Starting phenix.real_space_refine on Tue Jan 14 04:58:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9czl_46420/01_2025/9czl_46420_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9czl_46420/01_2025/9czl_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/cci-nas-00/data/ceres_data/9czl_46420/01_2025/9czl_46420.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9czl_46420/01_2025/9czl_46420.map" model { file = "/net/cci-nas-00/data/ceres_data/9czl_46420/01_2025/9czl_46420_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9czl_46420/01_2025/9czl_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-5571/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: 4.16, 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: 1.37 Conformation dependent library (CDL) restraints added in 739.0 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: 1.07 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: 1.68 Time building geometry restraints manager: 1.57 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: 0.01 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: 1.320 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: 0.060 Process input model: 17.850 Find NCS groups from input model: 0.210 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:13.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.470 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 0.663 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: 1.5394 time to fit residues: 383.2371 Evaluate side-chains 128 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.711 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.137300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.101023 restraints weight = 6649.102| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.88 r_work: 0.3443 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 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 to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 0.723 Fit side-chains REVERT: A 307 GLN cc_start: 0.8510 (mt0) cc_final: 0.8120 (mt0) REVERT: A 345 ASP cc_start: 0.8207 (t0) cc_final: 0.7701 (t70) REVERT: C 327 ASN cc_start: 0.9030 (t0) cc_final: 0.8705 (t0) REVERT: D 307 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7878 (tp40) REVERT: E 356 SER cc_start: 0.9044 (t) cc_final: 0.8723 (m) REVERT: F 336 GLN cc_start: 0.7957 (mm-40) cc_final: 0.7542 (mm110) REVERT: H 340 LYS cc_start: 0.7868 (ptpp) cc_final: 0.7447 (tmtt) REVERT: J 314 ASP cc_start: 0.8921 (t0) cc_final: 0.8582 (t0) REVERT: J 336 GLN cc_start: 0.8028 (mt0) cc_final: 0.7523 (mm-40) outliers start: 17 outliers final: 3 residues processed: 140 average time/residue: 0.9875 time to fit residues: 145.7530 Evaluate side-chains 126 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 122 time to evaluate : 0.725 ------------------------------------------------------------------------------- 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 47 optimal weight: 9.9990 chunk 20 optimal weight: 0.3980 chunk 61 optimal weight: 0.8980 chunk 23 optimal weight: 8.9990 chunk 66 optimal weight: 10.0000 chunk 45 optimal weight: 0.9990 chunk 13 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 55 optimal weight: 8.9990 chunk 10 optimal weight: 8.9990 chunk 5 optimal weight: 8.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN B 307 GLN C 336 GLN D 336 GLN E 327 ASN E 336 GLN G 368 ASN I 327 ASN I 368 ASN J 359 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.132701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.095424 restraints weight = 6873.294| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.96 r_work: 0.3323 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 5750 Z= 0.322 Angle : 0.671 6.572 7690 Z= 0.332 Chirality : 0.050 0.152 870 Planarity : 0.002 0.022 970 Dihedral : 5.118 13.946 750 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 2.46 % Allowed : 21.08 % Favored : 76.46 % 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: -0.99 (0.29), residues: 720 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.75 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS I 362 PHE 0.015 0.001 PHE G 346 TYR 0.013 0.002 TYR I 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 158 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 0.696 Fit side-chains REVERT: A 307 GLN cc_start: 0.8399 (mt0) cc_final: 0.7959 (mt0) REVERT: A 340 LYS cc_start: 0.7956 (OUTLIER) cc_final: 0.7472 (mttp) REVERT: A 345 ASP cc_start: 0.8060 (t0) cc_final: 0.7478 (t70) REVERT: B 338 GLU cc_start: 0.6840 (tp30) cc_final: 0.6636 (mm-30) REVERT: B 347 LYS cc_start: 0.6524 (mttp) cc_final: 0.5811 (mmpt) REVERT: C 327 ASN cc_start: 0.8965 (t0) cc_final: 0.8658 (t0) REVERT: D 307 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7688 (tp40) REVERT: D 340 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.7732 (tptt) REVERT: E 315 LEU cc_start: 0.9251 (mp) cc_final: 0.8962 (mt) REVERT: E 345 ASP cc_start: 0.7919 (t0) cc_final: 0.7628 (t70) REVERT: E 356 SER cc_start: 0.8724 (t) cc_final: 0.8432 (m) REVERT: F 336 GLN cc_start: 0.7991 (mm-40) cc_final: 0.7639 (mm110) REVERT: F 338 GLU cc_start: 0.7621 (pp20) cc_final: 0.7240 (pp20) REVERT: F 375 LYS cc_start: 0.8687 (tttt) cc_final: 0.8486 (tttm) REVERT: H 307 GLN cc_start: 0.8314 (mt0) cc_final: 0.8044 (mt0) REVERT: H 314 ASP cc_start: 0.9123 (t0) cc_final: 0.8807 (t0) REVERT: H 324 SER cc_start: 0.8721 (t) cc_final: 0.8337 (m) REVERT: H 340 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.7467 (tmtt) REVERT: J 314 ASP cc_start: 0.8969 (t0) cc_final: 0.8604 (t0) REVERT: J 336 GLN cc_start: 0.8210 (mt0) cc_final: 0.7694 (mm110) outliers start: 16 outliers final: 2 residues processed: 151 average time/residue: 1.1490 time to fit residues: 181.4692 Evaluate side-chains 146 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 140 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain D residue 307 GLN Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 340 LYS Chi-restraints excluded: chain H residue 340 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 10 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 27 optimal weight: 9.9990 chunk 13 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 E 336 GLN F 307 GLN I 327 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.133236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.095842 restraints weight = 6946.236| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.99 r_work: 0.3351 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5750 Z= 0.260 Angle : 0.611 5.556 7690 Z= 0.302 Chirality : 0.049 0.147 870 Planarity : 0.002 0.017 970 Dihedral : 4.974 13.527 750 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.62 % Allowed : 21.38 % Favored : 76.00 % 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: -1.08 (0.29), residues: 720 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.81 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 330 PHE 0.014 0.001 PHE G 346 TYR 0.010 0.002 TYR I 310 ARG 0.003 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 161 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 0.701 Fit side-chains REVERT: A 315 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.9134 (mp) REVERT: A 340 LYS cc_start: 0.7910 (OUTLIER) cc_final: 0.7418 (mttp) REVERT: A 343 LYS cc_start: 0.8416 (mmmt) cc_final: 0.8115 (tmtm) REVERT: A 345 ASP cc_start: 0.8087 (t0) cc_final: 0.7505 (t70) REVERT: A 375 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8474 (tttm) REVERT: B 347 LYS cc_start: 0.6472 (mttp) cc_final: 0.5729 (mmpt) REVERT: C 327 ASN cc_start: 0.8968 (t0) cc_final: 0.8688 (t0) REVERT: E 315 LEU cc_start: 0.9248 (mp) cc_final: 0.8938 (mt) REVERT: E 345 ASP cc_start: 0.7862 (t0) cc_final: 0.7527 (t70) REVERT: E 356 SER cc_start: 0.8733 (t) cc_final: 0.8399 (m) REVERT: F 316 SER cc_start: 0.9354 (p) cc_final: 0.9073 (p) REVERT: F 324 SER cc_start: 0.8645 (t) cc_final: 0.8335 (m) REVERT: F 336 GLN cc_start: 0.7950 (mm-40) cc_final: 0.7442 (mm110) REVERT: F 372 GLU cc_start: 0.8639 (tt0) cc_final: 0.8389 (tt0) REVERT: H 307 GLN cc_start: 0.8271 (mt0) cc_final: 0.7972 (mt0) REVERT: H 314 ASP cc_start: 0.9094 (t0) cc_final: 0.8786 (t0) REVERT: H 324 SER cc_start: 0.8656 (t) cc_final: 0.8229 (m) REVERT: H 340 LYS cc_start: 0.7706 (OUTLIER) cc_final: 0.7494 (tmtt) REVERT: J 314 ASP cc_start: 0.8962 (t0) cc_final: 0.8602 (t0) REVERT: J 336 GLN cc_start: 0.8239 (mt0) cc_final: 0.7710 (mm110) outliers start: 17 outliers final: 5 residues processed: 152 average time/residue: 1.0500 time to fit residues: 167.4575 Evaluate side-chains 150 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 141 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU 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 A residue 375 LYS 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 H residue 340 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 2 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 7 optimal weight: 0.0980 chunk 66 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 42 optimal weight: 0.6980 chunk 46 optimal weight: 10.0000 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 359 ASN E 327 ASN E 336 GLN H 336 GLN I 327 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.132488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.095125 restraints weight = 6827.232| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.97 r_work: 0.3321 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5750 Z= 0.286 Angle : 0.622 6.062 7690 Z= 0.306 Chirality : 0.049 0.147 870 Planarity : 0.002 0.015 970 Dihedral : 4.954 13.800 750 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 3.23 % Allowed : 21.08 % Favored : 75.69 % 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: -1.28 (0.29), residues: 720 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.97 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 330 PHE 0.014 0.001 PHE G 346 TYR 0.011 0.002 TYR I 310 ARG 0.002 0.000 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 172 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 151 time to evaluate : 0.729 Fit side-chains revert: symmetry clash REVERT: A 307 GLN cc_start: 0.8353 (mt0) cc_final: 0.7969 (mt0) REVERT: A 315 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9144 (mp) REVERT: A 340 LYS cc_start: 0.7885 (OUTLIER) cc_final: 0.7380 (mttp) REVERT: A 343 LYS cc_start: 0.8415 (mmmt) cc_final: 0.8093 (tmtm) REVERT: A 345 ASP cc_start: 0.8126 (t0) cc_final: 0.7521 (t70) REVERT: B 347 LYS cc_start: 0.6445 (mttp) cc_final: 0.5731 (mmpt) REVERT: C 327 ASN cc_start: 0.8964 (t0) cc_final: 0.8674 (t0) REVERT: C 331 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8573 (mttp) REVERT: D 307 GLN cc_start: 0.8318 (tt0) cc_final: 0.7975 (tt0) REVERT: D 317 LYS cc_start: 0.8815 (pttt) cc_final: 0.8607 (pttt) REVERT: E 315 LEU cc_start: 0.9245 (mp) cc_final: 0.8905 (mt) REVERT: E 345 ASP cc_start: 0.7855 (t0) cc_final: 0.7520 (t70) REVERT: E 356 SER cc_start: 0.8684 (t) cc_final: 0.8423 (m) REVERT: F 316 SER cc_start: 0.9362 (p) cc_final: 0.9120 (p) REVERT: F 336 GLN cc_start: 0.7971 (mm-40) cc_final: 0.7528 (mm110) REVERT: F 375 LYS cc_start: 0.8647 (tttm) cc_final: 0.8031 (ttmm) REVERT: G 353 LYS cc_start: 0.8911 (mtpp) cc_final: 0.8615 (ttpt) REVERT: H 307 GLN cc_start: 0.8266 (mt0) cc_final: 0.7967 (mt0) REVERT: H 324 SER cc_start: 0.8730 (t) cc_final: 0.8362 (m) REVERT: H 336 GLN cc_start: 0.7979 (mt0) cc_final: 0.7723 (mt0) REVERT: J 314 ASP cc_start: 0.9038 (t0) cc_final: 0.8581 (t0) REVERT: J 336 GLN cc_start: 0.8257 (mt0) cc_final: 0.7653 (mm110) outliers start: 21 outliers final: 6 residues processed: 160 average time/residue: 1.1598 time to fit residues: 194.0864 Evaluate side-chains 159 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 150 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain C residue 331 LYS 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 G residue 343 LYS 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 57 optimal weight: 8.9990 chunk 8 optimal weight: 3.9990 chunk 1 optimal weight: 0.4980 chunk 19 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 64 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 38 optimal weight: 20.0000 chunk 44 optimal weight: 8.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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 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 = 0.3945 r_free = 0.3945 target = 0.132701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.095366 restraints weight = 6778.498| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.96 r_work: 0.3334 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5750 Z= 0.263 Angle : 0.619 6.288 7690 Z= 0.305 Chirality : 0.049 0.146 870 Planarity : 0.002 0.016 970 Dihedral : 4.897 13.718 750 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.15 % Allowed : 22.92 % Favored : 74.92 % 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: -1.37 (0.29), residues: 720 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.04 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 330 PHE 0.014 0.001 PHE G 346 TYR 0.010 0.002 TYR I 310 ARG 0.002 0.000 ARG G 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 162 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 148 time to evaluate : 0.642 Fit side-chains revert: symmetry clash REVERT: A 307 GLN cc_start: 0.8353 (mt0) cc_final: 0.7955 (mt0) REVERT: A 315 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.9134 (mp) REVERT: A 340 LYS cc_start: 0.7856 (OUTLIER) cc_final: 0.7353 (mttp) REVERT: A 343 LYS cc_start: 0.8399 (mmmt) cc_final: 0.8077 (tmtm) REVERT: A 345 ASP cc_start: 0.8127 (t0) cc_final: 0.7487 (t70) REVERT: C 327 ASN cc_start: 0.8966 (t0) cc_final: 0.8677 (t0) REVERT: C 331 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8547 (mttp) REVERT: D 307 GLN cc_start: 0.8288 (tt0) cc_final: 0.7927 (tt0) REVERT: D 317 LYS cc_start: 0.8799 (pttt) cc_final: 0.8497 (pttt) REVERT: E 315 LEU cc_start: 0.9233 (mp) cc_final: 0.8877 (mt) REVERT: E 345 ASP cc_start: 0.7796 (t0) cc_final: 0.7463 (t70) REVERT: E 356 SER cc_start: 0.8650 (t) cc_final: 0.8418 (m) REVERT: F 316 SER cc_start: 0.9402 (p) cc_final: 0.9090 (p) REVERT: F 336 GLN cc_start: 0.8006 (mm-40) cc_final: 0.7557 (mm110) REVERT: F 375 LYS cc_start: 0.8659 (tttm) cc_final: 0.7992 (ttmm) REVERT: H 307 GLN cc_start: 0.8217 (mt0) cc_final: 0.7913 (mt0) REVERT: H 324 SER cc_start: 0.8756 (t) cc_final: 0.8383 (m) REVERT: J 307 GLN cc_start: 0.8403 (tt0) cc_final: 0.8187 (tt0) REVERT: J 314 ASP cc_start: 0.8954 (t0) cc_final: 0.8475 (t0) REVERT: J 336 GLN cc_start: 0.8305 (mt0) cc_final: 0.7761 (mm110) outliers start: 14 outliers final: 6 residues processed: 152 average time/residue: 1.1702 time to fit residues: 185.7053 Evaluate side-chains 152 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 143 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain G residue 343 LYS Chi-restraints excluded: chain J residue 340 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 52 optimal weight: 20.0000 chunk 21 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 47 optimal weight: 7.9990 chunk 13 optimal weight: 0.6980 chunk 66 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 E 327 ASN E 336 GLN F 307 GLN H 336 GLN I 327 ASN I 336 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.133274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.096039 restraints weight = 6868.583| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.96 r_work: 0.3353 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5750 Z= 0.247 Angle : 0.622 7.637 7690 Z= 0.306 Chirality : 0.049 0.148 870 Planarity : 0.002 0.016 970 Dihedral : 4.833 13.347 750 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 1.85 % Allowed : 24.00 % Favored : 74.15 % 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: -1.44 (0.29), residues: 720 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.09 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 330 PHE 0.013 0.001 PHE G 346 TYR 0.010 0.002 TYR G 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 159 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 147 time to evaluate : 0.705 Fit side-chains revert: symmetry clash REVERT: A 307 GLN cc_start: 0.8396 (mt0) cc_final: 0.7989 (mt0) REVERT: A 315 LEU cc_start: 0.9404 (OUTLIER) cc_final: 0.9174 (mp) REVERT: A 340 LYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7411 (mttp) REVERT: A 343 LYS cc_start: 0.8382 (mmmt) cc_final: 0.8059 (tmtm) REVERT: A 345 ASP cc_start: 0.8156 (t0) cc_final: 0.7552 (t70) REVERT: A 356 SER cc_start: 0.8716 (OUTLIER) cc_final: 0.8316 (m) REVERT: C 327 ASN cc_start: 0.8980 (t0) cc_final: 0.8684 (t0) REVERT: C 331 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8522 (mttp) REVERT: D 317 LYS cc_start: 0.8831 (pttt) cc_final: 0.8541 (pttt) REVERT: E 345 ASP cc_start: 0.7870 (t0) cc_final: 0.7526 (t70) REVERT: F 336 GLN cc_start: 0.7952 (mm-40) cc_final: 0.7423 (mm110) REVERT: F 375 LYS cc_start: 0.8696 (tttm) cc_final: 0.8050 (ttmm) REVERT: G 353 LYS cc_start: 0.8897 (mtpp) cc_final: 0.8475 (tttp) REVERT: H 307 GLN cc_start: 0.8222 (mt0) cc_final: 0.7919 (mt0) REVERT: H 324 SER cc_start: 0.8828 (t) cc_final: 0.8329 (m) REVERT: J 307 GLN cc_start: 0.8408 (tt0) cc_final: 0.8199 (tt0) REVERT: J 314 ASP cc_start: 0.8881 (t0) cc_final: 0.8459 (t0) REVERT: J 325 LEU cc_start: 0.9234 (tt) cc_final: 0.8936 (tp) REVERT: J 336 GLN cc_start: 0.8312 (mt0) cc_final: 0.7746 (mm110) outliers start: 12 outliers final: 7 residues processed: 151 average time/residue: 1.1764 time to fit residues: 185.6406 Evaluate side-chains 157 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 146 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain C residue 331 LYS 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 G residue 343 LYS 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 66 optimal weight: 9.9990 chunk 2 optimal weight: 0.0970 chunk 25 optimal weight: 20.0000 chunk 19 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 60 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 chunk 52 optimal weight: 30.0000 overall best weight: 4.6186 ------------------------------------------------------------------------------- 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 B 329 HIS E 327 ASN E 336 GLN F 307 GLN F 329 HIS I 327 ASN I 336 GLN ** I 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.129622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.092409 restraints weight = 6884.627| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.96 r_work: 0.3285 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.052 5750 Z= 0.511 Angle : 0.751 6.954 7690 Z= 0.370 Chirality : 0.051 0.165 870 Planarity : 0.003 0.016 970 Dihedral : 5.274 16.283 750 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 1.85 % Allowed : 24.15 % Favored : 74.00 % 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: -1.66 (0.28), residues: 720 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.26 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS I 362 PHE 0.023 0.002 PHE E 346 TYR 0.016 0.003 TYR I 310 ARG 0.006 0.001 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 169 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 157 time to evaluate : 0.678 Fit side-chains REVERT: A 307 GLN cc_start: 0.8361 (mt0) cc_final: 0.7986 (mt0) REVERT: A 315 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9104 (mp) REVERT: A 343 LYS cc_start: 0.8417 (mmmt) cc_final: 0.8194 (tmtt) REVERT: A 345 ASP cc_start: 0.8138 (t0) cc_final: 0.7634 (t70) REVERT: A 356 SER cc_start: 0.8768 (OUTLIER) cc_final: 0.8382 (m) REVERT: C 327 ASN cc_start: 0.9003 (t0) cc_final: 0.8690 (t0) REVERT: C 351 GLN cc_start: 0.8100 (tt0) cc_final: 0.7782 (tt0) REVERT: D 317 LYS cc_start: 0.8823 (pttt) cc_final: 0.8590 (pttt) REVERT: E 345 ASP cc_start: 0.7901 (t0) cc_final: 0.7530 (t70) REVERT: F 324 SER cc_start: 0.8607 (t) cc_final: 0.8289 (m) REVERT: F 336 GLN cc_start: 0.8139 (mm-40) cc_final: 0.7656 (mm110) REVERT: F 375 LYS cc_start: 0.8664 (tttm) cc_final: 0.8022 (ttmm) REVERT: H 307 GLN cc_start: 0.8319 (mt0) cc_final: 0.8023 (mt0) REVERT: H 324 SER cc_start: 0.8850 (t) cc_final: 0.8396 (m) REVERT: J 307 GLN cc_start: 0.8546 (tt0) cc_final: 0.8311 (tt0) REVERT: J 314 ASP cc_start: 0.8984 (t0) cc_final: 0.8466 (t0) REVERT: J 336 GLN cc_start: 0.8358 (mt0) cc_final: 0.7742 (mm-40) outliers start: 12 outliers final: 8 residues processed: 164 average time/residue: 1.0846 time to fit residues: 186.2591 Evaluate side-chains 164 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 154 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain B residue 371 ILE 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 G residue 352 SER Chi-restraints excluded: chain J residue 340 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 7.9990 chunk 25 optimal weight: 20.0000 chunk 38 optimal weight: 8.9990 chunk 16 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 39 optimal weight: 7.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN ** D 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 ASN E 336 GLN F 307 GLN H 327 ASN H 336 GLN I 327 ASN I 336 GLN ** I 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.130736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.093410 restraints weight = 6843.426| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.96 r_work: 0.3300 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3981 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= 0.391 Angle : 0.711 8.278 7690 Z= 0.351 Chirality : 0.050 0.157 870 Planarity : 0.002 0.016 970 Dihedral : 5.163 16.139 750 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 1.85 % Allowed : 24.15 % Favored : 74.00 % 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: -1.73 (0.28), residues: 720 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.31 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 362 PHE 0.018 0.002 PHE G 346 TYR 0.013 0.002 TYR I 310 ARG 0.005 0.001 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 161 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 149 time to evaluate : 0.708 Fit side-chains REVERT: A 307 GLN cc_start: 0.8347 (mt0) cc_final: 0.7980 (mt0) REVERT: A 340 LYS cc_start: 0.8068 (OUTLIER) cc_final: 0.7554 (mttp) REVERT: A 343 LYS cc_start: 0.8336 (mmmt) cc_final: 0.8121 (tmtt) REVERT: A 345 ASP cc_start: 0.8170 (t0) cc_final: 0.7660 (t70) REVERT: A 349 ARG cc_start: 0.8100 (ttm110) cc_final: 0.7851 (ttp80) REVERT: A 356 SER cc_start: 0.8775 (OUTLIER) cc_final: 0.8377 (m) REVERT: C 327 ASN cc_start: 0.8995 (t0) cc_final: 0.8670 (t0) REVERT: C 351 GLN cc_start: 0.8083 (tt0) cc_final: 0.7772 (tt0) REVERT: D 317 LYS cc_start: 0.8831 (pttt) cc_final: 0.8615 (pttt) REVERT: D 338 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7342 (mp0) REVERT: E 345 ASP cc_start: 0.7902 (t0) cc_final: 0.7526 (t70) REVERT: F 336 GLN cc_start: 0.8016 (mm-40) cc_final: 0.7335 (mp10) REVERT: F 375 LYS cc_start: 0.8664 (tttm) cc_final: 0.8017 (ttmm) REVERT: H 307 GLN cc_start: 0.8310 (mt0) cc_final: 0.8052 (mt0) REVERT: H 324 SER cc_start: 0.8826 (t) cc_final: 0.8356 (m) REVERT: H 336 GLN cc_start: 0.7947 (mt0) cc_final: 0.7170 (mp10) REVERT: J 307 GLN cc_start: 0.8558 (tt0) cc_final: 0.8319 (tt0) REVERT: J 314 ASP cc_start: 0.9027 (t0) cc_final: 0.8485 (t0) REVERT: J 336 GLN cc_start: 0.8358 (mt0) cc_final: 0.7762 (mm-40) outliers start: 12 outliers final: 6 residues processed: 157 average time/residue: 1.1021 time to fit residues: 181.2444 Evaluate side-chains 158 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 149 time to evaluate : 0.727 ------------------------------------------------------------------------------- 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 356 SER Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain E residue 324 SER 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 23 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN E 327 ASN E 336 GLN F 307 GLN I 327 ASN I 336 GLN I 362 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.133276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.096171 restraints weight = 6886.277| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.96 r_work: 0.3351 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5750 Z= 0.234 Angle : 0.656 9.041 7690 Z= 0.323 Chirality : 0.049 0.146 870 Planarity : 0.002 0.018 970 Dihedral : 4.833 13.874 750 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 1.08 % Allowed : 25.23 % Favored : 73.69 % 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: -1.65 (0.29), residues: 720 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.25 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 330 PHE 0.013 0.001 PHE G 346 TYR 0.009 0.002 TYR G 310 ARG 0.004 0.000 ARG G 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 153 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 146 time to evaluate : 0.676 Fit side-chains REVERT: A 307 GLN cc_start: 0.8446 (mt0) cc_final: 0.8108 (mt0) REVERT: A 340 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7639 (mttp) REVERT: A 345 ASP cc_start: 0.8200 (t0) cc_final: 0.7705 (t70) REVERT: C 327 ASN cc_start: 0.8979 (t0) cc_final: 0.8684 (t0) REVERT: D 317 LYS cc_start: 0.8860 (pttt) cc_final: 0.8577 (pttt) REVERT: D 338 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7429 (mp0) REVERT: E 307 GLN cc_start: 0.8449 (mt0) cc_final: 0.7954 (mt0) REVERT: E 345 ASP cc_start: 0.7870 (t0) cc_final: 0.7508 (t70) REVERT: F 324 SER cc_start: 0.8605 (t) cc_final: 0.8270 (m) REVERT: F 336 GLN cc_start: 0.8077 (mm-40) cc_final: 0.7403 (mp10) REVERT: F 375 LYS cc_start: 0.8740 (tttm) cc_final: 0.8122 (ttmm) REVERT: G 353 LYS cc_start: 0.8926 (mtpp) cc_final: 0.8495 (tttp) REVERT: H 307 GLN cc_start: 0.8259 (mt0) cc_final: 0.7938 (mt0) REVERT: H 324 SER cc_start: 0.8779 (t) cc_final: 0.8306 (m) REVERT: H 336 GLN cc_start: 0.7980 (mt0) cc_final: 0.7167 (mp10) REVERT: J 307 GLN cc_start: 0.8537 (tt0) cc_final: 0.8310 (tt0) REVERT: J 314 ASP cc_start: 0.8998 (t0) cc_final: 0.8538 (t0) REVERT: J 325 LEU cc_start: 0.9214 (tt) cc_final: 0.8977 (tp) REVERT: J 336 GLN cc_start: 0.8347 (mt0) cc_final: 0.7774 (mm110) outliers start: 7 outliers final: 4 residues processed: 149 average time/residue: 1.1640 time to fit residues: 181.2921 Evaluate side-chains 151 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 145 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain E residue 324 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 9 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 67 optimal weight: 9.9990 chunk 39 optimal weight: 20.0000 chunk 15 optimal weight: 10.0000 chunk 4 optimal weight: 0.3980 chunk 5 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN D 336 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 = 0.3929 r_free = 0.3929 target = 0.131487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.094106 restraints weight = 6925.820| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.99 r_work: 0.3310 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 5750 Z= 0.325 Angle : 0.697 9.430 7690 Z= 0.343 Chirality : 0.050 0.152 870 Planarity : 0.002 0.016 970 Dihedral : 4.973 15.082 750 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 1.23 % Allowed : 25.23 % Favored : 73.54 % 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: -1.73 (0.29), residues: 720 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.31 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 330 PHE 0.017 0.001 PHE G 346 TYR 0.012 0.002 TYR I 310 ARG 0.005 0.000 ARG G 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4736.30 seconds wall clock time: 85 minutes 34.35 seconds (5134.35 seconds total)