Starting phenix.real_space_refine on Thu Jun 5 07:55:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9czl_46420/06_2025/9czl_46420_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9czl_46420/06_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_46420/06_2025/9czl_46420.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9czl_46420/06_2025/9czl_46420.map" model { file = "/net/cci-nas-00/data/ceres_data/9czl_46420/06_2025/9czl_46420_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9czl_46420/06_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-5710/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: 3.92, per 1000 atoms: 0.69 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: 1.16 Conformation dependent library (CDL) restraints added in 627.6 milliseconds 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1300 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 56.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 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: 1.33 Time building geometry restraints manager: 1.41 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: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 16.270 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.023 0.111 5750 Z= 1.175 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 Details of bonding type rmsd hydrogen bonds : bond 0.06817 ( 120) hydrogen bonds : angle 9.23491 ( 360) covalent geometry : bond 0.02259 ( 5750) covalent geometry : angle 1.94679 ( 7690) *********************** 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 : 0.722 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: 1.4164 time to fit residues: 352.9174 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 : 0.678 ------------------------------------------------------------------------------- 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 = 38)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.101024 restraints weight = 6649.101| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.88 r_work: 0.3443 rms_B_bonded: 1.94 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= 0.144 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 Details of bonding type rmsd hydrogen bonds : bond 0.02743 ( 120) hydrogen bonds : angle 5.72316 ( 360) covalent geometry : bond 0.00338 ( 5750) covalent geometry : angle 0.66947 ( 7690) *********************** 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 : 0.641 Fit side-chains REVERT: A 307 GLN cc_start: 0.8510 (mt0) cc_final: 0.8119 (mt0) REVERT: A 345 ASP cc_start: 0.8207 (t0) cc_final: 0.7701 (t70) REVERT: C 327 ASN cc_start: 0.9031 (t0) cc_final: 0.8705 (t0) REVERT: D 307 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.7877 (tp40) REVERT: E 356 SER cc_start: 0.9043 (t) cc_final: 0.8723 (m) REVERT: F 336 GLN cc_start: 0.7956 (mm-40) cc_final: 0.7542 (mm110) REVERT: H 340 LYS cc_start: 0.7867 (ptpp) cc_final: 0.7446 (tmtt) REVERT: J 314 ASP cc_start: 0.8921 (t0) cc_final: 0.8583 (t0) REVERT: J 336 GLN cc_start: 0.8030 (mt0) cc_final: 0.7523 (mm-40) outliers start: 17 outliers final: 3 residues processed: 140 average time/residue: 0.9847 time to fit residues: 145.2014 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 : 0.686 ------------------------------------------------------------------------------- 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: 0.9980 chunk 61 optimal weight: 0.9980 chunk 23 optimal weight: 8.9990 chunk 66 optimal weight: 8.9990 chunk 45 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 chunk 55 optimal weight: 8.9990 chunk 10 optimal weight: 9.9990 chunk 5 optimal weight: 8.9990 overall best weight: 3.7986 ------------------------------------------------------------------------------- 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 J 359 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.131202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.093640 restraints weight = 6882.545| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.98 r_work: 0.3302 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 5750 Z= 0.276 Angle : 0.727 7.612 7690 Z= 0.359 Chirality : 0.051 0.159 870 Planarity : 0.003 0.023 970 Dihedral : 5.308 14.386 750 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 3.23 % Allowed : 20.77 % 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: -1.02 (0.29), residues: 720 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.76 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS I 362 PHE 0.021 0.002 PHE G 346 TYR 0.016 0.003 TYR I 310 ARG 0.004 0.001 ARG G 349 Details of bonding type rmsd hydrogen bonds : bond 0.02722 ( 120) hydrogen bonds : angle 5.36540 ( 360) covalent geometry : bond 0.00666 ( 5750) covalent geometry : angle 0.72694 ( 7690) *********************** 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 169 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 0.687 Fit side-chains REVERT: A 340 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.7487 (mttp) REVERT: A 345 ASP cc_start: 0.8074 (t0) cc_final: 0.7458 (t70) REVERT: A 375 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8474 (tttm) REVERT: B 347 LYS cc_start: 0.6543 (mttp) cc_final: 0.5771 (mmpt) REVERT: C 327 ASN cc_start: 0.9018 (t0) cc_final: 0.8702 (t0) REVERT: C 342 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7502 (mm-30) REVERT: D 340 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.7739 (tptt) REVERT: E 315 LEU cc_start: 0.9249 (mp) cc_final: 0.8944 (mt) REVERT: E 345 ASP cc_start: 0.7903 (t0) cc_final: 0.7605 (t70) REVERT: E 356 SER cc_start: 0.8705 (t) cc_final: 0.8441 (m) REVERT: F 324 SER cc_start: 0.8547 (t) cc_final: 0.8249 (m) REVERT: F 336 GLN cc_start: 0.7977 (mm-40) cc_final: 0.7618 (mm110) REVERT: F 338 GLU cc_start: 0.7660 (pp20) cc_final: 0.7269 (pp20) REVERT: F 372 GLU cc_start: 0.8635 (tt0) cc_final: 0.8423 (tt0) REVERT: H 307 GLN cc_start: 0.8339 (mt0) cc_final: 0.8029 (mt0) REVERT: H 314 ASP cc_start: 0.9063 (t0) cc_final: 0.8772 (t0) REVERT: H 324 SER cc_start: 0.8761 (t) cc_final: 0.8366 (m) REVERT: J 314 ASP cc_start: 0.8992 (t0) cc_final: 0.8496 (t0) REVERT: J 336 GLN cc_start: 0.8210 (mt0) cc_final: 0.7685 (mm110) outliers start: 21 outliers final: 5 residues processed: 160 average time/residue: 1.4402 time to fit residues: 240.5873 Evaluate side-chains 149 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 141 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 324 SER Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 340 LYS Chi-restraints excluded: chain E residue 324 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 10 optimal weight: 8.9990 chunk 15 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 13 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN C 336 GLN D 359 ASN E 327 ASN E 336 GLN F 307 GLN I 327 ASN I 368 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.135624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.098358 restraints weight = 6904.864| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.97 r_work: 0.3401 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5750 Z= 0.114 Angle : 0.567 5.077 7690 Z= 0.281 Chirality : 0.049 0.142 870 Planarity : 0.002 0.016 970 Dihedral : 4.807 13.210 750 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.85 % Allowed : 22.62 % Favored : 75.54 % 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: -1.07 (0.29), residues: 720 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.80 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 330 PHE 0.011 0.001 PHE G 346 TYR 0.008 0.002 TYR G 310 ARG 0.003 0.000 ARG E 349 Details of bonding type rmsd hydrogen bonds : bond 0.02006 ( 120) hydrogen bonds : angle 4.77066 ( 360) covalent geometry : bond 0.00263 ( 5750) covalent geometry : angle 0.56725 ( 7690) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 150 time to evaluate : 0.724 Fit side-chains REVERT: A 307 GLN cc_start: 0.8447 (mt0) cc_final: 0.8120 (mt0) REVERT: A 340 LYS cc_start: 0.7931 (OUTLIER) cc_final: 0.7453 (mttp) REVERT: A 343 LYS cc_start: 0.8405 (mmmt) cc_final: 0.8120 (tmtm) REVERT: A 345 ASP cc_start: 0.8107 (t0) cc_final: 0.7554 (t70) REVERT: A 353 LYS cc_start: 0.8948 (mtpp) cc_final: 0.8747 (ttpt) REVERT: B 347 LYS cc_start: 0.6430 (mttp) cc_final: 0.5705 (mmpt) REVERT: C 327 ASN cc_start: 0.8939 (t0) cc_final: 0.8656 (t0) REVERT: D 307 GLN cc_start: 0.8343 (tt0) cc_final: 0.8008 (tt0) REVERT: E 315 LEU cc_start: 0.9246 (mp) cc_final: 0.8926 (mt) REVERT: E 345 ASP cc_start: 0.7840 (t0) cc_final: 0.7469 (t70) REVERT: E 356 SER cc_start: 0.8745 (OUTLIER) cc_final: 0.8437 (m) REVERT: F 316 SER cc_start: 0.9372 (p) cc_final: 0.9108 (p) REVERT: F 324 SER cc_start: 0.8662 (t) cc_final: 0.8309 (m) REVERT: F 336 GLN cc_start: 0.7979 (mm-40) cc_final: 0.7513 (mm110) REVERT: F 372 GLU cc_start: 0.8615 (tt0) cc_final: 0.8404 (tt0) REVERT: H 307 GLN cc_start: 0.8244 (mt0) cc_final: 0.7923 (mt0) REVERT: H 314 ASP cc_start: 0.9061 (t0) cc_final: 0.8759 (t0) REVERT: H 324 SER cc_start: 0.8596 (t) cc_final: 0.8208 (m) REVERT: H 338 GLU cc_start: 0.7527 (pp20) cc_final: 0.7236 (pp20) REVERT: J 336 GLN cc_start: 0.8228 (mt0) cc_final: 0.7760 (mm110) outliers start: 12 outliers final: 2 residues processed: 155 average time/residue: 1.0546 time to fit residues: 171.4902 Evaluate side-chains 145 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 141 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 356 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 2 optimal weight: 7.9990 chunk 5 optimal weight: 0.9990 chunk 28 optimal weight: 8.9990 chunk 36 optimal weight: 9.9990 chunk 62 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 23 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 E 327 ASN H 336 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 = 0.132516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.094884 restraints weight = 6813.022| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.98 r_work: 0.3327 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 5750 Z= 0.197 Angle : 0.632 5.738 7690 Z= 0.310 Chirality : 0.049 0.148 870 Planarity : 0.002 0.016 970 Dihedral : 4.954 13.373 750 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.46 % Allowed : 23.23 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.29), residues: 720 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.96 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 330 PHE 0.016 0.001 PHE G 346 TYR 0.012 0.002 TYR I 310 ARG 0.003 0.000 ARG E 349 Details of bonding type rmsd hydrogen bonds : bond 0.02334 ( 120) hydrogen bonds : angle 4.75259 ( 360) covalent geometry : bond 0.00472 ( 5750) covalent geometry : angle 0.63222 ( 7690) *********************** 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 166 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 150 time to evaluate : 0.632 Fit side-chains revert: symmetry clash REVERT: A 340 LYS cc_start: 0.7897 (OUTLIER) cc_final: 0.7403 (mttp) REVERT: A 343 LYS cc_start: 0.8390 (mmmt) cc_final: 0.8063 (tmtm) REVERT: A 345 ASP cc_start: 0.8145 (t0) cc_final: 0.7522 (t70) REVERT: A 375 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8495 (tttm) REVERT: B 347 LYS cc_start: 0.6452 (mttp) cc_final: 0.5737 (mmpt) REVERT: C 327 ASN cc_start: 0.8988 (t0) cc_final: 0.8706 (t0) REVERT: C 349 ARG cc_start: 0.7755 (ttm170) cc_final: 0.7518 (ttp-170) REVERT: D 307 GLN cc_start: 0.8302 (tt0) cc_final: 0.7970 (tt0) REVERT: D 317 LYS cc_start: 0.8816 (pttt) cc_final: 0.8600 (pttt) REVERT: E 315 LEU cc_start: 0.9236 (mp) cc_final: 0.8893 (mt) REVERT: E 345 ASP cc_start: 0.7868 (t0) cc_final: 0.7536 (t70) REVERT: E 356 SER cc_start: 0.8685 (OUTLIER) cc_final: 0.8424 (m) REVERT: F 324 SER cc_start: 0.8635 (t) cc_final: 0.8291 (m) REVERT: F 336 GLN cc_start: 0.8061 (mm-40) cc_final: 0.7710 (mm110) REVERT: F 372 GLU cc_start: 0.8663 (tt0) cc_final: 0.8444 (tt0) REVERT: F 375 LYS cc_start: 0.8638 (tttm) cc_final: 0.8021 (ttmm) REVERT: G 353 LYS cc_start: 0.8906 (mtpp) cc_final: 0.8637 (ttpt) REVERT: H 307 GLN cc_start: 0.8267 (mt0) cc_final: 0.7977 (mt0) REVERT: H 324 SER cc_start: 0.8706 (t) cc_final: 0.8340 (m) REVERT: H 336 GLN cc_start: 0.7866 (mt0) cc_final: 0.7634 (mt0) REVERT: H 338 GLU cc_start: 0.7616 (pp20) cc_final: 0.7252 (pp20) REVERT: J 336 GLN cc_start: 0.8282 (mt0) cc_final: 0.7638 (mm110) outliers start: 16 outliers final: 8 residues processed: 157 average time/residue: 1.1081 time to fit residues: 182.1169 Evaluate side-chains 160 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 149 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain 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 E residue 356 SER Chi-restraints excluded: chain G residue 343 LYS Chi-restraints excluded: chain H residue 325 LEU 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: 2.9990 chunk 8 optimal weight: 1.9990 chunk 1 optimal weight: 0.4980 chunk 19 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 chunk 31 optimal weight: 8.9990 chunk 64 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 38 optimal weight: 20.0000 chunk 44 optimal weight: 2.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- 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 F 307 GLN F 329 HIS I 327 ASN I 336 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.132408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.094988 restraints weight = 6779.434| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.98 r_work: 0.3335 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 5750 Z= 0.192 Angle : 0.630 5.366 7690 Z= 0.310 Chirality : 0.049 0.147 870 Planarity : 0.002 0.016 970 Dihedral : 4.975 14.151 750 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 2.62 % Allowed : 23.08 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.29), residues: 720 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.06 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 330 PHE 0.016 0.001 PHE G 346 TYR 0.011 0.002 TYR I 310 ARG 0.005 0.000 ARG G 349 Details of bonding type rmsd hydrogen bonds : bond 0.02302 ( 120) hydrogen bonds : angle 4.65073 ( 360) covalent geometry : bond 0.00460 ( 5750) covalent geometry : angle 0.63003 ( 7690) *********************** 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 161 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 0.724 Fit side-chains revert: symmetry clash REVERT: A 307 GLN cc_start: 0.8465 (mt0) cc_final: 0.8099 (mt0) REVERT: A 340 LYS cc_start: 0.7910 (OUTLIER) cc_final: 0.7403 (mttp) REVERT: A 343 LYS cc_start: 0.8323 (mmmt) cc_final: 0.7981 (tmtm) REVERT: A 345 ASP cc_start: 0.8119 (t0) cc_final: 0.7504 (t70) REVERT: A 375 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.8526 (tttm) REVERT: C 327 ASN cc_start: 0.8977 (t0) cc_final: 0.8678 (t0) REVERT: C 349 ARG cc_start: 0.7740 (ttm170) cc_final: 0.7519 (ttp-170) REVERT: D 317 LYS cc_start: 0.8797 (pttt) cc_final: 0.8593 (pttt) REVERT: E 345 ASP cc_start: 0.7867 (t0) cc_final: 0.7510 (t70) REVERT: E 356 SER cc_start: 0.8658 (OUTLIER) cc_final: 0.8413 (m) REVERT: F 316 SER cc_start: 0.9409 (p) cc_final: 0.9120 (p) REVERT: F 336 GLN cc_start: 0.8156 (mm-40) cc_final: 0.7729 (mm110) REVERT: F 375 LYS cc_start: 0.8638 (tttm) cc_final: 0.7983 (ttmm) REVERT: H 307 GLN cc_start: 0.8241 (mt0) cc_final: 0.7941 (mt0) REVERT: H 324 SER cc_start: 0.8699 (t) cc_final: 0.8323 (m) REVERT: H 336 GLN cc_start: 0.7898 (mt0) cc_final: 0.7662 (mt0) REVERT: H 338 GLU cc_start: 0.7772 (pp20) cc_final: 0.7383 (pp20) REVERT: H 340 LYS cc_start: 0.7410 (tmtt) cc_final: 0.7169 (tmtt) REVERT: J 307 GLN cc_start: 0.8471 (tt0) cc_final: 0.8226 (tt0) REVERT: J 336 GLN cc_start: 0.8297 (mt0) cc_final: 0.7704 (mm110) outliers start: 17 outliers final: 9 residues processed: 152 average time/residue: 1.0951 time to fit residues: 174.2619 Evaluate side-chains 155 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 143 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain 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 E residue 356 SER Chi-restraints excluded: chain G residue 343 LYS Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain H residue 325 LEU 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: 30.0000 chunk 21 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 43 optimal weight: 9.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.132958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.095450 restraints weight = 6860.215| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.98 r_work: 0.3351 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3966 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= 0.162 Angle : 0.604 5.559 7690 Z= 0.298 Chirality : 0.049 0.143 870 Planarity : 0.002 0.017 970 Dihedral : 4.850 13.475 750 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 2.15 % Allowed : 24.00 % Favored : 73.85 % 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: -1.45 (0.29), residues: 720 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.10 (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 0.005 0.000 ARG G 349 Details of bonding type rmsd hydrogen bonds : bond 0.02263 ( 120) hydrogen bonds : angle 4.53943 ( 360) covalent geometry : bond 0.00386 ( 5750) covalent geometry : angle 0.60392 ( 7690) *********************** 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 162 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 148 time to evaluate : 0.693 Fit side-chains REVERT: A 307 GLN cc_start: 0.8451 (mt0) cc_final: 0.8084 (mt0) REVERT: A 340 LYS cc_start: 0.7957 (OUTLIER) cc_final: 0.7444 (mttp) REVERT: A 343 LYS cc_start: 0.8303 (mmmt) cc_final: 0.7965 (tmtm) REVERT: A 345 ASP cc_start: 0.8167 (t0) cc_final: 0.7534 (t70) REVERT: A 356 SER cc_start: 0.8697 (OUTLIER) cc_final: 0.8281 (m) REVERT: A 375 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8539 (tttm) REVERT: C 327 ASN cc_start: 0.8969 (t0) cc_final: 0.8674 (t0) REVERT: C 349 ARG cc_start: 0.7735 (ttm170) cc_final: 0.7529 (ttp-170) REVERT: D 317 LYS cc_start: 0.8808 (pttt) cc_final: 0.8512 (pttt) REVERT: E 345 ASP cc_start: 0.7881 (t0) cc_final: 0.7522 (t70) REVERT: E 356 SER cc_start: 0.8652 (OUTLIER) cc_final: 0.8447 (m) REVERT: F 336 GLN cc_start: 0.8124 (mm-40) cc_final: 0.7626 (mm110) REVERT: F 375 LYS cc_start: 0.8648 (tttm) cc_final: 0.7994 (ttmm) REVERT: H 307 GLN cc_start: 0.8220 (mt0) cc_final: 0.7912 (mt0) REVERT: H 314 ASP cc_start: 0.8833 (t0) cc_final: 0.8632 (t0) REVERT: H 324 SER cc_start: 0.8712 (t) cc_final: 0.8336 (m) REVERT: H 336 GLN cc_start: 0.7841 (mt0) cc_final: 0.7625 (mt0) REVERT: H 338 GLU cc_start: 0.7648 (pp20) cc_final: 0.7325 (pp20) REVERT: H 340 LYS cc_start: 0.7371 (tmtt) cc_final: 0.7090 (tmtt) REVERT: J 307 GLN cc_start: 0.8473 (tt0) cc_final: 0.8236 (tt0) REVERT: J 314 ASP cc_start: 0.9096 (t0) cc_final: 0.8574 (t0) REVERT: J 336 GLN cc_start: 0.8307 (mt0) cc_final: 0.7729 (mm110) outliers start: 14 outliers final: 5 residues processed: 154 average time/residue: 1.0185 time to fit residues: 164.5476 Evaluate side-chains 153 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 144 time to evaluate : 0.627 ------------------------------------------------------------------------------- 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 A residue 375 LYS Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain G residue 352 SER 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: 10.0000 chunk 2 optimal weight: 6.9990 chunk 25 optimal weight: 20.0000 chunk 19 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 60 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 52 optimal weight: 20.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 D 329 HIS D 359 ASN E 327 ASN E 336 GLN F 307 GLN I 327 ASN I 336 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.130965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.093540 restraints weight = 6858.822| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.97 r_work: 0.3310 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 5750 Z= 0.234 Angle : 0.672 6.121 7690 Z= 0.331 Chirality : 0.050 0.153 870 Planarity : 0.002 0.016 970 Dihedral : 5.053 15.024 750 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 2.31 % Allowed : 23.85 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.29), residues: 720 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.20 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 330 PHE 0.018 0.002 PHE G 346 TYR 0.013 0.002 TYR I 310 ARG 0.005 0.001 ARG G 349 Details of bonding type rmsd hydrogen bonds : bond 0.02493 ( 120) hydrogen bonds : angle 4.66117 ( 360) covalent geometry : bond 0.00564 ( 5750) covalent geometry : angle 0.67163 ( 7690) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1440 Ramachandran restraints generated. 720 Oldfield, 0 Emsley, 720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 148 time to evaluate : 0.653 Fit side-chains REVERT: A 307 GLN cc_start: 0.8384 (mt0) cc_final: 0.8011 (mt0) REVERT: A 315 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9099 (mp) REVERT: A 340 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7565 (mttp) REVERT: A 343 LYS cc_start: 0.8267 (mmmt) cc_final: 0.7904 (tmtm) REVERT: A 345 ASP cc_start: 0.8124 (t0) cc_final: 0.7536 (t70) REVERT: A 356 SER cc_start: 0.8729 (OUTLIER) cc_final: 0.8323 (m) REVERT: A 375 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8542 (tttm) REVERT: C 327 ASN cc_start: 0.8995 (t0) cc_final: 0.8684 (t0) REVERT: C 349 ARG cc_start: 0.7650 (ttm170) cc_final: 0.7440 (ttp-170) REVERT: C 351 GLN cc_start: 0.8071 (tt0) cc_final: 0.7758 (tt0) REVERT: D 317 LYS cc_start: 0.8821 (pttt) cc_final: 0.8609 (pttt) REVERT: D 338 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7306 (mp0) REVERT: E 345 ASP cc_start: 0.7868 (t0) cc_final: 0.7506 (t70) REVERT: E 356 SER cc_start: 0.8655 (OUTLIER) cc_final: 0.8429 (m) REVERT: F 336 GLN cc_start: 0.8075 (mm-40) cc_final: 0.7562 (mm110) REVERT: F 375 LYS cc_start: 0.8654 (tttm) cc_final: 0.8012 (ttmm) REVERT: H 307 GLN cc_start: 0.8252 (mt0) cc_final: 0.7977 (mt0) REVERT: H 324 SER cc_start: 0.8735 (t) cc_final: 0.8334 (m) REVERT: H 336 GLN cc_start: 0.7879 (mt0) cc_final: 0.7647 (mt0) REVERT: H 338 GLU cc_start: 0.7539 (pp20) cc_final: 0.7197 (pp20) REVERT: J 307 GLN cc_start: 0.8533 (tt0) cc_final: 0.8301 (tt0) REVERT: J 314 ASP cc_start: 0.9117 (t0) cc_final: 0.8515 (t0) REVERT: J 336 GLN cc_start: 0.8303 (mt0) cc_final: 0.7701 (mm110) outliers start: 15 outliers final: 8 residues processed: 158 average time/residue: 1.1492 time to fit residues: 189.7636 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 : 0.704 ------------------------------------------------------------------------------- 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 356 SER Chi-restraints excluded: chain A residue 375 LYS 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 E residue 356 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: 10.0000 chunk 25 optimal weight: 20.0000 chunk 38 optimal weight: 20.0000 chunk 16 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- 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 ** I 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.130045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.092675 restraints weight = 6857.763| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.93 r_work: 0.3287 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 5750 Z= 0.284 Angle : 0.724 8.448 7690 Z= 0.357 Chirality : 0.051 0.163 870 Planarity : 0.003 0.019 970 Dihedral : 5.194 16.017 750 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 2.15 % Allowed : 24.46 % Favored : 73.38 % 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: -1.75 (0.28), residues: 720 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.33 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 362 PHE 0.020 0.002 PHE E 346 TYR 0.015 0.003 TYR I 310 ARG 0.005 0.001 ARG G 349 Details of bonding type rmsd hydrogen bonds : bond 0.02778 ( 120) hydrogen bonds : angle 4.81739 ( 360) covalent geometry : bond 0.00686 ( 5750) covalent geometry : angle 0.72356 ( 7690) *********************** 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 167 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 153 time to evaluate : 1.279 Fit side-chains REVERT: A 307 GLN cc_start: 0.8386 (mt0) cc_final: 0.8020 (mt0) REVERT: A 340 LYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7550 (mttp) REVERT: A 343 LYS cc_start: 0.8307 (mmmt) cc_final: 0.8080 (tmtt) REVERT: A 345 ASP cc_start: 0.8174 (t0) cc_final: 0.7688 (t70) REVERT: A 356 SER cc_start: 0.8859 (OUTLIER) cc_final: 0.8474 (m) REVERT: C 327 ASN cc_start: 0.9030 (t0) cc_final: 0.8730 (t0) REVERT: C 349 ARG cc_start: 0.7647 (ttm170) cc_final: 0.7424 (ttp-170) REVERT: C 351 GLN cc_start: 0.8121 (tt0) cc_final: 0.7784 (tt0) REVERT: D 317 LYS cc_start: 0.8851 (pttt) cc_final: 0.8631 (pttt) REVERT: D 338 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7330 (mp0) REVERT: E 345 ASP cc_start: 0.7929 (t0) cc_final: 0.7550 (t70) REVERT: E 356 SER cc_start: 0.8628 (OUTLIER) cc_final: 0.8395 (m) REVERT: F 324 SER cc_start: 0.8624 (t) cc_final: 0.8271 (m) REVERT: F 336 GLN cc_start: 0.8130 (mm-40) cc_final: 0.7618 (mm110) REVERT: F 375 LYS cc_start: 0.8691 (tttm) cc_final: 0.8055 (ttmm) REVERT: H 307 GLN cc_start: 0.8320 (mt0) cc_final: 0.8020 (mt0) REVERT: H 324 SER cc_start: 0.8779 (t) cc_final: 0.8338 (m) REVERT: H 338 GLU cc_start: 0.7577 (pp20) cc_final: 0.7202 (pp20) REVERT: J 307 GLN cc_start: 0.8556 (tt0) cc_final: 0.8328 (tt0) REVERT: J 314 ASP cc_start: 0.9091 (t0) cc_final: 0.8499 (t0) REVERT: J 336 GLN cc_start: 0.8355 (mt0) cc_final: 0.8041 (pt0) outliers start: 14 outliers final: 7 residues processed: 161 average time/residue: 1.2660 time to fit residues: 213.8185 Evaluate side-chains 164 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 153 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain 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 E residue 356 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: 0.9990 chunk 47 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 36 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- 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 E 327 ASN E 336 GLN F 307 GLN H 327 ASN I 327 ASN I 336 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.134886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.097638 restraints weight = 6873.550| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.96 r_work: 0.3394 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5750 Z= 0.123 Angle : 0.624 9.075 7690 Z= 0.307 Chirality : 0.049 0.142 870 Planarity : 0.002 0.016 970 Dihedral : 4.710 13.635 750 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 1.54 % Allowed : 25.08 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.29), residues: 720 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.22 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS G 330 PHE 0.012 0.001 PHE G 346 TYR 0.008 0.002 TYR G 310 ARG 0.004 0.000 ARG G 349 Details of bonding type rmsd hydrogen bonds : bond 0.02206 ( 120) hydrogen bonds : angle 4.45527 ( 360) covalent geometry : bond 0.00294 ( 5750) covalent geometry : angle 0.62406 ( 7690) ********************** 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 157 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 147 time to evaluate : 0.777 Fit side-chains REVERT: A 307 GLN cc_start: 0.8477 (mt0) cc_final: 0.8085 (mt0) REVERT: A 340 LYS cc_start: 0.8102 (OUTLIER) cc_final: 0.7590 (mttp) REVERT: A 345 ASP cc_start: 0.8206 (t0) cc_final: 0.7702 (t70) REVERT: B 344 LEU cc_start: 0.7446 (mp) cc_final: 0.7143 (mt) REVERT: C 327 ASN cc_start: 0.8991 (t0) cc_final: 0.8694 (t0) REVERT: D 317 LYS cc_start: 0.8897 (pttt) cc_final: 0.8627 (pttt) REVERT: E 345 ASP cc_start: 0.7855 (t0) cc_final: 0.7469 (t70) REVERT: F 324 SER cc_start: 0.8619 (t) cc_final: 0.8310 (m) REVERT: F 336 GLN cc_start: 0.8061 (mm-40) cc_final: 0.7402 (mp10) REVERT: F 375 LYS cc_start: 0.8753 (tttm) cc_final: 0.8148 (ttmm) REVERT: H 307 GLN cc_start: 0.8257 (mt0) cc_final: 0.7985 (mt0) REVERT: H 324 SER cc_start: 0.8805 (t) cc_final: 0.8397 (m) REVERT: H 336 GLN cc_start: 0.7915 (mt0) cc_final: 0.7105 (mp10) REVERT: H 338 GLU cc_start: 0.7686 (pp20) cc_final: 0.7298 (pp20) REVERT: J 307 GLN cc_start: 0.8480 (tt0) cc_final: 0.8251 (tt0) REVERT: J 314 ASP cc_start: 0.8964 (t0) cc_final: 0.8524 (t0) REVERT: J 336 GLN cc_start: 0.8308 (mt0) cc_final: 0.7926 (pt0) outliers start: 10 outliers final: 5 residues processed: 150 average time/residue: 1.3933 time to fit residues: 219.1402 Evaluate side-chains 147 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 141 time to evaluate : 0.660 ------------------------------------------------------------------------------- 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 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 9 optimal weight: 0.6980 chunk 6 optimal weight: 7.9990 chunk 67 optimal weight: 6.9990 chunk 39 optimal weight: 20.0000 chunk 15 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 2 optimal weight: 0.0970 chunk 46 optimal weight: 10.0000 overall best weight: 2.7382 ------------------------------------------------------------------------------- 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 ** I 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.131842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.094358 restraints weight = 6930.207| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.00 r_work: 0.3317 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 5750 Z= 0.209 Angle : 0.683 8.597 7690 Z= 0.334 Chirality : 0.050 0.152 870 Planarity : 0.002 0.018 970 Dihedral : 4.932 14.934 750 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 1.08 % Allowed : 25.85 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.29), residues: 720 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.30 (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 Details of bonding type rmsd hydrogen bonds : bond 0.02555 ( 120) hydrogen bonds : angle 4.57655 ( 360) covalent geometry : bond 0.00504 ( 5750) covalent geometry : angle 0.68271 ( 7690) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5192.89 seconds wall clock time: 93 minutes 50.30 seconds (5630.30 seconds total)