Starting phenix.real_space_refine on Wed Oct 9 23:56:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9czl_46420/10_2024/9czl_46420_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9czl_46420/10_2024/9czl_46420.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/9czl_46420/10_2024/9czl_46420.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9czl_46420/10_2024/9czl_46420.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9czl_46420/10_2024/9czl_46420_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9czl_46420/10_2024/9czl_46420_neut.cif" } 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= -0.006 sd= 0.986 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 3570 2.51 5 N 1030 2.21 5 O 1050 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 5660 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 566 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "B" Number of atoms: 566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 566 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "C" Number of atoms: 566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 566 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "D" Number of atoms: 566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 566 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "E" Number of atoms: 566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 566 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "F" Number of atoms: 566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 566 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "G" Number of atoms: 566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 566 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "H" Number of atoms: 566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 566 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "I" Number of atoms: 566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 566 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "J" Number of atoms: 566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 566 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Time building chain proxies: 4.13, per 1000 atoms: 0.73 Number of scatterers: 5660 At special positions: 0 Unit cell: (100.13, 132.804, 46.376, 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 1050 8.00 N 1030 7.00 C 3570 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 - 3.00 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: 1.24 Conformation dependent library (CDL) restraints added in 662.9 milliseconds 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1300 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 56.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 306 through 310 removed outlier: 6.572A pdb=" N GLN A 307 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N TYR C 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N VAL A 309 " --> pdb=" O TYR C 310 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLN C 307 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N TYR E 310 " --> pdb=" O GLN C 307 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL C 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLN E 307 " --> pdb=" O ILE G 308 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N TYR G 310 " --> pdb=" O GLN E 307 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL E 309 " --> pdb=" O TYR G 310 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLN G 307 " --> pdb=" O ILE I 308 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N TYR I 310 " --> pdb=" O GLN G 307 " (cutoff:3.500A) removed outlier: 6.423A 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: 6.625A pdb=" N VAL A 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL C 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL E 313 " --> pdb=" O ASP G 314 " (cutoff:3.500A) removed outlier: 6.626A 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 330 removed outlier: 6.486A pdb=" N LYS A 317 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N SER C 320 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR A 319 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N CYS C 322 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LYS A 321 " --> pdb=" O CYS C 322 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N SER C 324 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N GLY A 323 " --> pdb=" O SER C 324 " (cutoff:3.500A) removed outlier: 9.988A pdb=" N GLY C 326 " --> pdb=" O GLY A 323 " (cutoff:3.500A) removed outlier: 8.785A pdb=" N LEU A 325 " --> pdb=" O GLY C 326 " (cutoff:3.500A) removed outlier: 9.570A pdb=" N ILE C 328 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ASN A 327 " --> pdb=" O ILE C 328 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N HIS C 330 " --> pdb=" O ASN A 327 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N HIS A 329 " --> pdb=" O HIS C 330 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LYS C 317 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N SER E 320 " --> pdb=" O LYS C 317 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR C 319 " --> pdb=" O SER E 320 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N CYS E 322 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LYS C 321 " --> pdb=" O CYS E 322 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N SER E 324 " --> pdb=" O LYS C 321 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N GLY C 323 " --> pdb=" O SER E 324 " (cutoff:3.500A) removed outlier: 9.988A pdb=" N GLY E 326 " --> pdb=" O GLY C 323 " (cutoff:3.500A) removed outlier: 8.784A pdb=" N LEU C 325 " --> pdb=" O GLY E 326 " (cutoff:3.500A) removed outlier: 9.570A pdb=" N ILE E 328 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ASN C 327 " --> pdb=" O ILE E 328 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N HIS E 330 " --> pdb=" O ASN C 327 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N HIS C 329 " --> pdb=" O HIS E 330 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LYS E 317 " --> pdb=" O VAL G 318 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N SER G 320 " --> pdb=" O LYS E 317 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR E 319 " --> pdb=" O SER G 320 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N CYS G 322 " --> pdb=" O THR E 319 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LYS E 321 " --> pdb=" O CYS G 322 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N SER G 324 " --> pdb=" O LYS E 321 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N GLY E 323 " --> pdb=" O SER G 324 " (cutoff:3.500A) removed outlier: 9.987A pdb=" N GLY G 326 " --> pdb=" O GLY E 323 " (cutoff:3.500A) removed outlier: 8.785A pdb=" N LEU E 325 " --> pdb=" O GLY G 326 " (cutoff:3.500A) removed outlier: 9.569A pdb=" N ILE G 328 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ASN E 327 " --> pdb=" O ILE G 328 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N HIS G 330 " --> pdb=" O ASN E 327 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N HIS E 329 " --> pdb=" O HIS G 330 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LYS G 317 " --> pdb=" O VAL I 318 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N SER I 320 " --> pdb=" O LYS G 317 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR G 319 " --> pdb=" O SER I 320 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N CYS I 322 " --> pdb=" O THR G 319 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LYS G 321 " --> pdb=" O CYS I 322 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N SER I 324 " --> pdb=" O LYS G 321 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N GLY G 323 " --> pdb=" O SER I 324 " (cutoff:3.500A) removed outlier: 9.988A pdb=" N GLY I 326 " --> pdb=" O GLY G 323 " (cutoff:3.500A) removed outlier: 8.785A pdb=" N LEU G 325 " --> pdb=" O GLY I 326 " (cutoff:3.500A) removed outlier: 9.568A pdb=" N ILE I 328 " --> pdb=" O LEU G 325 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ASN G 327 " --> pdb=" O ILE I 328 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N HIS I 330 " --> pdb=" O ASN G 327 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N HIS G 329 " --> pdb=" O HIS I 330 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 336 through 340 Processing sheet with id=AA5, first strand: chain 'A' and resid 343 through 347 Processing sheet with id=AA6, first strand: chain 'A' and resid 351 through 362 removed outlier: 6.932A pdb=" N SER A 352 " --> pdb=" O GLN C 351 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LYS C 353 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ILE A 354 " --> pdb=" O LYS C 353 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLY C 355 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N SER C 352 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LYS E 353 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ILE C 354 " --> pdb=" O LYS E 353 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLY E 355 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N SER E 352 " --> pdb=" O GLN G 351 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LYS G 353 " --> pdb=" O SER E 352 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ILE E 354 " --> pdb=" O LYS G 353 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLY G 355 " --> pdb=" O ILE E 354 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N SER G 352 " --> pdb=" O GLN I 351 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LYS I 353 " --> pdb=" O SER G 352 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ILE G 354 " --> pdb=" O LYS I 353 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLY I 355 " --> pdb=" O ILE G 354 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 369 through 377 removed outlier: 6.523A pdb=" N LYS A 369 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N GLU C 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ILE A 371 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N HIS C 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N THR A 373 " --> pdb=" O HIS C 374 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N LEU C 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LYS A 375 " --> pdb=" O LEU C 376 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LYS C 369 " --> pdb=" O LYS E 370 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N GLU E 372 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE C 371 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N HIS E 374 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N THR C 373 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N LEU E 376 " --> pdb=" O THR C 373 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LYS C 375 " --> pdb=" O LEU E 376 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LYS E 369 " --> pdb=" O LYS G 370 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N GLU G 372 " --> pdb=" O LYS E 369 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ILE E 371 " --> pdb=" O GLU G 372 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N HIS G 374 " --> pdb=" O ILE E 371 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N THR E 373 " --> pdb=" O HIS G 374 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N LEU G 376 " --> pdb=" O THR E 373 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LYS E 375 " --> pdb=" O LEU G 376 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LYS G 369 " --> pdb=" O LYS I 370 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N GLU I 372 " --> pdb=" O LYS G 369 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ILE G 371 " --> pdb=" O GLU I 372 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N HIS I 374 " --> pdb=" O ILE G 371 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N THR G 373 " --> pdb=" O HIS I 374 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N LEU I 376 " --> pdb=" O THR G 373 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LYS G 375 " --> pdb=" O LEU I 376 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 306 through 310 removed outlier: 6.525A pdb=" N GLN B 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N TYR D 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL B 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLN D 307 " --> pdb=" O ILE F 308 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N TYR F 310 " --> pdb=" O GLN D 307 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL D 309 " --> pdb=" O TYR F 310 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLN F 307 " --> pdb=" O ILE H 308 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N TYR H 310 " --> pdb=" O GLN F 307 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL F 309 " --> pdb=" O TYR H 310 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLN H 307 " --> pdb=" O ILE J 308 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N TYR J 310 " --> pdb=" O GLN H 307 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL H 309 " --> pdb=" O TYR J 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.594A pdb=" N VAL B 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL D 313 " --> pdb=" O ASP F 314 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL F 313 " --> pdb=" O ASP H 314 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL H 313 " --> pdb=" O ASP J 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 317 through 326 removed outlier: 8.843A pdb=" N VAL B 318 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 10.515A pdb=" N LYS D 321 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 9.021A pdb=" N SER B 320 " --> pdb=" O LYS D 321 " (cutoff:3.500A) removed outlier: 10.140A pdb=" N GLY D 323 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 6.172A 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: 6.247A pdb=" N SER B 324 " --> pdb=" O LEU D 325 " (cutoff:3.500A) removed outlier: 8.843A pdb=" N VAL D 318 " --> pdb=" O THR F 319 " (cutoff:3.500A) removed outlier: 10.515A pdb=" N LYS F 321 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 9.020A pdb=" N SER D 320 " --> pdb=" O LYS F 321 " (cutoff:3.500A) removed outlier: 10.139A pdb=" N GLY F 323 " --> pdb=" O SER D 320 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N CYS D 322 " --> pdb=" O GLY F 323 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N LEU F 325 " --> pdb=" O CYS D 322 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N SER D 324 " --> pdb=" O LEU F 325 " (cutoff:3.500A) removed outlier: 8.844A pdb=" N VAL F 318 " --> pdb=" O THR H 319 " (cutoff:3.500A) removed outlier: 10.515A pdb=" N LYS H 321 " --> pdb=" O VAL F 318 " (cutoff:3.500A) removed outlier: 9.021A pdb=" N SER F 320 " --> pdb=" O LYS H 321 " (cutoff:3.500A) removed outlier: 10.140A pdb=" N GLY H 323 " --> pdb=" O SER F 320 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N CYS F 322 " --> pdb=" O GLY H 323 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N LEU H 325 " --> pdb=" O CYS F 322 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N SER F 324 " --> pdb=" O LEU H 325 " (cutoff:3.500A) removed outlier: 8.845A pdb=" N VAL H 318 " --> pdb=" O THR J 319 " (cutoff:3.500A) removed outlier: 10.515A pdb=" N LYS J 321 " --> pdb=" O VAL H 318 " (cutoff:3.500A) removed outlier: 9.022A pdb=" N SER H 320 " --> pdb=" O LYS J 321 " (cutoff:3.500A) removed outlier: 10.140A pdb=" N GLY J 323 " --> pdb=" O SER H 320 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N CYS H 322 " --> pdb=" O GLY J 323 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N LEU J 325 " --> pdb=" O CYS H 322 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N SER H 324 " --> pdb=" O LEU J 325 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 329 through 330 removed outlier: 6.484A pdb=" N HIS B 329 " --> pdb=" O HIS D 330 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N HIS D 329 " --> pdb=" O HIS F 330 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N HIS F 329 " --> pdb=" O HIS H 330 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N HIS H 329 " --> pdb=" O HIS J 330 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 336 through 340 Processing sheet with id=AB4, first strand: chain 'B' and resid 343 through 347 Processing sheet with id=AB5, first strand: chain 'B' and resid 351 through 356 removed outlier: 6.977A pdb=" N SER D 356 " --> pdb=" O GLY B 355 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N SER F 356 " --> pdb=" O GLY D 355 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N SER H 356 " --> pdb=" O GLY F 355 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N SER J 356 " --> pdb=" O GLY H 355 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 359 through 362 Processing sheet with id=AB7, first strand: chain 'B' and resid 369 through 377 removed outlier: 6.601A pdb=" N LYS B 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N GLU D 372 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE B 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N HIS D 374 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N THR B 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N LEU D 376 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LYS B 375 " --> pdb=" O LEU D 376 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LYS D 369 " --> pdb=" O LYS F 370 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N GLU F 372 " --> pdb=" O LYS D 369 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE D 371 " --> pdb=" O GLU F 372 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N HIS F 374 " --> pdb=" O ILE D 371 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N THR D 373 " --> pdb=" O HIS F 374 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N LEU F 376 " --> pdb=" O THR D 373 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LYS D 375 " --> pdb=" O LEU F 376 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LYS F 369 " --> pdb=" O LYS H 370 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N GLU H 372 " --> pdb=" O LYS F 369 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE F 371 " --> pdb=" O GLU H 372 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N HIS H 374 " --> pdb=" O ILE F 371 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N THR F 373 " --> pdb=" O HIS H 374 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N LEU H 376 " --> pdb=" O THR F 373 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LYS F 375 " --> pdb=" O LEU H 376 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LYS H 369 " --> pdb=" O LYS J 370 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N GLU J 372 " --> pdb=" O LYS H 369 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE H 371 " --> pdb=" O GLU J 372 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N HIS J 374 " --> pdb=" O ILE H 371 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N THR H 373 " --> pdb=" O HIS J 374 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N LEU J 376 " --> pdb=" O THR H 373 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LYS H 375 " --> pdb=" O LEU J 376 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 120 hydrogen bonds defined for protein. 360 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: 1.56 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1228 1.32 - 1.43: 1079 1.43 - 1.54: 3266 1.54 - 1.65: 167 1.65 - 1.76: 10 Bond restraints: 5750 Sorted by residual: bond pdb=" CB HIS C 374 " pdb=" CG HIS C 374 " ideal model delta sigma weight residual 1.497 1.407 0.090 1.40e-02 5.10e+03 4.14e+01 bond pdb=" CB HIS G 374 " pdb=" CG HIS G 374 " ideal model delta sigma weight residual 1.497 1.407 0.090 1.40e-02 5.10e+03 4.13e+01 bond pdb=" CB HIS A 374 " pdb=" CG HIS A 374 " ideal model delta sigma weight residual 1.497 1.408 0.089 1.40e-02 5.10e+03 4.07e+01 bond pdb=" CB HIS I 374 " pdb=" CG HIS I 374 " ideal model delta sigma weight residual 1.497 1.408 0.089 1.40e-02 5.10e+03 4.03e+01 bond pdb=" CB HIS E 374 " pdb=" CG HIS E 374 " ideal model delta sigma weight residual 1.497 1.408 0.089 1.40e-02 5.10e+03 4.00e+01 ... (remaining 5745 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 6218 2.25 - 4.49: 1161 4.49 - 6.74: 251 6.74 - 8.99: 50 8.99 - 11.23: 10 Bond angle restraints: 7690 Sorted by residual: angle pdb=" CA ASP G 358 " pdb=" CB ASP G 358 " pdb=" CG ASP G 358 " ideal model delta sigma weight residual 112.60 119.23 -6.63 1.00e+00 1.00e+00 4.40e+01 angle pdb=" CA ASP A 358 " pdb=" CB ASP A 358 " pdb=" CG ASP A 358 " ideal model delta sigma weight residual 112.60 119.21 -6.61 1.00e+00 1.00e+00 4.37e+01 angle pdb=" CA ASP C 358 " pdb=" CB ASP C 358 " pdb=" CG ASP C 358 " ideal model delta sigma weight residual 112.60 119.21 -6.61 1.00e+00 1.00e+00 4.36e+01 angle pdb=" CA ASP E 358 " pdb=" CB ASP E 358 " pdb=" CG ASP E 358 " ideal model delta sigma weight residual 112.60 119.19 -6.59 1.00e+00 1.00e+00 4.35e+01 angle pdb=" CA ASP I 358 " pdb=" CB ASP I 358 " pdb=" CG ASP I 358 " ideal model delta sigma weight residual 112.60 119.19 -6.59 1.00e+00 1.00e+00 4.34e+01 ... (remaining 7685 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.40: 3345 12.40 - 24.79: 95 24.79 - 37.19: 35 37.19 - 49.58: 10 49.58 - 61.98: 25 Dihedral angle restraints: 3510 sinusoidal: 1470 harmonic: 2040 Sorted by residual: dihedral pdb=" C ASP E 358 " pdb=" N ASP E 358 " pdb=" CA ASP E 358 " pdb=" CB ASP E 358 " ideal model delta harmonic sigma weight residual -122.60 -130.24 7.64 0 2.50e+00 1.60e-01 9.34e+00 dihedral pdb=" C ASP I 358 " pdb=" N ASP I 358 " pdb=" CA ASP I 358 " pdb=" CB ASP I 358 " ideal model delta harmonic sigma weight residual -122.60 -130.21 7.61 0 2.50e+00 1.60e-01 9.27e+00 dihedral pdb=" C ASP A 358 " pdb=" N ASP A 358 " pdb=" CA ASP A 358 " pdb=" CB ASP A 358 " ideal model delta harmonic sigma weight residual -122.60 -130.19 7.59 0 2.50e+00 1.60e-01 9.22e+00 ... (remaining 3507 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 490 0.071 - 0.142: 296 0.142 - 0.213: 68 0.213 - 0.284: 11 0.284 - 0.355: 5 Chirality restraints: 870 Sorted by residual: chirality pdb=" CA ASP E 358 " pdb=" N ASP E 358 " pdb=" C ASP E 358 " pdb=" CB ASP E 358 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.36 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" CA ASP A 358 " pdb=" N ASP A 358 " pdb=" C ASP A 358 " pdb=" CB ASP A 358 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" CA ASP I 358 " pdb=" N ASP I 358 " pdb=" C ASP I 358 " pdb=" CB ASP I 358 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.11e+00 ... (remaining 867 not shown) Planarity restraints: 970 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO D 364 " 0.017 2.00e-02 2.50e+03 3.40e-02 1.16e+01 pdb=" C PRO D 364 " -0.059 2.00e-02 2.50e+03 pdb=" O PRO D 364 " 0.022 2.00e-02 2.50e+03 pdb=" N GLY D 365 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO H 364 " 0.017 2.00e-02 2.50e+03 3.37e-02 1.14e+01 pdb=" C PRO H 364 " -0.058 2.00e-02 2.50e+03 pdb=" O PRO H 364 " 0.022 2.00e-02 2.50e+03 pdb=" N GLY H 365 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO F 364 " 0.017 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C PRO F 364 " -0.058 2.00e-02 2.50e+03 pdb=" O PRO F 364 " 0.022 2.00e-02 2.50e+03 pdb=" N GLY F 365 " 0.020 2.00e-02 2.50e+03 ... (remaining 967 not shown) Histogram of nonbonded interaction distances: 2.46 - 2.95: 2744 2.95 - 3.44: 4522 3.44 - 3.93: 9333 3.93 - 4.41: 10577 4.41 - 4.90: 20013 Nonbonded interactions: 47189 Sorted by model distance: nonbonded pdb=" NZ LYS A 370 " pdb=" OE1 GLU A 372 " model vdw 2.463 3.120 nonbonded pdb=" NZ LYS C 370 " pdb=" OE1 GLU C 372 " model vdw 2.464 3.120 nonbonded pdb=" NZ LYS I 370 " pdb=" OE1 GLU I 372 " model vdw 2.464 3.120 nonbonded pdb=" NZ LYS E 370 " pdb=" OE1 GLU E 372 " model vdw 2.464 3.120 nonbonded pdb=" NZ LYS G 370 " pdb=" OE1 GLU G 372 " model vdw 2.464 3.120 ... (remaining 47184 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: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 17.200 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 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 0.111 5750 Z= 1.511 Angle : 1.947 11.232 7690 Z= 1.237 Chirality : 0.091 0.355 870 Planarity : 0.008 0.034 970 Dihedral : 9.529 61.979 2210 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 0.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % 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: -1.27 (0.27), residues: 720 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.96 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS E 362 PHE 0.026 0.007 PHE E 346 TYR 0.007 0.004 TYR G 310 ARG 0.001 0.001 ARG H 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 241 time to evaluate : 0.717 Fit side-chains revert: symmetry clash REVERT: A 369 LYS cc_start: 0.8393 (mttt) cc_final: 0.8049 (mttp) REVERT: C 327 ASN cc_start: 0.8764 (t0) cc_final: 0.8467 (t160) REVERT: E 369 LYS cc_start: 0.8463 (mttt) cc_final: 0.8131 (mttp) REVERT: G 338 GLU cc_start: 0.7262 (tt0) cc_final: 0.7050 (tt0) REVERT: G 369 LYS cc_start: 0.8610 (mttt) cc_final: 0.8391 (mttm) REVERT: I 369 LYS cc_start: 0.8490 (mttt) cc_final: 0.8081 (mttm) outliers start: 0 outliers final: 0 residues processed: 241 average time/residue: 1.5049 time to fit residues: 374.5835 Evaluate side-chains 128 residues out of total 650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 0.811 ------------------------------------------------------------------------------- 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: 9.9990 chunk 53 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN B 336 GLN C 336 GLN C 368 ASN D 336 GLN ** D 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 362 HIS G 368 ASN H 336 GLN I 327 ASN J 336 GLN ** J 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5750 Z= 0.221 Angle : 0.669 5.895 7690 Z= 0.334 Chirality : 0.051 0.127 870 Planarity : 0.002 0.028 970 Dihedral : 5.216 15.331 750 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.62 % Allowed : 21.08 % Favored : 76.31 % 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: -0.97 (0.29), residues: 720 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.73 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS J 374 PHE 0.010 0.002 PHE G 346 TYR 0.011 0.002 TYR E 310 ARG 0.003 0.001 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 133 time to evaluate : 0.716 Fit side-chains REVERT: A 307 GLN cc_start: 0.8374 (mt0) cc_final: 0.8123 (mt0) REVERT: B 319 THR cc_start: 0.9115 (p) cc_final: 0.8911 (p) REVERT: C 327 ASN cc_start: 0.8856 (t0) cc_final: 0.8557 (t0) REVERT: D 307 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.7622 (tp40) outliers start: 17 outliers final: 3 residues processed: 140 average time/residue: 0.9782 time to fit residues: 144.3741 Evaluate side-chains 126 residues out of total 650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 122 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 307 GLN Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain E residue 343 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 52 optimal weight: 8.9990 chunk 43 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 63 optimal weight: 0.8980 chunk 68 optimal weight: 9.9990 chunk 56 optimal weight: 7.9990 chunk 21 optimal weight: 0.7980 chunk 51 optimal weight: 0.0470 chunk 62 optimal weight: 0.9980 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN B 307 GLN C 336 GLN D 336 GLN E 327 ASN F 307 GLN G 368 ASN H 336 GLN H 362 HIS I 327 ASN J 359 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5750 Z= 0.147 Angle : 0.557 6.121 7690 Z= 0.277 Chirality : 0.049 0.136 870 Planarity : 0.002 0.016 970 Dihedral : 4.653 13.744 750 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.15 % Allowed : 21.69 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.30), residues: 720 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.67 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 330 PHE 0.006 0.001 PHE G 346 TYR 0.007 0.002 TYR E 310 ARG 0.004 0.001 ARG G 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 149 time to evaluate : 0.675 Fit side-chains REVERT: A 307 GLN cc_start: 0.8322 (mt0) cc_final: 0.8080 (mt0) REVERT: A 340 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8206 (mttp) REVERT: A 343 LYS cc_start: 0.8558 (mmmt) cc_final: 0.8146 (mmtt) REVERT: C 327 ASN cc_start: 0.8772 (t0) cc_final: 0.8529 (t0) outliers start: 14 outliers final: 1 residues processed: 157 average time/residue: 1.1434 time to fit residues: 187.6521 Evaluate side-chains 134 residues out of total 650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 132 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain I residue 324 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 30 optimal weight: 7.9990 chunk 42 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 67 optimal weight: 20.0000 chunk 60 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN B 327 ASN C 336 GLN D 336 GLN E 327 ASN ** H 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 368 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5750 Z= 0.192 Angle : 0.604 10.016 7690 Z= 0.291 Chirality : 0.049 0.134 870 Planarity : 0.002 0.015 970 Dihedral : 4.670 12.959 750 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.31 % Allowed : 22.62 % Favored : 75.08 % 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: -1.02 (0.30), residues: 720 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.77 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 362 PHE 0.005 0.001 PHE G 346 TYR 0.009 0.002 TYR I 310 ARG 0.002 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 147 time to evaluate : 0.732 Fit side-chains REVERT: A 340 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.8211 (mttp) REVERT: A 343 LYS cc_start: 0.8560 (mmmt) cc_final: 0.8131 (mmtt) REVERT: C 327 ASN cc_start: 0.8805 (t0) cc_final: 0.8577 (t0) REVERT: D 307 GLN cc_start: 0.8246 (tt0) cc_final: 0.8013 (tt0) REVERT: G 353 LYS cc_start: 0.8457 (mtpp) cc_final: 0.8246 (tttp) outliers start: 15 outliers final: 7 residues processed: 155 average time/residue: 1.0974 time to fit residues: 178.2096 Evaluate side-chains 149 residues out of total 650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 141 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain I residue 324 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 7.9990 chunk 50 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 57 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 13 optimal weight: 0.9990 chunk 39 optimal weight: 20.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN C 336 GLN D 359 ASN E 327 ASN E 336 GLN F 307 GLN ** H 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 327 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 5750 Z= 0.386 Angle : 0.685 9.272 7690 Z= 0.333 Chirality : 0.050 0.144 870 Planarity : 0.002 0.017 970 Dihedral : 5.019 14.149 750 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 2.31 % Allowed : 23.38 % Favored : 74.31 % 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: -1.21 (0.29), residues: 720 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.91 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 362 PHE 0.013 0.001 PHE G 346 TYR 0.013 0.003 TYR I 310 ARG 0.003 0.001 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 150 time to evaluate : 0.615 Fit side-chains REVERT: A 307 GLN cc_start: 0.8400 (mt0) cc_final: 0.8155 (mt0) REVERT: A 340 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8103 (mttp) REVERT: C 327 ASN cc_start: 0.8900 (t0) cc_final: 0.8609 (t0) REVERT: D 307 GLN cc_start: 0.8264 (tt0) cc_final: 0.8010 (tt0) outliers start: 15 outliers final: 10 residues processed: 157 average time/residue: 1.1048 time to fit residues: 181.4008 Evaluate side-chains 159 residues out of total 650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 148 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain J residue 340 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 65 optimal weight: 0.0030 chunk 7 optimal weight: 0.7980 chunk 38 optimal weight: 20.0000 chunk 49 optimal weight: 0.5980 overall best weight: 1.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN E 327 ASN E 336 GLN F 307 GLN ** H 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 327 ASN I 327 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5750 Z= 0.214 Angle : 0.622 8.793 7690 Z= 0.302 Chirality : 0.049 0.140 870 Planarity : 0.002 0.016 970 Dihedral : 4.795 13.210 750 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.15 % Allowed : 24.92 % Favored : 72.92 % 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: -1.25 (0.29), residues: 720 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.95 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 330 PHE 0.008 0.001 PHE G 346 TYR 0.009 0.002 TYR I 310 ARG 0.002 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 141 time to evaluate : 0.690 Fit side-chains REVERT: A 307 GLN cc_start: 0.8355 (mt0) cc_final: 0.8104 (mt0) REVERT: A 340 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8185 (mttp) REVERT: B 338 GLU cc_start: 0.6950 (tp30) cc_final: 0.6665 (mm-30) REVERT: C 327 ASN cc_start: 0.8857 (t0) cc_final: 0.8606 (t0) REVERT: D 307 GLN cc_start: 0.8225 (tt0) cc_final: 0.7982 (tt0) outliers start: 14 outliers final: 9 residues processed: 149 average time/residue: 1.0808 time to fit residues: 168.9051 Evaluate side-chains 149 residues out of total 650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 139 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain G 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: 20.0000 chunk 57 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 67 optimal weight: 8.9990 chunk 42 optimal weight: 8.9990 chunk 41 optimal weight: 8.9990 chunk 31 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 40 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN B 329 HIS D 359 ASN E 327 ASN E 336 GLN F 329 HIS ** H 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 327 ASN I 336 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 5750 Z= 0.389 Angle : 0.713 9.483 7690 Z= 0.345 Chirality : 0.050 0.156 870 Planarity : 0.002 0.016 970 Dihedral : 5.020 14.577 750 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.62 % Allowed : 25.08 % Favored : 72.31 % 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: -1.42 (0.29), residues: 720 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.07 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 362 PHE 0.013 0.001 PHE G 346 TYR 0.013 0.002 TYR I 310 ARG 0.002 0.000 ARG G 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 149 time to evaluate : 0.673 Fit side-chains REVERT: A 307 GLN cc_start: 0.8416 (mt0) cc_final: 0.8192 (mt0) REVERT: A 340 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8156 (mttp) REVERT: B 338 GLU cc_start: 0.7051 (tp30) cc_final: 0.6783 (mm-30) REVERT: C 327 ASN cc_start: 0.8917 (t0) cc_final: 0.8638 (t0) REVERT: J 307 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7969 (tt0) outliers start: 17 outliers final: 10 residues processed: 158 average time/residue: 1.0688 time to fit residues: 177.1782 Evaluate side-chains 156 residues out of total 650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 144 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain J residue 307 GLN Chi-restraints excluded: chain J residue 340 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 4.9990 chunk 42 optimal weight: 7.9990 chunk 45 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 53 optimal weight: 20.0000 chunk 61 optimal weight: 0.6980 chunk 64 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 37 optimal weight: 9.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN B 307 GLN E 327 ASN E 336 GLN F 307 GLN H 307 GLN ** H 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 327 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.4098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 5750 Z= 0.346 Angle : 0.703 9.563 7690 Z= 0.341 Chirality : 0.050 0.152 870 Planarity : 0.002 0.015 970 Dihedral : 5.049 14.987 750 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 2.62 % Allowed : 25.69 % Favored : 71.69 % 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: -1.52 (0.29), residues: 720 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.15 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 362 PHE 0.012 0.001 PHE G 346 TYR 0.013 0.002 TYR I 310 ARG 0.002 0.000 ARG G 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 146 time to evaluate : 0.693 Fit side-chains REVERT: A 307 GLN cc_start: 0.8414 (mt0) cc_final: 0.8181 (mt0) REVERT: A 340 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8217 (mttp) REVERT: C 327 ASN cc_start: 0.8937 (t0) cc_final: 0.8651 (t0) REVERT: J 307 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7942 (tt0) outliers start: 17 outliers final: 11 residues processed: 156 average time/residue: 1.1272 time to fit residues: 184.2125 Evaluate side-chains 157 residues out of total 650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 144 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain H residue 327 ASN Chi-restraints excluded: chain J residue 307 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 56 optimal weight: 0.0370 chunk 59 optimal weight: 7.9990 chunk 62 optimal weight: 0.7980 chunk 41 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 40 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 46 optimal weight: 9.9990 overall best weight: 2.1062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN B 307 GLN ** D 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 ASN F 307 GLN I 327 ASN I 336 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5750 Z= 0.274 Angle : 0.679 9.325 7690 Z= 0.330 Chirality : 0.049 0.148 870 Planarity : 0.002 0.017 970 Dihedral : 4.870 13.998 750 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 2.15 % Allowed : 25.85 % Favored : 72.00 % 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: -1.53 (0.29), residues: 720 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.16 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 330 PHE 0.009 0.001 PHE G 346 TYR 0.010 0.002 TYR I 310 ARG 0.002 0.000 ARG G 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 146 time to evaluate : 0.710 Fit side-chains REVERT: A 307 GLN cc_start: 0.8377 (mt0) cc_final: 0.8131 (mt0) REVERT: A 340 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8218 (mttp) REVERT: C 327 ASN cc_start: 0.8894 (t0) cc_final: 0.8635 (t0) outliers start: 14 outliers final: 11 residues processed: 154 average time/residue: 1.0899 time to fit residues: 176.2052 Evaluate side-chains 156 residues out of total 650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 144 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain J residue 340 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 6.9990 chunk 64 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 chunk 42 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 chunk 44 optimal weight: 0.4980 chunk 59 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN B 307 GLN E 327 ASN E 336 GLN F 307 GLN ** H 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 327 ASN I 336 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5750 Z= 0.351 Angle : 0.733 9.571 7690 Z= 0.356 Chirality : 0.050 0.152 870 Planarity : 0.002 0.016 970 Dihedral : 5.023 15.060 750 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.00 % Allowed : 26.46 % Favored : 71.54 % 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: -1.62 (0.29), residues: 720 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.23 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 362 PHE 0.011 0.001 PHE G 346 TYR 0.013 0.002 TYR I 310 ARG 0.002 0.000 ARG C 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 142 time to evaluate : 0.664 Fit side-chains REVERT: A 307 GLN cc_start: 0.8413 (mt0) cc_final: 0.8175 (mt0) REVERT: A 340 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8223 (mttp) REVERT: B 338 GLU cc_start: 0.6972 (tp30) cc_final: 0.6742 (mm-30) REVERT: C 327 ASN cc_start: 0.8937 (t0) cc_final: 0.8654 (t0) outliers start: 13 outliers final: 11 residues processed: 150 average time/residue: 1.0603 time to fit residues: 166.9084 Evaluate side-chains 154 residues out of total 650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 142 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain G residue 352 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 63 optimal weight: 0.0970 chunk 37 optimal weight: 4.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN B 307 GLN ** D 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 ASN E 336 GLN F 307 GLN I 327 ASN I 336 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.131533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.094935 restraints weight = 6753.542| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.91 r_work: 0.3360 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.4221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5750 Z= 0.273 Angle : 0.710 9.278 7690 Z= 0.347 Chirality : 0.050 0.149 870 Planarity : 0.002 0.022 970 Dihedral : 4.886 14.504 750 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 2.15 % Allowed : 26.62 % Favored : 71.23 % 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: -1.60 (0.29), residues: 720 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.21 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 330 PHE 0.009 0.001 PHE G 346 TYR 0.010 0.002 TYR I 310 ARG 0.002 0.000 ARG C 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3136.08 seconds wall clock time: 57 minutes 9.97 seconds (3429.97 seconds total)