Starting phenix.real_space_refine on Wed Sep 25 22:01:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkg_23890/09_2024/7mkg_23890.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkg_23890/09_2024/7mkg_23890.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkg_23890/09_2024/7mkg_23890.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkg_23890/09_2024/7mkg_23890.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkg_23890/09_2024/7mkg_23890.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkg_23890/09_2024/7mkg_23890.cif" } resolution = 3.07 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= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 10 5.16 5 C 3510 2.51 5 N 1010 2.21 5 O 1040 1.98 5 H 5800 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 11370 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "B" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "E" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "F" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "C" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "D" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "G" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "H" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "I" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "J" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Time building chain proxies: 5.73, per 1000 atoms: 0.50 Number of scatterers: 11370 At special positions: 0 Unit cell: (115.346, 114.268, 48.51, 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 10 16.00 O 1040 8.00 N 1010 7.00 C 3510 6.00 H 5800 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 - 3.00 Amino acid : True - 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: 2.82 Conformation dependent library (CDL) restraints added in 807.1 milliseconds 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1280 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 17 sheets defined 0.0% alpha, 52.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 307 through 310 removed outlier: 6.550A pdb=" N GLN A 307 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N TYR E 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL A 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLN E 307 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N TYR C 310 " --> pdb=" O GLN E 307 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL E 309 " --> pdb=" O TYR C 310 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLN C 307 " --> pdb=" O ILE G 308 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N TYR G 310 " --> pdb=" O GLN C 307 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL C 309 " --> pdb=" O TYR G 310 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLN G 307 " --> pdb=" O ILE I 308 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N TYR I 310 " --> pdb=" O GLN G 307 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL G 309 " --> pdb=" O TYR I 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314 removed outlier: 6.617A pdb=" N VAL A 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL E 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL C 313 " --> pdb=" O ASP G 314 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL G 313 " --> pdb=" O ASP I 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 317 through 324 removed outlier: 6.683A pdb=" N SER E 324 " --> pdb=" O GLY A 323 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N SER C 324 " --> pdb=" O GLY E 323 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N SER G 324 " --> pdb=" O GLY C 323 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N SER I 324 " --> pdb=" O GLY G 323 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 328 through 330 Processing sheet with id=AA5, first strand: chain 'A' and resid 335 through 340 Processing sheet with id=AA6, first strand: chain 'A' and resid 343 through 347 Processing sheet with id=AA7, first strand: chain 'A' and resid 351 through 362 removed outlier: 8.843A pdb=" N SER A 352 " --> pdb=" O LYS E 353 " (cutoff:3.500A) removed outlier: 10.239A pdb=" N GLY E 355 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ILE A 354 " --> pdb=" O GLY E 355 " (cutoff:3.500A) removed outlier: 9.401A pdb=" N LEU E 357 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N SER A 356 " --> pdb=" O LEU E 357 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N ASN E 359 " --> pdb=" O SER A 356 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ASP A 358 " --> pdb=" O ASN E 359 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N THR E 361 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ILE A 360 " --> pdb=" O THR E 361 " (cutoff:3.500A) removed outlier: 8.843A pdb=" N SER E 352 " --> pdb=" O LYS C 353 " (cutoff:3.500A) removed outlier: 10.239A pdb=" N GLY C 355 " --> pdb=" O SER E 352 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ILE E 354 " --> pdb=" O GLY C 355 " (cutoff:3.500A) removed outlier: 9.401A pdb=" N LEU C 357 " --> pdb=" O ILE E 354 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N SER E 356 " --> pdb=" O LEU C 357 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ASN C 359 " --> pdb=" O SER E 356 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ASP E 358 " --> pdb=" O ASN C 359 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N THR C 361 " --> pdb=" O ASP E 358 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE E 360 " --> pdb=" O THR C 361 " (cutoff:3.500A) removed outlier: 8.843A pdb=" N SER C 352 " --> pdb=" O LYS G 353 " (cutoff:3.500A) removed outlier: 10.240A pdb=" N GLY G 355 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ILE C 354 " --> pdb=" O GLY G 355 " (cutoff:3.500A) removed outlier: 9.401A pdb=" N LEU G 357 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N SER C 356 " --> pdb=" O LEU G 357 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ASN G 359 " --> pdb=" O SER C 356 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ASP C 358 " --> pdb=" O ASN G 359 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N THR G 361 " --> pdb=" O ASP C 358 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ILE C 360 " --> pdb=" O THR G 361 " (cutoff:3.500A) removed outlier: 8.843A pdb=" N SER G 352 " --> pdb=" O LYS I 353 " (cutoff:3.500A) removed outlier: 10.239A pdb=" N GLY I 355 " --> pdb=" O SER G 352 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ILE G 354 " --> pdb=" O GLY I 355 " (cutoff:3.500A) removed outlier: 9.399A pdb=" N LEU I 357 " --> pdb=" O ILE G 354 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N SER G 356 " --> pdb=" O LEU I 357 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ASN I 359 " --> pdb=" O SER G 356 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ASP G 358 " --> pdb=" O ASN I 359 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N THR I 361 " --> pdb=" O ASP G 358 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ILE G 360 " --> pdb=" O THR I 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 369 through 377 removed outlier: 6.562A pdb=" N LYS A 369 " --> pdb=" O LYS E 370 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N GLU E 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE A 371 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N HIS E 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N THR A 373 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N LEU E 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LYS A 375 " --> pdb=" O LEU E 376 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LYS E 369 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N GLU C 372 " --> pdb=" O LYS E 369 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE E 371 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N HIS C 374 " --> pdb=" O ILE E 371 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N THR E 373 " --> pdb=" O HIS C 374 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N LEU C 376 " --> pdb=" O THR E 373 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LYS E 375 " --> pdb=" O LEU C 376 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LYS C 369 " --> pdb=" O LYS G 370 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N GLU G 372 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE C 371 " --> pdb=" O GLU G 372 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N HIS G 374 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N THR C 373 " --> pdb=" O HIS G 374 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N LEU G 376 " --> pdb=" O THR C 373 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LYS C 375 " --> pdb=" O LEU G 376 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LYS G 369 " --> pdb=" O LYS I 370 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N GLU I 372 " --> pdb=" O LYS G 369 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE G 371 " --> pdb=" O GLU I 372 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N HIS I 374 " --> pdb=" O ILE G 371 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N THR G 373 " --> pdb=" O HIS I 374 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N LEU I 376 " --> pdb=" O THR G 373 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LYS G 375 " --> pdb=" O LEU I 376 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 307 through 310 removed outlier: 6.531A pdb=" N GLN B 307 " --> pdb=" O ILE F 308 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N TYR F 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL B 309 " --> pdb=" O TYR F 310 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N GLN F 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N TYR D 310 " --> pdb=" O GLN F 307 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL F 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N GLN D 307 " --> pdb=" O ILE H 308 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N TYR H 310 " --> pdb=" O GLN D 307 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL D 309 " --> pdb=" O TYR H 310 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N GLN H 307 " --> pdb=" O ILE J 308 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N TYR J 310 " --> pdb=" O GLN H 307 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL H 309 " --> pdb=" O TYR J 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.623A pdb=" N VAL B 313 " --> pdb=" O ASP F 314 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL F 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL D 313 " --> pdb=" O ASP H 314 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL H 313 " --> pdb=" O ASP J 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 317 through 322 removed outlier: 6.567A pdb=" N LYS B 317 " --> pdb=" O VAL F 318 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N SER F 320 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N THR B 319 " --> pdb=" O SER F 320 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N CYS F 322 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LYS B 321 " --> pdb=" O CYS F 322 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LYS F 317 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N SER D 320 " --> pdb=" O LYS F 317 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N THR F 319 " --> pdb=" O SER D 320 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N CYS D 322 " --> pdb=" O THR F 319 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LYS F 321 " --> pdb=" O CYS D 322 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LYS D 317 " --> pdb=" O VAL H 318 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N SER H 320 " --> pdb=" O LYS D 317 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N THR D 319 " --> pdb=" O SER H 320 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N CYS H 322 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LYS D 321 " --> pdb=" O CYS H 322 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LYS H 317 " --> pdb=" O VAL J 318 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N SER J 320 " --> pdb=" O LYS H 317 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N THR H 319 " --> pdb=" O SER J 320 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N CYS J 322 " --> pdb=" O THR H 319 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LYS H 321 " --> pdb=" O CYS J 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 327 through 330 Processing sheet with id=AB4, first strand: chain 'B' and resid 335 through 340 Processing sheet with id=AB5, first strand: chain 'B' and resid 343 through 347 Processing sheet with id=AB6, first strand: chain 'B' and resid 350 through 362 removed outlier: 9.080A pdb=" N VAL B 350 " --> pdb=" O GLN F 351 " (cutoff:3.500A) removed outlier: 10.596A pdb=" N LYS F 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 9.209A pdb=" N SER B 352 " --> pdb=" O LYS F 353 " (cutoff:3.500A) removed outlier: 10.127A pdb=" N GLY F 355 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ILE B 354 " --> pdb=" O GLY F 355 " (cutoff:3.500A) removed outlier: 9.169A pdb=" N LEU F 357 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N SER B 356 " --> pdb=" O LEU F 357 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N ASN F 359 " --> pdb=" O SER B 356 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ASP B 358 " --> pdb=" O ASN F 359 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N THR F 361 " --> pdb=" O ASP B 358 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE B 360 " --> pdb=" O THR F 361 " (cutoff:3.500A) removed outlier: 9.080A pdb=" N VAL F 350 " --> pdb=" O GLN D 351 " (cutoff:3.500A) removed outlier: 10.596A pdb=" N LYS D 353 " --> pdb=" O VAL F 350 " (cutoff:3.500A) removed outlier: 9.209A pdb=" N SER F 352 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 10.126A pdb=" N GLY D 355 " --> pdb=" O SER F 352 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N ILE F 354 " --> pdb=" O GLY D 355 " (cutoff:3.500A) removed outlier: 9.168A pdb=" N LEU D 357 " --> pdb=" O ILE F 354 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N SER F 356 " --> pdb=" O LEU D 357 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ASN D 359 " --> pdb=" O SER F 356 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ASP F 358 " --> pdb=" O ASN D 359 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N THR D 361 " --> pdb=" O ASP F 358 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE F 360 " --> pdb=" O THR D 361 " (cutoff:3.500A) removed outlier: 9.080A pdb=" N VAL D 350 " --> pdb=" O GLN H 351 " (cutoff:3.500A) removed outlier: 10.596A pdb=" N LYS H 353 " --> pdb=" O VAL D 350 " (cutoff:3.500A) removed outlier: 9.209A pdb=" N SER D 352 " --> pdb=" O LYS H 353 " (cutoff:3.500A) removed outlier: 10.126A pdb=" N GLY H 355 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ILE D 354 " --> pdb=" O GLY H 355 " (cutoff:3.500A) removed outlier: 9.168A pdb=" N LEU H 357 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N SER D 356 " --> pdb=" O LEU H 357 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ASN H 359 " --> pdb=" O SER D 356 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ASP D 358 " --> pdb=" O ASN H 359 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N THR H 361 " --> pdb=" O ASP D 358 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE D 360 " --> pdb=" O THR H 361 " (cutoff:3.500A) removed outlier: 9.081A pdb=" N VAL H 350 " --> pdb=" O GLN J 351 " (cutoff:3.500A) removed outlier: 10.595A pdb=" N LYS J 353 " --> pdb=" O VAL H 350 " (cutoff:3.500A) removed outlier: 9.210A pdb=" N SER H 352 " --> pdb=" O LYS J 353 " (cutoff:3.500A) removed outlier: 10.126A pdb=" N GLY J 355 " --> pdb=" O SER H 352 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ILE H 354 " --> pdb=" O GLY J 355 " (cutoff:3.500A) removed outlier: 9.168A pdb=" N LEU J 357 " --> pdb=" O ILE H 354 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N SER H 356 " --> pdb=" O LEU J 357 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N ASN J 359 " --> pdb=" O SER H 356 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ASP H 358 " --> pdb=" O ASN J 359 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N THR J 361 " --> pdb=" O ASP H 358 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE H 360 " --> pdb=" O THR J 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 369 through 370 removed outlier: 6.485A pdb=" N LYS B 369 " --> pdb=" O LYS F 370 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LYS F 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LYS D 369 " --> pdb=" O LYS H 370 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LYS H 369 " --> pdb=" O LYS J 370 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 374 through 376 124 hydrogen bonds defined for protein. 372 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: 3.71 Time building geometry restraints manager: 3.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.12: 5790 1.12 - 1.27: 930 1.27 - 1.43: 1434 1.43 - 1.59: 3296 1.59 - 1.75: 10 Bond restraints: 11460 Sorted by residual: bond pdb=" NE2 HIS C 374 " pdb=" HE2 HIS C 374 " ideal model delta sigma weight residual 0.860 1.052 -0.192 2.00e-02 2.50e+03 9.25e+01 bond pdb=" NE2 HIS E 374 " pdb=" HE2 HIS E 374 " ideal model delta sigma weight residual 0.860 1.052 -0.192 2.00e-02 2.50e+03 9.24e+01 bond pdb=" NE2 HIS G 374 " pdb=" HE2 HIS G 374 " ideal model delta sigma weight residual 0.860 1.052 -0.192 2.00e-02 2.50e+03 9.24e+01 bond pdb=" NE2 HIS A 374 " pdb=" HE2 HIS A 374 " ideal model delta sigma weight residual 0.860 1.052 -0.192 2.00e-02 2.50e+03 9.21e+01 bond pdb=" NE2 HIS I 374 " pdb=" HE2 HIS I 374 " ideal model delta sigma weight residual 0.860 1.052 -0.192 2.00e-02 2.50e+03 9.19e+01 ... (remaining 11455 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.02: 18111 3.02 - 6.03: 1965 6.03 - 9.05: 714 9.05 - 12.06: 110 12.06 - 15.08: 10 Bond angle restraints: 20910 Sorted by residual: angle pdb=" N SER C 352 " pdb=" CA SER C 352 " pdb=" C SER C 352 " ideal model delta sigma weight residual 108.79 118.10 -9.31 1.53e+00 4.27e-01 3.70e+01 angle pdb=" N SER I 352 " pdb=" CA SER I 352 " pdb=" C SER I 352 " ideal model delta sigma weight residual 108.79 118.07 -9.28 1.53e+00 4.27e-01 3.68e+01 angle pdb=" N SER E 352 " pdb=" CA SER E 352 " pdb=" C SER E 352 " ideal model delta sigma weight residual 108.79 118.07 -9.28 1.53e+00 4.27e-01 3.68e+01 angle pdb=" N SER G 352 " pdb=" CA SER G 352 " pdb=" C SER G 352 " ideal model delta sigma weight residual 108.79 118.06 -9.27 1.53e+00 4.27e-01 3.67e+01 angle pdb=" N SER A 352 " pdb=" CA SER A 352 " pdb=" C SER A 352 " ideal model delta sigma weight residual 108.79 118.06 -9.27 1.53e+00 4.27e-01 3.67e+01 ... (remaining 20905 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.24: 4765 12.24 - 24.48: 255 24.48 - 36.72: 100 36.72 - 48.96: 54 48.96 - 61.20: 106 Dihedral angle restraints: 5280 sinusoidal: 3010 harmonic: 2270 Sorted by residual: dihedral pdb=" CD2 HIS C 329 " pdb=" CG HIS C 329 " pdb=" ND1 HIS C 329 " pdb=" HD1 HIS C 329 " ideal model delta harmonic sigma weight residual 180.00 -154.40 -25.60 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CD2 HIS A 329 " pdb=" CG HIS A 329 " pdb=" ND1 HIS A 329 " pdb=" HD1 HIS A 329 " ideal model delta harmonic sigma weight residual -180.00 -154.43 -25.57 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CD2 HIS I 329 " pdb=" CG HIS I 329 " pdb=" ND1 HIS I 329 " pdb=" HD1 HIS I 329 " ideal model delta harmonic sigma weight residual 180.00 -154.44 -25.56 0 5.00e+00 4.00e-02 2.61e+01 ... (remaining 5277 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 458 0.060 - 0.120: 232 0.120 - 0.179: 120 0.179 - 0.239: 30 0.239 - 0.299: 20 Chirality restraints: 860 Sorted by residual: chirality pdb=" CA LEU F 325 " pdb=" N LEU F 325 " pdb=" C LEU F 325 " pdb=" CB LEU F 325 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CA LEU B 325 " pdb=" N LEU B 325 " pdb=" C LEU B 325 " pdb=" CB LEU B 325 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" CA LEU D 325 " pdb=" N LEU D 325 " pdb=" C LEU D 325 " pdb=" CB LEU D 325 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 857 not shown) Planarity restraints: 1650 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 329 " -0.095 2.00e-02 2.50e+03 9.41e-02 1.99e+02 pdb=" CG HIS A 329 " -0.051 2.00e-02 2.50e+03 pdb=" ND1 HIS A 329 " -0.082 2.00e-02 2.50e+03 pdb=" CD2 HIS A 329 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 HIS A 329 " -0.045 2.00e-02 2.50e+03 pdb=" NE2 HIS A 329 " 0.010 2.00e-02 2.50e+03 pdb=" HD1 HIS A 329 " 0.217 2.00e-02 2.50e+03 pdb=" HD2 HIS A 329 " 0.083 2.00e-02 2.50e+03 pdb=" HE1 HIS A 329 " -0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 329 " -0.095 2.00e-02 2.50e+03 9.40e-02 1.99e+02 pdb=" CG HIS C 329 " -0.051 2.00e-02 2.50e+03 pdb=" ND1 HIS C 329 " -0.082 2.00e-02 2.50e+03 pdb=" CD2 HIS C 329 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 HIS C 329 " -0.046 2.00e-02 2.50e+03 pdb=" NE2 HIS C 329 " 0.010 2.00e-02 2.50e+03 pdb=" HD1 HIS C 329 " 0.217 2.00e-02 2.50e+03 pdb=" HD2 HIS C 329 " 0.082 2.00e-02 2.50e+03 pdb=" HE1 HIS C 329 " -0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS I 329 " -0.095 2.00e-02 2.50e+03 9.40e-02 1.99e+02 pdb=" CG HIS I 329 " -0.051 2.00e-02 2.50e+03 pdb=" ND1 HIS I 329 " -0.082 2.00e-02 2.50e+03 pdb=" CD2 HIS I 329 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 HIS I 329 " -0.045 2.00e-02 2.50e+03 pdb=" NE2 HIS I 329 " 0.010 2.00e-02 2.50e+03 pdb=" HD1 HIS I 329 " 0.217 2.00e-02 2.50e+03 pdb=" HD2 HIS I 329 " 0.082 2.00e-02 2.50e+03 pdb=" HE1 HIS I 329 " -0.066 2.00e-02 2.50e+03 ... (remaining 1647 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 2016 2.28 - 2.86: 24683 2.86 - 3.44: 29858 3.44 - 4.02: 41507 4.02 - 4.60: 60201 Nonbonded interactions: 158265 Sorted by model distance: nonbonded pdb=" HG SER A 320 " pdb=" O GLY E 365 " model vdw 1.699 2.450 nonbonded pdb=" HG SER G 320 " pdb=" O GLY I 365 " model vdw 1.700 2.450 nonbonded pdb=" HG SER E 320 " pdb=" O GLY C 365 " model vdw 1.700 2.450 nonbonded pdb=" HG SER C 320 " pdb=" O GLY G 365 " model vdw 1.700 2.450 nonbonded pdb=" OE1 GLN A 351 " pdb="HE22 GLN E 351 " model vdw 1.716 2.450 ... (remaining 158260 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 2.250 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: 0.190 Extract box with map and model: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 26.690 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6626 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 : 0.023 0.132 5660 Z= 1.577 Angle : 1.979 9.309 7580 Z= 1.256 Chirality : 0.095 0.299 860 Planarity : 0.009 0.035 960 Dihedral : 10.383 61.202 2160 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 0.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -1.46 (0.27), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.10 (0.20), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.004 HIS H 330 PHE 0.019 0.007 PHE A 346 TYR 0.018 0.005 TYR H 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 279 time to evaluate : 0.998 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 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 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 REVERT: F 339 VAL cc_start: 0.7984 (t) cc_final: 0.7759 (m) outliers start: 0 outliers final: 0 residues processed: 279 average time/residue: 0.5164 time to fit residues: 174.5926 Evaluate side-chains 148 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 54 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 GLN D 307 GLN ** G 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.6710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 5660 Z= 0.362 Angle : 0.731 6.435 7580 Z= 0.377 Chirality : 0.049 0.159 860 Planarity : 0.003 0.020 960 Dihedral : 5.998 19.710 740 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.34 % Allowed : 16.25 % Favored : 81.41 % 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 (0.25), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.20 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.003 HIS C 329 PHE 0.010 0.001 PHE B 378 TYR 0.016 0.003 TYR C 310 ARG 0.001 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 152 time to evaluate : 0.916 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: D 346 PHE cc_start: 0.8480 (m-80) cc_final: 0.8088 (m-10) REVERT: G 322 CYS cc_start: 0.6943 (OUTLIER) cc_final: 0.6583 (t) outliers start: 15 outliers final: 10 residues processed: 163 average time/residue: 0.3693 time to fit residues: 77.6916 Evaluate side-chains 134 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 123 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 CYS Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain C residue 322 CYS Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain G residue 322 CYS Chi-restraints excluded: chain I residue 322 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 3.9990 chunk 19 optimal weight: 8.9990 chunk 52 optimal weight: 8.9990 chunk 43 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.7735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5660 Z= 0.233 Angle : 0.612 4.909 7580 Z= 0.310 Chirality : 0.048 0.133 860 Planarity : 0.003 0.024 960 Dihedral : 5.295 20.585 740 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.03 % Allowed : 19.22 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.26), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.22 (0.20), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 374 PHE 0.007 0.001 PHE F 378 TYR 0.010 0.002 TYR C 310 ARG 0.005 0.001 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 131 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 344 LEU cc_start: 0.7609 (mp) cc_final: 0.7130 (mt) REVERT: D 346 PHE cc_start: 0.8555 (m-80) cc_final: 0.8105 (m-10) REVERT: G 322 CYS cc_start: 0.7069 (OUTLIER) cc_final: 0.6797 (t) REVERT: H 346 PHE cc_start: 0.8647 (m-80) cc_final: 0.8260 (m-10) REVERT: I 325 LEU cc_start: 0.5941 (mt) cc_final: 0.5557 (mt) REVERT: J 346 PHE cc_start: 0.8343 (m-80) cc_final: 0.8068 (m-10) outliers start: 13 outliers final: 9 residues processed: 138 average time/residue: 0.3324 time to fit residues: 61.1570 Evaluate side-chains 122 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 112 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 CYS Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain C residue 322 CYS Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain G residue 322 CYS Chi-restraints excluded: chain I residue 322 CYS Chi-restraints excluded: chain I residue 353 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 30 optimal weight: 8.9990 chunk 42 optimal weight: 9.9990 chunk 63 optimal weight: 6.9990 chunk 67 optimal weight: 0.2980 chunk 60 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 38 optimal weight: 20.0000 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.8128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5660 Z= 0.178 Angle : 0.550 4.228 7580 Z= 0.277 Chirality : 0.048 0.130 860 Planarity : 0.003 0.020 960 Dihedral : 5.041 19.376 740 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.56 % Allowed : 18.12 % Favored : 80.31 % 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: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.21 (0.20), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 330 PHE 0.004 0.001 PHE B 378 TYR 0.011 0.002 TYR I 310 ARG 0.003 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 117 time to evaluate : 0.922 Fit side-chains revert: symmetry clash REVERT: C 344 LEU cc_start: 0.7717 (mp) cc_final: 0.7333 (mt) REVERT: D 346 PHE cc_start: 0.8592 (m-80) cc_final: 0.8037 (m-10) REVERT: H 346 PHE cc_start: 0.8635 (m-80) cc_final: 0.8308 (m-10) REVERT: J 346 PHE cc_start: 0.8304 (m-80) cc_final: 0.8097 (m-10) outliers start: 10 outliers final: 10 residues processed: 123 average time/residue: 0.2588 time to fit residues: 46.3087 Evaluate side-chains 123 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 113 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 CYS Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain C residue 322 CYS Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain I residue 353 LYS Chi-restraints excluded: chain J residue 311 LYS Chi-restraints excluded: chain J residue 319 THR 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: 8.9990 chunk 27 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 60 optimal weight: 7.9990 chunk 17 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 13 optimal weight: 0.0970 chunk 39 optimal weight: 7.9990 overall best weight: 7.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.9005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 5660 Z= 0.354 Angle : 0.636 4.920 7580 Z= 0.328 Chirality : 0.048 0.135 860 Planarity : 0.004 0.026 960 Dihedral : 5.716 18.465 740 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 3.75 % Allowed : 17.50 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.25), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.67 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS A 329 PHE 0.010 0.002 PHE E 346 TYR 0.011 0.002 TYR A 310 ARG 0.002 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 113 time to evaluate : 0.934 Fit side-chains revert: symmetry clash REVERT: C 325 LEU cc_start: 0.7063 (mt) cc_final: 0.6459 (mt) REVERT: D 346 PHE cc_start: 0.8602 (m-80) cc_final: 0.8325 (m-10) REVERT: H 346 PHE cc_start: 0.8606 (m-80) cc_final: 0.8248 (m-10) REVERT: J 346 PHE cc_start: 0.8516 (m-80) cc_final: 0.8315 (m-10) outliers start: 24 outliers final: 20 residues processed: 126 average time/residue: 0.2583 time to fit residues: 47.6690 Evaluate side-chains 126 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 106 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 CYS Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 358 ASP Chi-restraints excluded: chain C residue 322 CYS Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 358 ASP Chi-restraints excluded: chain G residue 337 VAL Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain I residue 322 CYS Chi-restraints excluded: chain I residue 342 GLU Chi-restraints excluded: chain J residue 311 LYS Chi-restraints excluded: chain J residue 319 THR Chi-restraints excluded: chain J residue 358 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 1.9990 chunk 67 optimal weight: 0.4980 chunk 56 optimal weight: 0.1980 chunk 31 optimal weight: 4.9990 chunk 5 optimal weight: 8.9990 chunk 22 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 38 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.9080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5660 Z= 0.151 Angle : 0.536 3.865 7580 Z= 0.270 Chirality : 0.049 0.133 860 Planarity : 0.003 0.022 960 Dihedral : 5.004 18.429 740 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.56 % Allowed : 20.78 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.26), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.51 (0.20), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 362 PHE 0.004 0.001 PHE D 346 TYR 0.008 0.001 TYR I 310 ARG 0.001 0.000 ARG G 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 120 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 346 PHE cc_start: 0.8596 (m-80) cc_final: 0.8133 (m-10) outliers start: 10 outliers final: 9 residues processed: 125 average time/residue: 0.2254 time to fit residues: 42.0777 Evaluate side-chains 125 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 116 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 344 LEU Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain I residue 342 GLU Chi-restraints excluded: chain J residue 311 LYS Chi-restraints excluded: chain J residue 319 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 67 optimal weight: 6.9990 chunk 42 optimal weight: 7.9990 chunk 41 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 13 optimal weight: 0.9980 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.9420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5660 Z= 0.303 Angle : 0.586 4.374 7580 Z= 0.301 Chirality : 0.047 0.133 860 Planarity : 0.003 0.023 960 Dihedral : 5.378 17.599 740 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 2.97 % Allowed : 19.69 % Favored : 77.34 % 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: -2.36 (0.25), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.79 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 329 PHE 0.006 0.001 PHE H 378 TYR 0.010 0.002 TYR A 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 106 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 325 LEU cc_start: 0.7010 (mt) cc_final: 0.6622 (mt) REVERT: G 307 GLN cc_start: 0.6682 (OUTLIER) cc_final: 0.6341 (mm110) REVERT: I 344 LEU cc_start: 0.7930 (mp) cc_final: 0.7560 (mt) outliers start: 19 outliers final: 12 residues processed: 117 average time/residue: 0.2379 time to fit residues: 41.1673 Evaluate side-chains 118 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 105 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain C residue 322 CYS Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain G residue 307 GLN Chi-restraints excluded: chain I residue 342 GLU Chi-restraints excluded: chain J residue 319 THR Chi-restraints excluded: chain J residue 337 VAL Chi-restraints excluded: chain J residue 358 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 0.8980 chunk 42 optimal weight: 7.9990 chunk 45 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 61 optimal weight: 7.9990 chunk 64 optimal weight: 10.0000 chunk 58 optimal weight: 0.4980 chunk 62 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.9527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5660 Z= 0.197 Angle : 0.538 4.082 7580 Z= 0.273 Chirality : 0.048 0.136 860 Planarity : 0.003 0.023 960 Dihedral : 5.092 18.374 740 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.03 % Allowed : 21.56 % Favored : 76.41 % 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: -2.35 (0.25), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.78 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 362 PHE 0.004 0.001 PHE E 346 TYR 0.008 0.001 TYR I 310 ARG 0.001 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 111 time to evaluate : 0.958 Fit side-chains revert: symmetry clash REVERT: D 346 PHE cc_start: 0.8587 (m-80) cc_final: 0.8173 (m-10) REVERT: H 346 PHE cc_start: 0.8636 (m-80) cc_final: 0.8259 (m-10) outliers start: 13 outliers final: 12 residues processed: 120 average time/residue: 0.2292 time to fit residues: 40.6422 Evaluate side-chains 120 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 108 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 CYS Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain C residue 322 CYS Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain G residue 344 LEU Chi-restraints excluded: chain I residue 342 GLU Chi-restraints excluded: chain J residue 319 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 19 optimal weight: 8.9990 chunk 56 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.9639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5660 Z= 0.248 Angle : 0.569 9.804 7580 Z= 0.289 Chirality : 0.048 0.134 860 Planarity : 0.003 0.024 960 Dihedral : 5.148 17.383 740 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 2.34 % Allowed : 21.88 % Favored : 75.78 % 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: -2.50 (0.25), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.90 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 329 PHE 0.024 0.001 PHE J 346 TYR 0.008 0.002 TYR A 310 ARG 0.001 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 105 time to evaluate : 0.962 Fit side-chains revert: symmetry clash REVERT: D 346 PHE cc_start: 0.8570 (m-80) cc_final: 0.7761 (m-10) REVERT: H 346 PHE cc_start: 0.8618 (m-80) cc_final: 0.8140 (m-10) outliers start: 15 outliers final: 13 residues processed: 116 average time/residue: 0.2419 time to fit residues: 41.4435 Evaluate side-chains 116 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 103 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 CYS Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain C residue 322 CYS Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain G residue 344 LEU Chi-restraints excluded: chain I residue 342 GLU Chi-restraints excluded: chain J residue 319 THR Chi-restraints excluded: chain J residue 342 GLU 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: 3.9990 chunk 55 optimal weight: 5.9990 chunk 5 optimal weight: 0.4980 chunk 42 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 8 optimal weight: 10.0000 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.9762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5660 Z= 0.195 Angle : 0.555 8.729 7580 Z= 0.280 Chirality : 0.048 0.133 860 Planarity : 0.003 0.022 960 Dihedral : 4.979 18.075 740 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.03 % Allowed : 22.03 % 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: -2.46 (0.25), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.87 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 362 PHE 0.012 0.001 PHE J 346 TYR 0.007 0.001 TYR C 310 ARG 0.001 0.000 ARG H 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 104 time to evaluate : 0.940 Fit side-chains revert: symmetry clash REVERT: J 346 PHE cc_start: 0.8158 (m-10) cc_final: 0.7846 (m-10) outliers start: 13 outliers final: 13 residues processed: 113 average time/residue: 0.2320 time to fit residues: 38.9119 Evaluate side-chains 116 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 103 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 CYS Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain C residue 322 CYS Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain G residue 344 LEU Chi-restraints excluded: chain I residue 342 GLU Chi-restraints excluded: chain J residue 319 THR Chi-restraints excluded: chain J residue 342 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 chunk 48 optimal weight: 8.9990 chunk 3 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 362 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.108813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.092348 restraints weight = 57361.121| |-----------------------------------------------------------------------------| r_work (start): 0.4347 rms_B_bonded: 5.51 r_work: 0.4372 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.4372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.9924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5660 Z= 0.219 Angle : 0.563 8.641 7580 Z= 0.285 Chirality : 0.048 0.132 860 Planarity : 0.003 0.022 960 Dihedral : 4.976 17.426 740 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 2.19 % Allowed : 22.03 % Favored : 75.78 % 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: -2.53 (0.25), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.92 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 362 PHE 0.014 0.001 PHE J 346 TYR 0.008 0.001 TYR C 310 ARG 0.001 0.000 ARG D 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3414.45 seconds wall clock time: 60 minutes 29.83 seconds (3629.83 seconds total)