Starting phenix.real_space_refine on Wed Sep 17 05:54:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9czl_46420/09_2025/9czl_46420_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9czl_46420/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9czl_46420/09_2025/9czl_46420_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9czl_46420/09_2025/9czl_46420_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9czl_46420/09_2025/9czl_46420.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9czl_46420/09_2025/9czl_46420.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.44, per 1000 atoms: 0.25 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: 0.43 Conformation dependent library (CDL) restraints added in 202.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.16 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: 0.74 Time building geometry restraints manager: 0.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1228 1.32 - 1.43: 1079 1.43 - 1.54: 3266 1.54 - 1.65: 167 1.65 - 1.76: 10 Bond restraints: 5750 Sorted by residual: bond pdb=" CB HIS C 374 " pdb=" CG HIS C 374 " ideal model delta sigma weight residual 1.497 1.407 0.090 1.40e-02 5.10e+03 4.14e+01 bond pdb=" CB HIS G 374 " pdb=" CG HIS G 374 " ideal model delta sigma weight residual 1.497 1.407 0.090 1.40e-02 5.10e+03 4.13e+01 bond pdb=" CB HIS A 374 " pdb=" CG HIS A 374 " ideal model delta sigma weight residual 1.497 1.408 0.089 1.40e-02 5.10e+03 4.07e+01 bond pdb=" CB HIS I 374 " pdb=" CG HIS I 374 " ideal model delta sigma weight residual 1.497 1.408 0.089 1.40e-02 5.10e+03 4.03e+01 bond pdb=" CB HIS E 374 " pdb=" CG HIS E 374 " ideal model delta sigma weight residual 1.497 1.408 0.089 1.40e-02 5.10e+03 4.00e+01 ... (remaining 5745 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 6218 2.25 - 4.49: 1161 4.49 - 6.74: 251 6.74 - 8.99: 50 8.99 - 11.23: 10 Bond angle restraints: 7690 Sorted by residual: angle pdb=" CA ASP G 358 " pdb=" CB ASP G 358 " pdb=" CG ASP G 358 " ideal model delta sigma weight residual 112.60 119.23 -6.63 1.00e+00 1.00e+00 4.40e+01 angle pdb=" CA ASP A 358 " pdb=" CB ASP A 358 " pdb=" CG ASP A 358 " ideal model delta sigma weight residual 112.60 119.21 -6.61 1.00e+00 1.00e+00 4.37e+01 angle pdb=" CA ASP C 358 " pdb=" CB ASP C 358 " pdb=" CG ASP C 358 " ideal model delta sigma weight residual 112.60 119.21 -6.61 1.00e+00 1.00e+00 4.36e+01 angle pdb=" CA ASP E 358 " pdb=" CB ASP E 358 " pdb=" CG ASP E 358 " ideal model delta sigma weight residual 112.60 119.19 -6.59 1.00e+00 1.00e+00 4.35e+01 angle pdb=" CA ASP I 358 " pdb=" CB ASP I 358 " pdb=" CG ASP I 358 " ideal model delta sigma weight residual 112.60 119.19 -6.59 1.00e+00 1.00e+00 4.34e+01 ... (remaining 7685 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.40: 3345 12.40 - 24.79: 95 24.79 - 37.19: 35 37.19 - 49.58: 10 49.58 - 61.98: 25 Dihedral angle restraints: 3510 sinusoidal: 1470 harmonic: 2040 Sorted by residual: dihedral pdb=" C ASP E 358 " pdb=" N ASP E 358 " pdb=" CA ASP E 358 " pdb=" CB ASP E 358 " ideal model delta harmonic sigma weight residual -122.60 -130.24 7.64 0 2.50e+00 1.60e-01 9.34e+00 dihedral pdb=" C ASP I 358 " pdb=" N ASP I 358 " pdb=" CA ASP I 358 " pdb=" CB ASP I 358 " ideal model delta harmonic sigma weight residual -122.60 -130.21 7.61 0 2.50e+00 1.60e-01 9.27e+00 dihedral pdb=" C ASP A 358 " pdb=" N ASP A 358 " pdb=" CA ASP A 358 " pdb=" CB ASP A 358 " ideal model delta harmonic sigma weight residual -122.60 -130.19 7.59 0 2.50e+00 1.60e-01 9.22e+00 ... (remaining 3507 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 490 0.071 - 0.142: 296 0.142 - 0.213: 68 0.213 - 0.284: 11 0.284 - 0.355: 5 Chirality restraints: 870 Sorted by residual: chirality pdb=" CA ASP E 358 " pdb=" N ASP E 358 " pdb=" C ASP E 358 " pdb=" CB ASP E 358 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.36 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" CA ASP A 358 " pdb=" N ASP A 358 " pdb=" C ASP A 358 " pdb=" CB ASP A 358 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" CA ASP I 358 " pdb=" N ASP I 358 " pdb=" C ASP I 358 " pdb=" CB ASP I 358 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.11e+00 ... (remaining 867 not shown) Planarity restraints: 970 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO D 364 " 0.017 2.00e-02 2.50e+03 3.40e-02 1.16e+01 pdb=" C PRO D 364 " -0.059 2.00e-02 2.50e+03 pdb=" O PRO D 364 " 0.022 2.00e-02 2.50e+03 pdb=" N GLY D 365 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO H 364 " 0.017 2.00e-02 2.50e+03 3.37e-02 1.14e+01 pdb=" C PRO H 364 " -0.058 2.00e-02 2.50e+03 pdb=" O PRO H 364 " 0.022 2.00e-02 2.50e+03 pdb=" N GLY H 365 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO F 364 " 0.017 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C PRO F 364 " -0.058 2.00e-02 2.50e+03 pdb=" O PRO F 364 " 0.022 2.00e-02 2.50e+03 pdb=" N GLY F 365 " 0.020 2.00e-02 2.50e+03 ... (remaining 967 not shown) Histogram of nonbonded interaction distances: 2.46 - 2.95: 2744 2.95 - 3.44: 4522 3.44 - 3.93: 9333 3.93 - 4.41: 10577 4.41 - 4.90: 20013 Nonbonded interactions: 47189 Sorted by model distance: nonbonded pdb=" NZ LYS A 370 " pdb=" OE1 GLU A 372 " model vdw 2.463 3.120 nonbonded pdb=" NZ LYS C 370 " pdb=" OE1 GLU C 372 " model vdw 2.464 3.120 nonbonded pdb=" NZ LYS I 370 " pdb=" OE1 GLU I 372 " model vdw 2.464 3.120 nonbonded pdb=" NZ LYS E 370 " pdb=" OE1 GLU E 372 " model vdw 2.464 3.120 nonbonded pdb=" NZ LYS G 370 " pdb=" OE1 GLU G 372 " model vdw 2.464 3.120 ... (remaining 47184 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.620 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.800 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 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:6.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.010 Internal consistency checks: 0.000 Total: 14.800 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.001 0.001 ARG H 349 TYR 0.007 0.004 TYR G 310 PHE 0.026 0.007 PHE E 346 HIS 0.006 0.002 HIS E 362 Details of bonding type rmsd covalent geometry : bond 0.02259 ( 5750) covalent geometry : angle 1.94679 ( 7690) hydrogen bonds : bond 0.06817 ( 120) hydrogen bonds : angle 9.23491 ( 360) *********************** 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 : 0.217 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: 0.7051 (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: 0.7063 time to fit residues: 175.6870 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 : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 20.0000 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 = 0.4014 r_free = 0.4014 target = 0.136903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.100538 restraints weight = 6787.301| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.90 r_work: 0.3434 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 5750 Z= 0.158 Angle : 0.667 6.005 7690 Z= 0.333 Chirality : 0.051 0.127 870 Planarity : 0.002 0.029 970 Dihedral : 5.247 15.288 750 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.46 % Allowed : 20.77 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.29), residues: 720 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.72 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 349 TYR 0.011 0.002 TYR E 310 PHE 0.009 0.001 PHE G 346 HIS 0.003 0.001 HIS I 362 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 5750) covalent geometry : angle 0.66665 ( 7690) hydrogen bonds : bond 0.02598 ( 120) hydrogen bonds : angle 5.64045 ( 360) *********************** 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 153 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 0.177 Fit side-chains REVERT: A 307 GLN cc_start: 0.8522 (mt0) cc_final: 0.8131 (mt0) REVERT: A 345 ASP cc_start: 0.8185 (t0) cc_final: 0.7682 (t70) REVERT: C 327 ASN cc_start: 0.9034 (t0) cc_final: 0.8713 (t0) REVERT: D 307 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.7866 (tp40) REVERT: E 356 SER cc_start: 0.9025 (t) cc_final: 0.8732 (m) REVERT: F 336 GLN cc_start: 0.7993 (mm-40) cc_final: 0.7574 (mm110) REVERT: H 340 LYS cc_start: 0.7864 (ptpp) cc_final: 0.7455 (tmtt) REVERT: J 314 ASP cc_start: 0.8857 (t0) cc_final: 0.8573 (t0) REVERT: J 336 GLN cc_start: 0.8039 (mt0) cc_final: 0.7529 (mm-40) outliers start: 16 outliers final: 2 residues processed: 143 average time/residue: 0.4284 time to fit residues: 64.5110 Evaluate side-chains 123 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 120 time to evaluate : 0.144 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 39 optimal weight: 20.0000 chunk 42 optimal weight: 0.7980 chunk 1 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 43 optimal weight: 9.9990 chunk 11 optimal weight: 8.9990 chunk 19 optimal weight: 8.9990 chunk 49 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 overall best weight: 2.9186 ------------------------------------------------------------------------------- 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 I 327 ASN I 368 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 = 0.3939 r_free = 0.3939 target = 0.132160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.094794 restraints weight = 6779.281| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.95 r_work: 0.3313 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: 0.8140 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 5750 Z= 0.222 Angle : 0.685 6.852 7690 Z= 0.339 Chirality : 0.051 0.156 870 Planarity : 0.002 0.019 970 Dihedral : 5.153 13.752 750 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 2.46 % Allowed : 21.85 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.99 (0.29), residues: 720 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.75 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 349 TYR 0.013 0.003 TYR I 310 PHE 0.017 0.002 PHE G 346 HIS 0.004 0.001 HIS I 362 Details of bonding type rmsd covalent geometry : bond 0.00533 ( 5750) covalent geometry : angle 0.68486 ( 7690) hydrogen bonds : bond 0.02555 ( 120) hydrogen bonds : angle 5.20568 ( 360) *********************** 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 160 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 0.241 Fit side-chains REVERT: A 340 LYS cc_start: 0.7967 (OUTLIER) cc_final: 0.7474 (mttp) REVERT: A 345 ASP cc_start: 0.8072 (t0) cc_final: 0.7466 (t70) REVERT: A 375 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8503 (tttm) REVERT: B 338 GLU cc_start: 0.6841 (tp30) cc_final: 0.6641 (mm-30) REVERT: B 347 LYS cc_start: 0.6500 (mttp) cc_final: 0.5796 (mmpt) REVERT: C 327 ASN cc_start: 0.8982 (t0) cc_final: 0.8676 (t0) REVERT: C 342 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7468 (mm-30) REVERT: D 340 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.7712 (tptt) REVERT: E 315 LEU cc_start: 0.9253 (mt) cc_final: 0.8956 (mt) REVERT: E 345 ASP cc_start: 0.7873 (t0) cc_final: 0.7587 (t70) REVERT: E 356 SER cc_start: 0.8713 (t) cc_final: 0.8432 (m) REVERT: F 336 GLN cc_start: 0.8010 (mm-40) cc_final: 0.7667 (mm110) REVERT: F 338 GLU cc_start: 0.7618 (pp20) cc_final: 0.7208 (pp20) REVERT: H 307 GLN cc_start: 0.8296 (mt0) cc_final: 0.8063 (mt0) REVERT: H 314 ASP cc_start: 0.9121 (t0) cc_final: 0.8815 (t0) REVERT: H 324 SER cc_start: 0.8729 (t) cc_final: 0.8359 (m) REVERT: H 340 LYS cc_start: 0.7683 (OUTLIER) cc_final: 0.7430 (tmtt) REVERT: J 314 ASP cc_start: 0.8983 (t0) cc_final: 0.8603 (t0) REVERT: J 336 GLN cc_start: 0.8216 (mt0) cc_final: 0.7681 (mm110) outliers start: 16 outliers final: 3 residues processed: 153 average time/residue: 0.5052 time to fit residues: 80.9154 Evaluate side-chains 147 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 140 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 LYS 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 H residue 340 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 68 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 27 optimal weight: 9.9990 chunk 44 optimal weight: 0.9990 chunk 25 optimal weight: 20.0000 chunk 48 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 D 359 ASN E 327 ASN E 336 GLN F 307 GLN I 327 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.133479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.096252 restraints weight = 6844.618| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.96 r_work: 0.3365 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 5750 Z= 0.149 Angle : 0.600 5.309 7690 Z= 0.296 Chirality : 0.049 0.147 870 Planarity : 0.002 0.015 970 Dihedral : 4.932 13.531 750 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.31 % Allowed : 22.15 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.11 (0.29), residues: 720 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.83 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 349 TYR 0.010 0.002 TYR G 310 PHE 0.013 0.001 PHE G 346 HIS 0.003 0.001 HIS G 330 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 5750) covalent geometry : angle 0.59994 ( 7690) hydrogen bonds : bond 0.02152 ( 120) hydrogen bonds : angle 4.79992 ( 360) *********************** 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 159 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 0.266 Fit side-chains revert: symmetry clash REVERT: A 307 GLN cc_start: 0.8480 (mt0) cc_final: 0.8133 (mt0) REVERT: A 340 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7473 (mttp) REVERT: A 345 ASP cc_start: 0.8146 (t0) cc_final: 0.7567 (t70) REVERT: B 347 LYS cc_start: 0.6523 (mttp) cc_final: 0.5761 (mmpt) REVERT: C 327 ASN cc_start: 0.8987 (t0) cc_final: 0.8685 (t0) REVERT: D 307 GLN cc_start: 0.8394 (tt0) cc_final: 0.8056 (tt0) REVERT: E 315 LEU cc_start: 0.9263 (mt) cc_final: 0.8941 (mt) REVERT: E 345 ASP cc_start: 0.7922 (t0) cc_final: 0.7584 (t70) REVERT: E 356 SER cc_start: 0.8792 (OUTLIER) cc_final: 0.8464 (m) REVERT: F 316 SER cc_start: 0.9372 (p) cc_final: 0.9099 (p) REVERT: F 324 SER cc_start: 0.8681 (t) cc_final: 0.8398 (m) REVERT: F 336 GLN cc_start: 0.8022 (mm-40) cc_final: 0.7509 (mm110) REVERT: F 338 GLU cc_start: 0.7398 (pp20) cc_final: 0.7188 (pp20) REVERT: F 372 GLU cc_start: 0.8621 (tt0) cc_final: 0.8380 (tt0) REVERT: H 307 GLN cc_start: 0.8279 (mt0) cc_final: 0.8041 (mt0) REVERT: H 314 ASP cc_start: 0.9074 (t0) cc_final: 0.8793 (t0) REVERT: H 324 SER cc_start: 0.8615 (t) cc_final: 0.8226 (m) REVERT: H 340 LYS cc_start: 0.7735 (ptpp) cc_final: 0.7485 (tmtt) REVERT: J 314 ASP cc_start: 0.8932 (t0) cc_final: 0.8610 (t0) REVERT: J 325 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8944 (tp) REVERT: J 336 GLN cc_start: 0.8248 (mt0) cc_final: 0.7729 (mm110) outliers start: 15 outliers final: 5 residues processed: 153 average time/residue: 0.5238 time to fit residues: 83.8834 Evaluate side-chains 146 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 138 time to evaluate : 0.243 ------------------------------------------------------------------------------- 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 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 J residue 325 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 chunk 52 optimal weight: 30.0000 chunk 58 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 31 optimal weight: 7.9990 chunk 39 optimal weight: 30.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 F 307 GLN F 329 HIS H 336 GLN I 327 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.131988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.094483 restraints weight = 6984.844| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.98 r_work: 0.3317 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 5750 Z= 0.210 Angle : 0.643 6.040 7690 Z= 0.316 Chirality : 0.050 0.150 870 Planarity : 0.002 0.020 970 Dihedral : 5.022 14.024 750 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 2.92 % Allowed : 22.15 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.30 (0.29), residues: 720 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.98 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 349 TYR 0.012 0.002 TYR I 310 PHE 0.017 0.001 PHE G 346 HIS 0.003 0.001 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00504 ( 5750) covalent geometry : angle 0.64286 ( 7690) hydrogen bonds : bond 0.02309 ( 120) hydrogen bonds : angle 4.78464 ( 360) *********************** 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 170 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 151 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: A 307 GLN cc_start: 0.8454 (mt0) cc_final: 0.8067 (mt0) REVERT: A 340 LYS cc_start: 0.7908 (OUTLIER) cc_final: 0.7396 (mttp) REVERT: A 345 ASP cc_start: 0.8143 (t0) cc_final: 0.7499 (t70) REVERT: A 375 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8559 (tttm) REVERT: B 347 LYS cc_start: 0.6450 (mttp) cc_final: 0.5733 (mmpt) REVERT: C 327 ASN cc_start: 0.9029 (t0) cc_final: 0.8737 (t0) REVERT: C 351 GLN cc_start: 0.8122 (tt0) cc_final: 0.7839 (tt0) REVERT: D 317 LYS cc_start: 0.8813 (pttt) cc_final: 0.8585 (pttt) REVERT: E 315 LEU cc_start: 0.9238 (mt) cc_final: 0.8891 (mt) REVERT: E 345 ASP cc_start: 0.7915 (t0) cc_final: 0.7569 (t70) REVERT: E 356 SER cc_start: 0.8677 (t) cc_final: 0.8426 (m) REVERT: F 324 SER cc_start: 0.8637 (t) cc_final: 0.8365 (m) REVERT: F 336 GLN cc_start: 0.8149 (mm-40) cc_final: 0.7696 (mm110) REVERT: F 372 GLU cc_start: 0.8659 (tt0) cc_final: 0.8412 (tt0) REVERT: F 375 LYS cc_start: 0.8697 (tttm) cc_final: 0.8043 (ttmm) REVERT: H 307 GLN cc_start: 0.8230 (mt0) cc_final: 0.7983 (mt0) REVERT: H 324 SER cc_start: 0.8716 (t) cc_final: 0.8350 (m) REVERT: H 336 GLN cc_start: 0.7996 (mt0) cc_final: 0.7743 (mt0) REVERT: J 314 ASP cc_start: 0.8981 (t0) cc_final: 0.8553 (t0) REVERT: J 336 GLN cc_start: 0.8264 (mt0) cc_final: 0.7646 (mm110) outliers start: 19 outliers final: 9 residues processed: 160 average time/residue: 0.5232 time to fit residues: 87.5390 Evaluate side-chains 161 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 150 time to evaluate : 0.240 ------------------------------------------------------------------------------- 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 B residue 371 ILE 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 E residue 324 SER Chi-restraints excluded: chain G residue 343 LYS Chi-restraints excluded: chain J residue 340 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 27 optimal weight: 7.9990 chunk 68 optimal weight: 8.9990 chunk 58 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 26 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN B 307 GLN B 329 HIS D 329 HIS D 359 ASN E 327 ASN E 336 GLN F 307 GLN H 327 ASN I 327 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.130580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.093349 restraints weight = 6916.742| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 1.97 r_work: 0.3290 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3869 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= 0.258 Angle : 0.687 6.226 7690 Z= 0.337 Chirality : 0.050 0.157 870 Planarity : 0.003 0.020 970 Dihedral : 5.162 15.189 750 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 3.23 % Allowed : 22.92 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.51 (0.28), residues: 720 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.14 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 349 TYR 0.013 0.003 TYR I 310 PHE 0.020 0.002 PHE G 346 HIS 0.003 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00620 ( 5750) covalent geometry : angle 0.68705 ( 7690) hydrogen bonds : bond 0.02487 ( 120) hydrogen bonds : angle 4.80227 ( 360) *********************** 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 170 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: A 307 GLN cc_start: 0.8378 (mt0) cc_final: 0.7985 (mt0) REVERT: A 345 ASP cc_start: 0.8146 (t0) cc_final: 0.7528 (t70) REVERT: A 375 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8579 (tttm) REVERT: C 327 ASN cc_start: 0.9013 (t0) cc_final: 0.8699 (t0) REVERT: C 349 ARG cc_start: 0.7458 (ttp-170) cc_final: 0.7255 (ttp-170) REVERT: C 351 GLN cc_start: 0.8092 (tt0) cc_final: 0.7777 (tt0) REVERT: D 317 LYS cc_start: 0.8829 (pttt) cc_final: 0.8600 (pttt) REVERT: E 345 ASP cc_start: 0.7945 (t0) cc_final: 0.7544 (t70) REVERT: E 356 SER cc_start: 0.8662 (t) cc_final: 0.8401 (m) REVERT: F 324 SER cc_start: 0.8575 (t) cc_final: 0.8225 (m) REVERT: F 336 GLN cc_start: 0.8175 (mm-40) cc_final: 0.7737 (mm110) REVERT: F 375 LYS cc_start: 0.8671 (tttm) cc_final: 0.8030 (ttmm) REVERT: H 307 GLN cc_start: 0.8273 (mt0) cc_final: 0.8034 (mt0) REVERT: H 324 SER cc_start: 0.8737 (t) cc_final: 0.8347 (m) REVERT: H 327 ASN cc_start: 0.8586 (m-40) cc_final: 0.8383 (m110) REVERT: J 307 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.8237 (tt0) REVERT: J 314 ASP cc_start: 0.8991 (t0) cc_final: 0.8444 (t0) REVERT: J 336 GLN cc_start: 0.8327 (mt0) cc_final: 0.7781 (mm110) outliers start: 21 outliers final: 10 residues processed: 161 average time/residue: 0.5392 time to fit residues: 90.8200 Evaluate side-chains 161 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 149 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER 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 E residue 324 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 307 GLN 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 67 optimal weight: 2.9990 chunk 24 optimal weight: 20.0000 chunk 0 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 4 optimal weight: 0.9990 chunk 50 optimal weight: 7.9990 chunk 63 optimal weight: 0.4980 chunk 29 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN B 307 GLN E 327 ASN E 336 GLN F 307 GLN H 336 GLN I 327 ASN ** 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 = 0.3931 r_free = 0.3931 target = 0.131616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.094256 restraints weight = 6989.312| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.99 r_work: 0.3321 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 5750 Z= 0.204 Angle : 0.649 6.458 7690 Z= 0.319 Chirality : 0.049 0.154 870 Planarity : 0.002 0.018 970 Dihedral : 5.042 14.703 750 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.62 % Allowed : 24.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.59 (0.28), 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 ARG 0.004 0.000 ARG G 349 TYR 0.011 0.002 TYR I 310 PHE 0.016 0.001 PHE G 346 HIS 0.003 0.001 HIS G 330 Details of bonding type rmsd covalent geometry : bond 0.00488 ( 5750) covalent geometry : angle 0.64948 ( 7690) hydrogen bonds : bond 0.02400 ( 120) hydrogen bonds : angle 4.69060 ( 360) *********************** 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 164 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 0.185 Fit side-chains REVERT: A 307 GLN cc_start: 0.8388 (mt0) cc_final: 0.8026 (mt0) REVERT: A 340 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7521 (mttp) REVERT: A 345 ASP cc_start: 0.8145 (t0) cc_final: 0.7541 (t70) REVERT: A 375 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8578 (tttm) REVERT: C 327 ASN cc_start: 0.9006 (t0) cc_final: 0.8703 (t0) REVERT: C 351 GLN cc_start: 0.8097 (tt0) cc_final: 0.7787 (tt0) REVERT: D 317 LYS cc_start: 0.8850 (pttt) cc_final: 0.8633 (pttt) REVERT: E 345 ASP cc_start: 0.7884 (t0) cc_final: 0.7520 (t70) REVERT: E 356 SER cc_start: 0.8678 (OUTLIER) cc_final: 0.8438 (m) REVERT: F 324 SER cc_start: 0.8612 (t) cc_final: 0.8228 (m) REVERT: F 336 GLN cc_start: 0.8127 (mm-40) cc_final: 0.7577 (mp10) REVERT: F 375 LYS cc_start: 0.8682 (tttm) cc_final: 0.8050 (ttmm) REVERT: G 353 LYS cc_start: 0.8992 (tttt) cc_final: 0.8507 (tttp) REVERT: H 307 GLN cc_start: 0.8252 (mt0) cc_final: 0.8005 (mt0) REVERT: H 324 SER cc_start: 0.8737 (t) cc_final: 0.8336 (m) REVERT: H 327 ASN cc_start: 0.8559 (m-40) cc_final: 0.8355 (m110) REVERT: J 307 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.8222 (tt0) REVERT: J 314 ASP cc_start: 0.9030 (t0) cc_final: 0.8500 (t0) REVERT: J 336 GLN cc_start: 0.8335 (mt0) cc_final: 0.7699 (mm110) outliers start: 17 outliers final: 7 residues processed: 156 average time/residue: 0.5314 time to fit residues: 86.6846 Evaluate side-chains 157 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 146 time to evaluate : 0.235 ------------------------------------------------------------------------------- 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 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 352 SER Chi-restraints excluded: chain H residue 325 LEU Chi-restraints excluded: chain J residue 307 GLN Chi-restraints excluded: chain J residue 340 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 28 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 25 optimal weight: 20.0000 chunk 57 optimal weight: 0.3980 chunk 47 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN B 307 GLN D 359 ASN E 327 ASN E 336 GLN F 307 GLN H 336 GLN I 327 ASN I 362 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.134345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.097250 restraints weight = 6807.045| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.96 r_work: 0.3370 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5750 Z= 0.126 Angle : 0.606 7.136 7690 Z= 0.299 Chirality : 0.049 0.145 870 Planarity : 0.002 0.015 970 Dihedral : 4.712 13.294 750 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 1.38 % Allowed : 24.92 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.52 (0.29), residues: 720 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.15 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 349 TYR 0.008 0.002 TYR G 310 PHE 0.011 0.001 PHE G 346 HIS 0.004 0.001 HIS G 330 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 5750) covalent geometry : angle 0.60565 ( 7690) hydrogen bonds : bond 0.02183 ( 120) hydrogen bonds : angle 4.46048 ( 360) *********************** 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 156 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 147 time to evaluate : 0.176 Fit side-chains REVERT: A 307 GLN cc_start: 0.8439 (mt0) cc_final: 0.8008 (mt0) REVERT: A 340 LYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7511 (mttp) REVERT: A 343 LYS cc_start: 0.8411 (mmmt) cc_final: 0.7545 (mmtt) REVERT: A 345 ASP cc_start: 0.8187 (t0) cc_final: 0.7580 (t70) REVERT: A 375 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8526 (tttm) REVERT: C 327 ASN cc_start: 0.8982 (t0) cc_final: 0.8695 (t0) REVERT: C 349 ARG cc_start: 0.7553 (ttp-170) cc_final: 0.7345 (ttp-170) REVERT: D 317 LYS cc_start: 0.8861 (pttt) cc_final: 0.8590 (pttt) REVERT: E 345 ASP cc_start: 0.7813 (t0) cc_final: 0.7471 (t70) REVERT: F 324 SER cc_start: 0.8615 (t) cc_final: 0.8265 (m) REVERT: F 336 GLN cc_start: 0.8030 (mm-40) cc_final: 0.7444 (mm110) REVERT: F 340 LYS cc_start: 0.8396 (mmtm) cc_final: 0.8083 (mmtm) REVERT: F 375 LYS cc_start: 0.8698 (tttm) cc_final: 0.8049 (ttmm) REVERT: H 307 GLN cc_start: 0.8160 (mt0) cc_final: 0.7916 (mt0) REVERT: H 324 SER cc_start: 0.8682 (t) cc_final: 0.8262 (m) REVERT: H 336 GLN cc_start: 0.7985 (mt0) cc_final: 0.7184 (mp10) REVERT: H 340 LYS cc_start: 0.7478 (tmtt) cc_final: 0.7249 (tptt) REVERT: J 307 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.8190 (tt0) REVERT: J 314 ASP cc_start: 0.8995 (t0) cc_final: 0.8621 (t0) REVERT: J 325 LEU cc_start: 0.9191 (tt) cc_final: 0.8980 (tp) REVERT: J 336 GLN cc_start: 0.8310 (mt0) cc_final: 0.7713 (mm110) outliers start: 9 outliers final: 5 residues processed: 152 average time/residue: 0.5328 time to fit residues: 84.6375 Evaluate side-chains 151 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 143 time to evaluate : 0.225 ------------------------------------------------------------------------------- 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 375 LYS Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain H residue 325 LEU Chi-restraints excluded: chain J residue 307 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 33 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 9 optimal weight: 0.0270 chunk 38 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 11 optimal weight: 20.0000 chunk 5 optimal weight: 5.9990 overall best weight: 3.4046 ------------------------------------------------------------------------------- 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 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.130506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.093252 restraints weight = 6938.515| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.96 r_work: 0.3307 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 5750 Z= 0.247 Angle : 0.712 8.259 7690 Z= 0.348 Chirality : 0.050 0.157 870 Planarity : 0.003 0.020 970 Dihedral : 5.056 15.213 750 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 1.85 % Allowed : 24.77 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.69 (0.28), residues: 720 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.28 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 349 TYR 0.013 0.002 TYR I 310 PHE 0.019 0.002 PHE E 346 HIS 0.003 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00596 ( 5750) covalent geometry : angle 0.71165 ( 7690) hydrogen bonds : bond 0.02631 ( 120) hydrogen bonds : angle 4.63329 ( 360) *********************** 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 163 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 151 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: A 307 GLN cc_start: 0.8398 (mt0) cc_final: 0.8008 (mt0) REVERT: A 315 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9123 (mp) REVERT: A 345 ASP cc_start: 0.8163 (t0) cc_final: 0.7617 (t70) REVERT: A 375 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8578 (tttm) REVERT: C 327 ASN cc_start: 0.9026 (t0) cc_final: 0.8727 (t0) REVERT: C 351 GLN cc_start: 0.8087 (tt0) cc_final: 0.7785 (tt0) REVERT: D 317 LYS cc_start: 0.8858 (pttt) cc_final: 0.8636 (pttt) REVERT: E 307 GLN cc_start: 0.8366 (mt0) cc_final: 0.7939 (mt0) REVERT: E 345 ASP cc_start: 0.7894 (t0) cc_final: 0.7535 (t70) REVERT: F 324 SER cc_start: 0.8657 (t) cc_final: 0.8301 (m) REVERT: F 336 GLN cc_start: 0.8106 (mm-40) cc_final: 0.7421 (mp10) REVERT: F 340 LYS cc_start: 0.8473 (mmtm) cc_final: 0.8224 (mmtm) REVERT: F 375 LYS cc_start: 0.8686 (tttm) cc_final: 0.8045 (ttmm) REVERT: G 353 LYS cc_start: 0.9050 (tttt) cc_final: 0.8561 (tttp) REVERT: H 307 GLN cc_start: 0.8258 (mt0) cc_final: 0.8002 (mt0) REVERT: H 324 SER cc_start: 0.8769 (t) cc_final: 0.8365 (m) REVERT: H 327 ASN cc_start: 0.8544 (m-40) cc_final: 0.8342 (m110) REVERT: H 336 GLN cc_start: 0.8004 (mt0) cc_final: 0.7203 (mp10) REVERT: J 307 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.8229 (tt0) REVERT: J 314 ASP cc_start: 0.9108 (t0) cc_final: 0.8582 (t0) REVERT: J 336 GLN cc_start: 0.8340 (mt0) cc_final: 0.7752 (mm110) outliers start: 12 outliers final: 6 residues processed: 157 average time/residue: 0.5206 time to fit residues: 85.4151 Evaluate side-chains 159 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 150 time to evaluate : 0.233 ------------------------------------------------------------------------------- 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 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 G residue 352 SER Chi-restraints excluded: chain J residue 307 GLN Chi-restraints excluded: chain J residue 340 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 50 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 48 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- 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 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 = 0.3921 r_free = 0.3921 target = 0.130876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.093650 restraints weight = 7014.144| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.99 r_work: 0.3314 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 5750 Z= 0.234 Angle : 0.713 9.073 7690 Z= 0.349 Chirality : 0.050 0.156 870 Planarity : 0.002 0.024 970 Dihedral : 5.074 15.770 750 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 1.69 % Allowed : 24.15 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.76 (0.28), residues: 720 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.33 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 349 TYR 0.013 0.002 TYR I 310 PHE 0.018 0.002 PHE G 346 HIS 0.003 0.001 HIS G 330 Details of bonding type rmsd covalent geometry : bond 0.00563 ( 5750) covalent geometry : angle 0.71265 ( 7690) hydrogen bonds : bond 0.02592 ( 120) hydrogen bonds : angle 4.67160 ( 360) ********************** 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 156 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 145 time to evaluate : 0.237 Fit side-chains revert: symmetry clash REVERT: A 307 GLN cc_start: 0.8376 (mt0) cc_final: 0.7988 (mt0) REVERT: A 315 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.9098 (mp) REVERT: A 345 ASP cc_start: 0.8195 (t0) cc_final: 0.7617 (t70) REVERT: C 327 ASN cc_start: 0.9002 (t0) cc_final: 0.8698 (t0) REVERT: C 351 GLN cc_start: 0.8076 (tt0) cc_final: 0.7772 (tt0) REVERT: D 317 LYS cc_start: 0.8831 (pttt) cc_final: 0.8620 (pttt) REVERT: E 307 GLN cc_start: 0.8326 (mt0) cc_final: 0.7921 (mt0) REVERT: E 345 ASP cc_start: 0.7877 (t0) cc_final: 0.7511 (t70) REVERT: F 324 SER cc_start: 0.8625 (t) cc_final: 0.8230 (m) REVERT: F 336 GLN cc_start: 0.8114 (mm-40) cc_final: 0.7621 (mp10) REVERT: F 340 LYS cc_start: 0.8413 (mmtm) cc_final: 0.8117 (mmtm) REVERT: F 375 LYS cc_start: 0.8674 (tttm) cc_final: 0.8025 (ttmm) REVERT: G 353 LYS cc_start: 0.8986 (tttt) cc_final: 0.8499 (tttp) REVERT: H 307 GLN cc_start: 0.8236 (mt0) cc_final: 0.7982 (mt0) REVERT: H 324 SER cc_start: 0.8713 (t) cc_final: 0.8279 (m) REVERT: J 307 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.8212 (tt0) REVERT: J 336 GLN cc_start: 0.8344 (mt0) cc_final: 0.7724 (mm110) outliers start: 11 outliers final: 5 residues processed: 149 average time/residue: 0.5578 time to fit residues: 86.7398 Evaluate side-chains 153 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 146 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain J residue 307 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 55 optimal weight: 8.9990 chunk 35 optimal weight: 0.9990 chunk 43 optimal weight: 8.9990 chunk 12 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 53 optimal weight: 20.0000 chunk 3 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 59 optimal weight: 8.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN E 327 ASN E 336 GLN F 307 GLN I 327 ASN I 336 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.132506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.095414 restraints weight = 6819.370| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.95 r_work: 0.3344 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5750 Z= 0.167 Angle : 0.670 9.036 7690 Z= 0.328 Chirality : 0.050 0.150 870 Planarity : 0.002 0.018 970 Dihedral : 4.885 14.631 750 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 1.38 % Allowed : 24.77 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.73 (0.29), residues: 720 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.31 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 349 TYR 0.010 0.002 TYR I 310 PHE 0.014 0.001 PHE G 346 HIS 0.004 0.001 HIS G 330 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 5750) covalent geometry : angle 0.66994 ( 7690) hydrogen bonds : bond 0.02417 ( 120) hydrogen bonds : angle 4.53564 ( 360) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2357.07 seconds wall clock time: 41 minutes 17.73 seconds (2477.73 seconds total)