 0.8869 (mttt) cc_final: 0.8645 (mtpm) REVERT: G 342 GLU cc_start: 0.9086 (mt-10) cc_final: 0.8743 (mp0) REVERT: H 317 LYS cc_start: 0.8336 (pttt) cc_final: 0.8135 (ptmt) REVERT: H 338 GLU cc_start: 0.8326 (tt0) cc_final: 0.8112 (tm-30) REVERT: I 349 ARG cc_start: 0.8445 (mtt180) cc_final: 0.6841 (mmm160) outliers start: 22 outliers final: 11 residues processed: 90 average time/residue: 1.2397 time to fit residues: 116.7416 Evaluate side-chains 78 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 65 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain G residue 311 LYS Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain H residue 348 ASP Chi-restraints excluded: chain H residue 350 VAL Chi-restraints excluded: chain J residue 350 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 57 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 60 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 13 optimal weight: 0.7980 chunk 39 optimal weight: 9.9990 overall best weight: 5.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 5875 Z= 0.458 Angle : 0.772 7.782 7870 Z= 0.392 Chirality : 0.052 0.129 885 Planarity : 0.004 0.019 1000 Dihedral : 6.517 46.880 785 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 4.06 % Allowed : 18.80 % Favored : 77.14 % 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: -1.78 (0.25), residues: 735 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.35 (0.19), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS D 362 PHE 0.020 0.002 PHE A 378 TYR 0.028 0.007 TYR B 310 ARG 0.003 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 73 time to evaluate : 0.744 Fit side-chains REVERT: B 348 ASP cc_start: 0.8989 (OUTLIER) cc_final: 0.8548 (t0) REVERT: C 342 GLU cc_start: 0.8787 (mt-10) cc_final: 0.8357 (mp0) REVERT: D 348 ASP cc_start: 0.8880 (OUTLIER) cc_final: 0.8275 (t0) REVERT: E 340 LYS cc_start: 0.8401 (mttt) cc_final: 0.8060 (mtpp) REVERT: E 342 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8264 (mp0) REVERT: E 378 PHE cc_start: 0.7715 (t80) cc_final: 0.7214 (t80) REVERT: F 343 LYS cc_start: 0.7825 (OUTLIER) cc_final: 0.7608 (ttpp) REVERT: G 340 LYS cc_start: 0.8846 (mttt) cc_final: 0.8633 (mtpm) REVERT: G 342 GLU cc_start: 0.9050 (mt-10) cc_final: 0.8688 (mp0) REVERT: G 378 PHE cc_start: 0.7528 (t80) cc_final: 0.6976 (m-80) REVERT: I 318 VAL cc_start: 0.8770 (t) cc_final: 0.8516 (m) REVERT: I 342 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8231 (mp0) REVERT: I 349 ARG cc_start: 0.8430 (mtt180) cc_final: 0.6906 (mmm160) outliers start: 27 outliers final: 12 residues processed: 93 average time/residue: 1.1684 time to fit residues: 114.2255 Evaluate side-chains 87 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 72 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain F residue 343 LYS Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain H residue 348 ASP Chi-restraints excluded: chain H residue 350 VAL Chi-restraints excluded: chain I residue 311 LYS Chi-restraints excluded: chain J residue 350 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 4.9990 chunk 67 optimal weight: 7.9990 chunk 56 optimal weight: 7.9990 chunk 31 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 5875 Z= 0.349 Angle : 0.725 8.184 7870 Z= 0.361 Chirality : 0.050 0.127 885 Planarity : 0.003 0.017 1000 Dihedral : 6.158 43.354 785 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 3.91 % Allowed : 20.00 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.26), residues: 735 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.32 (0.19), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 362 PHE 0.017 0.002 PHE C 378 TYR 0.023 0.005 TYR F 310 ARG 0.002 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 75 time to evaluate : 0.713 Fit side-chains REVERT: B 348 ASP cc_start: 0.8964 (OUTLIER) cc_final: 0.8519 (t0) REVERT: C 342 GLU cc_start: 0.8782 (mt-10) cc_final: 0.8367 (mp0) REVERT: D 348 ASP cc_start: 0.8878 (OUTLIER) cc_final: 0.8234 (t0) REVERT: E 340 LYS cc_start: 0.8385 (mttt) cc_final: 0.8044 (mtpp) REVERT: E 342 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8270 (mp0) REVERT: E 378 PHE cc_start: 0.7573 (t80) cc_final: 0.7108 (t80) REVERT: F 343 LYS cc_start: 0.7840 (OUTLIER) cc_final: 0.7623 (ttpp) REVERT: G 340 LYS cc_start: 0.8831 (mttt) cc_final: 0.8612 (mtpm) REVERT: G 342 GLU cc_start: 0.9037 (mt-10) cc_final: 0.8662 (mp0) REVERT: G 378 PHE cc_start: 0.7404 (t80) cc_final: 0.6794 (m-80) REVERT: H 338 GLU cc_start: 0.8345 (tt0) cc_final: 0.8126 (tm-30) REVERT: I 318 VAL cc_start: 0.8748 (t) cc_final: 0.8502 (m) REVERT: I 342 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8278 (mp0) REVERT: I 349 ARG cc_start: 0.8438 (mtt180) cc_final: 0.6856 (mmm160) REVERT: J 348 ASP cc_start: 0.8714 (OUTLIER) cc_final: 0.8251 (t0) outliers start: 26 outliers final: 11 residues processed: 95 average time/residue: 1.1458 time to fit residues: 114.1768 Evaluate side-chains 87 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 72 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain F residue 343 LYS Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain H residue 348 ASP Chi-restraints excluded: chain H residue 350 VAL Chi-restraints excluded: chain I residue 311 LYS Chi-restraints excluded: chain J residue 348 ASP Chi-restraints excluded: chain J residue 350 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 5.9990 chunk 57 optimal weight: 7.9990 chunk 37 optimal weight: 0.9990 chunk 67 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 20 optimal weight: 8.9990 chunk 13 optimal weight: 0.5980 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 5875 Z= 0.248 Angle : 0.673 8.549 7870 Z= 0.328 Chirality : 0.049 0.127 885 Planarity : 0.003 0.016 1000 Dihedral : 5.698 38.467 785 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 3.31 % Allowed : 20.90 % Favored : 75.79 % 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: -1.61 (0.26), residues: 735 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.22 (0.20), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 362 PHE 0.018 0.001 PHE C 378 TYR 0.019 0.004 TYR F 310 ARG 0.002 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 74 time to evaluate : 0.626 Fit side-chains REVERT: B 348 ASP cc_start: 0.8968 (OUTLIER) cc_final: 0.8539 (t0) REVERT: C 342 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8395 (mp0) REVERT: D 348 ASP cc_start: 0.8864 (OUTLIER) cc_final: 0.8223 (t0) REVERT: E 340 LYS cc_start: 0.8358 (mttt) cc_final: 0.8027 (mtpp) REVERT: E 342 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8267 (mp0) REVERT: E 378 PHE cc_start: 0.7509 (t80) cc_final: 0.7012 (t80) REVERT: F 338 GLU cc_start: 0.8405 (tt0) cc_final: 0.8180 (tm-30) REVERT: G 340 LYS cc_start: 0.8860 (mttt) cc_final: 0.8616 (mtpm) REVERT: G 342 GLU cc_start: 0.9028 (mt-10) cc_final: 0.8653 (mp0) REVERT: G 378 PHE cc_start: 0.7348 (t80) cc_final: 0.6703 (m-80) REVERT: H 338 GLU cc_start: 0.8329 (tt0) cc_final: 0.8078 (tm-30) REVERT: I 318 VAL cc_start: 0.8732 (t) cc_final: 0.8477 (m) REVERT: I 342 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8252 (mp0) REVERT: I 349 ARG cc_start: 0.8440 (mtt180) cc_final: 0.6848 (mmm160) REVERT: J 348 ASP cc_start: 0.8679 (OUTLIER) cc_final: 0.8221 (t0) outliers start: 22 outliers final: 12 residues processed: 87 average time/residue: 1.2228 time to fit residues: 111.3487 Evaluate side-chains 87 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 72 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain G residue 311 LYS Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain H residue 348 ASP Chi-restraints excluded: chain H residue 350 VAL Chi-restraints excluded: chain I residue 311 LYS Chi-restraints excluded: chain J residue 348 ASP Chi-restraints excluded: chain J residue 350 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 0.0980 chunk 42 optimal weight: 0.0870 chunk 45 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 61 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 overall best weight: 1.1960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 5875 Z= 0.152 Angle : 0.619 9.007 7870 Z= 0.293 Chirality : 0.048 0.123 885 Planarity : 0.002 0.017 1000 Dihedral : 4.958 26.034 785 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 3.16 % Allowed : 20.90 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.26), residues: 735 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.12 (0.20), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 330 PHE 0.015 0.001 PHE C 378 TYR 0.013 0.002 TYR H 310 ARG 0.001 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 73 time to evaluate : 0.622 Fit side-chains REVERT: B 348 ASP cc_start: 0.8927 (OUTLIER) cc_final: 0.8519 (t0) REVERT: C 342 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8385 (mp0) REVERT: D 348 ASP cc_start: 0.8860 (OUTLIER) cc_final: 0.8340 (t0) REVERT: E 342 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8211 (mp0) REVERT: F 338 GLU cc_start: 0.8391 (tt0) cc_final: 0.8187 (tm-30) REVERT: G 342 GLU cc_start: 0.9034 (mt-10) cc_final: 0.8644 (mp0) REVERT: G 378 PHE cc_start: 0.7297 (t80) cc_final: 0.6717 (m-80) REVERT: H 338 GLU cc_start: 0.8352 (tt0) cc_final: 0.8127 (tm-30) REVERT: I 342 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8251 (mp0) REVERT: I 349 ARG cc_start: 0.8439 (mtt180) cc_final: 0.6805 (mmm160) REVERT: J 348 ASP cc_start: 0.8638 (OUTLIER) cc_final: 0.7096 (p0) outliers start: 21 outliers final: 9 residues processed: 84 average time/residue: 1.0822 time to fit residues: 95.5795 Evaluate side-chains 78 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 66 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain H residue 350 VAL Chi-restraints excluded: chain I residue 311 LYS Chi-restraints excluded: chain J residue 348 ASP Chi-restraints excluded: chain J residue 350 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 56 optimal weight: 0.7980 chunk 59 optimal weight: 8.9990 chunk 62 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 66 optimal weight: 0.0010 chunk 40 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 46 optimal weight: 7.9990 overall best weight: 5.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 5875 Z= 0.495 Angle : 0.803 8.731 7870 Z= 0.410 Chirality : 0.053 0.130 885 Planarity : 0.004 0.019 1000 Dihedral : 6.507 47.146 785 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.16 % Allowed : 21.20 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.26), residues: 735 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.33 (0.20), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS D 362 PHE 0.017 0.002 PHE I 378 TYR 0.031 0.007 TYR F 310 ARG 0.002 0.000 ARG G 379 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 70 time to evaluate : 0.685 Fit side-chains REVERT: B 348 ASP cc_start: 0.8986 (OUTLIER) cc_final: 0.8540 (t0) REVERT: C 342 GLU cc_start: 0.8791 (mt-10) cc_final: 0.8382 (mp0) REVERT: D 348 ASP cc_start: 0.8899 (OUTLIER) cc_final: 0.8247 (t0) REVERT: E 340 LYS cc_start: 0.8383 (mttt) cc_final: 0.8037 (mtpp) REVERT: E 342 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8289 (mp0) REVERT: E 378 PHE cc_start: 0.7688 (t80) cc_final: 0.7191 (t80) REVERT: F 343 LYS cc_start: 0.7781 (OUTLIER) cc_final: 0.7567 (ttpp) REVERT: G 340 LYS cc_start: 0.8836 (mttt) cc_final: 0.8620 (mtpm) REVERT: G 342 GLU cc_start: 0.9034 (mt-10) cc_final: 0.8660 (mp0) REVERT: G 378 PHE cc_start: 0.7529 (t80) cc_final: 0.6821 (m-80) REVERT: H 338 GLU cc_start: 0.8371 (tt0) cc_final: 0.8096 (tm-30) REVERT: I 342 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8348 (mp0) REVERT: I 349 ARG cc_start: 0.8436 (mtt180) cc_final: 0.6910 (mmm160) REVERT: J 348 ASP cc_start: 0.8719 (OUTLIER) cc_final: 0.8250 (t0) outliers start: 21 outliers final: 10 residues processed: 85 average time/residue: 1.1244 time to fit residues: 100.4445 Evaluate side-chains 83 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 69 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain F residue 343 LYS Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain H residue 350 VAL Chi-restraints excluded: chain I residue 311 LYS Chi-restraints excluded: chain J residue 348 ASP Chi-restraints excluded: chain J residue 350 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 7.9990 chunk 64 optimal weight: 8.9990 chunk 55 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 34 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5875 Z= 0.227 Angle : 0.687 9.160 7870 Z= 0.333 Chirality : 0.049 0.125 885 Planarity : 0.002 0.018 1000 Dihedral : 5.775 38.875 785 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 2.26 % Allowed : 21.95 % Favored : 75.79 % 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: -1.59 (0.26), residues: 735 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.20 (0.20), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 330 PHE 0.017 0.001 PHE C 378 TYR 0.018 0.003 TYR F 310 ARG 0.002 0.000 ARG J 379 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 68 time to evaluate : 0.683 Fit side-chains REVERT: A 378 PHE cc_start: 0.7937 (t80) cc_final: 0.7308 (m-80) REVERT: B 348 ASP cc_start: 0.8953 (OUTLIER) cc_final: 0.8521 (t0) REVERT: C 342 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8397 (mp0) REVERT: D 348 ASP cc_start: 0.8848 (OUTLIER) cc_final: 0.8226 (t0) REVERT: E 342 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8204 (mp0) REVERT: E 378 PHE cc_start: 0.7471 (t80) cc_final: 0.6957 (t80) REVERT: G 342 GLU cc_start: 0.9026 (mt-10) cc_final: 0.8607 (mp0) REVERT: G 378 PHE cc_start: 0.7391 (t80) cc_final: 0.6687 (m-80) REVERT: H 338 GLU cc_start: 0.8313 (tt0) cc_final: 0.8062 (tm-30) REVERT: I 318 VAL cc_start: 0.8759 (t) cc_final: 0.8537 (m) REVERT: I 342 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8293 (mp0) REVERT: I 349 ARG cc_start: 0.8435 (mtt180) cc_final: 0.6850 (mmm160) REVERT: J 348 ASP cc_start: 0.8708 (OUTLIER) cc_final: 0.8234 (t0) outliers start: 15 outliers final: 10 residues processed: 77 average time/residue: 1.0395 time to fit residues: 84.6293 Evaluate side-chains 81 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 68 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain H residue 350 VAL Chi-restraints excluded: chain I residue 311 LYS Chi-restraints excluded: chain J residue 348 ASP Chi-restraints excluded: chain J residue 350 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 48 optimal weight: 0.5980 chunk 3 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 63 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.129478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.097966 restraints weight = 17973.051| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 4.19 r_work: 0.3821 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3785 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3785 r_free = 0.3785 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3784 r_free = 0.3784 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3784 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 5875 Z= 0.423 Angle : 0.777 8.836 7870 Z= 0.392 Chirality : 0.052 0.130 885 Planarity : 0.003 0.020 1000 Dihedral : 6.243 43.425 785 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.41 % Allowed : 22.11 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.26), residues: 735 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.30 (0.20), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS D 362 PHE 0.022 0.002 PHE C 378 TYR 0.029 0.006 TYR F 310 ARG 0.002 0.000 ARG J 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2859.88 seconds wall clock time: 51 minutes 19.59 seconds (3079.59 seconds total)